Starting phenix.real_space_refine on Fri Sep 11 23:25:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6c9a_7435/09_2026/6c9a_7435.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c9a_7435/09_2026/6c9a_7435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6c9a_7435/09_2026/6c9a_7435.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6c9a_7435/09_2026/6c9a_7435.cif" model { file = "/net/cci-nas-00/data/ceres_data/6c9a_7435/09_2026/6c9a_7435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c9a_7435/09_2026/6c9a_7435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c9a_7435/09_2026/6c9a_7435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c9a_7435/09_2026/6c9a_7435.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 76 5.16 5 C 8010 2.51 5 N 1978 2.21 5 O 2112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12182 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 6002 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 20, 'TRANS': 702} Chain breaks: 1 Chain: "A" Number of atoms: 6002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 6002 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 20, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'EUJ': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'EUJ': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.62, per 1000 atoms: 0.22 Number of scatterers: 12182 At special positions: 0 Unit cell: (129.47, 111.28, 120.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 6 15.00 O 2112 8.00 N 1978 7.00 C 8010 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1003 " - " ASN A 612 " " NAG B1003 " - " ASN B 612 " " NAG C 1 " - " ASN B 600 " " NAG D 1 " - " ASN A 600 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 569.0 milliseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 77.0% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.717A pdb=" N THR B 90 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B 91 " --> pdb=" O PHE B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 107 through 124 Processing helix chain 'B' and resid 137 through 163 removed outlier: 3.751A pdb=" N HIS B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.776A pdb=" N ARG B 170 " --> pdb=" O HIS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 195 Processing helix chain 'B' and resid 201 through 206 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 216 through 229 removed outlier: 3.548A pdb=" N ASN B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 256 removed outlier: 3.755A pdb=" N ASP B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.625A pdb=" N THR B 279 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 removed outlier: 3.657A pdb=" N MET B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 297 through 309 removed outlier: 4.151A pdb=" N PHE B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 350 removed outlier: 3.585A pdb=" N ALA B 342 " --> pdb=" O HIS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 369 Processing helix chain 'B' and resid 376 through 389 removed outlier: 4.461A pdb=" N GLN B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 443 through 466 Processing helix chain 'B' and resid 468 through 472 removed outlier: 3.944A pdb=" N PHE B 471 " --> pdb=" O GLY B 468 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR B 472 " --> pdb=" O GLY B 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 468 through 472' Processing helix chain 'B' and resid 477 through 499 removed outlier: 3.556A pdb=" N LEU B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 528 removed outlier: 3.614A pdb=" N LEU B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 533 Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 550 removed outlier: 3.652A pdb=" N ARG B 546 " --> pdb=" O GLN B 543 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 550 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 562 removed outlier: 3.653A pdb=" N ARG B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 590 removed outlier: 4.131A pdb=" N THR B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.648A pdb=" N ASN B 629 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 removed outlier: 3.600A pdb=" N SER B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 4.377A pdb=" N ILE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 699 removed outlier: 3.586A pdb=" N LEU B 667 " --> pdb=" O HIS B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.964A pdb=" N ALA B 723 " --> pdb=" O GLU B 719 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 724 " --> pdb=" O GLU B 720 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 728 " --> pdb=" O VAL B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 751 removed outlier: 4.062A pdb=" N TYR B 751 " --> pdb=" O GLN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 774 removed outlier: 3.804A pdb=" N LEU B 769 " --> pdb=" O THR B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 778 through 794 Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.717A pdb=" N THR A 90 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A 91 " --> pdb=" O PHE A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 107 through 124 Processing helix chain 'A' and resid 137 through 163 removed outlier: 3.752A pdb=" N HIS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.776A pdb=" N ARG A 170 " --> pdb=" O HIS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 195 Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.549A pdb=" N ASN A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 256 removed outlier: 3.756A pdb=" N ASP A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.625A pdb=" N THR A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.657A pdb=" N MET A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 297 through 309 removed outlier: 4.151A pdb=" N PHE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 350 removed outlier: 3.585A pdb=" N ALA A 342 " --> pdb=" O HIS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 369 Processing helix chain 'A' and resid 376 through 389 removed outlier: 4.461A pdb=" N GLN A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 443 through 466 Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.943A pdb=" N PHE A 471 " --> pdb=" O GLY A 468 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 472 " --> pdb=" O GLY A 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 468 through 472' Processing helix chain 'A' and resid 477 through 499 removed outlier: 3.556A pdb=" N LEU A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 528 removed outlier: 3.614A pdb=" N LEU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 533 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.652A pdb=" N ARG A 546 " --> pdb=" O GLN A 543 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 550 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 removed outlier: 3.653A pdb=" N ARG A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 590 removed outlier: 4.130A pdb=" N THR A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.648A pdb=" N ASN A 629 " --> pdb=" O TYR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 removed outlier: 3.600A pdb=" N SER A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 4.377A pdb=" N ILE A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 699 removed outlier: 3.586A pdb=" N LEU A 667 " --> pdb=" O HIS A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.964A pdb=" N ALA A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 724 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 728 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 751 removed outlier: 4.062A pdb=" N TYR A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 774 removed outlier: 3.803A pdb=" N LEU A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 777 No H-bonds generated for 'chain 'A' and resid 775 through 777' Processing helix chain 'A' and resid 778 through 794 Processing sheet with id=AA1, first strand: chain 'B' and resid 410 through 412 removed outlier: 3.547A pdb=" N LYS B 714 " --> pdb=" O PHE B 758 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 762 " --> pdb=" O ILE B 710 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 610 through 611 Processing sheet with id=AA3, first strand: chain 'A' and resid 410 through 412 removed outlier: 3.548A pdb=" N LYS A 714 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 762 " --> pdb=" O ILE A 710 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 610 through 611 776 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1812 1.30 - 1.43: 3668 1.43 - 1.56: 6872 1.56 - 1.68: 8 1.68 - 1.81: 136 Bond restraints: 12496 Sorted by residual: bond pdb=" O3 EUJ A1000 " pdb=" P3 EUJ A1000 " ideal model delta sigma weight residual 1.727 1.636 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" O3 EUJ B1000 " pdb=" P3 EUJ B1000 " ideal model delta sigma weight residual 1.727 1.638 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1B EUJ B1000 " pdb=" O3C EUJ B1000 " ideal model delta sigma weight residual 1.330 1.396 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1B EUJ A1000 " pdb=" O3C EUJ A1000 " ideal model delta sigma weight residual 1.330 1.396 -0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C1A EUJ A1000 " pdb=" O2C EUJ A1000 " ideal model delta sigma weight residual 1.332 1.396 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 12491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 16313 2.55 - 5.11: 487 5.11 - 7.66: 84 7.66 - 10.22: 32 10.22 - 12.77: 6 Bond angle restraints: 16922 Sorted by residual: angle pdb=" C ARG B 426 " pdb=" N THR B 427 " pdb=" CA THR B 427 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C ARG A 426 " pdb=" N THR A 427 " pdb=" CA THR A 427 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" O11 EUJ B1000 " pdb=" P1 EUJ B1000 " pdb=" O12 EUJ B1000 " ideal model delta sigma weight residual 121.88 109.11 12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" O11 EUJ A1000 " pdb=" P1 EUJ A1000 " pdb=" O12 EUJ A1000 " ideal model delta sigma weight residual 121.88 109.28 12.60 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N LEU B 230 " pdb=" CA LEU B 230 " pdb=" C LEU B 230 " ideal model delta sigma weight residual 109.81 118.85 -9.04 2.21e+00 2.05e-01 1.67e+01 ... (remaining 16917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 6883 15.08 - 30.16: 391 30.16 - 45.23: 76 45.23 - 60.31: 20 60.31 - 75.39: 10 Dihedral angle restraints: 7380 sinusoidal: 3076 harmonic: 4304 Sorted by residual: dihedral pdb=" CA GLU A 127 " pdb=" C GLU A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual 180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLU B 127 " pdb=" C GLU B 127 " pdb=" N SER B 128 " pdb=" CA SER B 128 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA SER A 128 " pdb=" C SER A 128 " pdb=" N PRO A 129 " pdb=" CA PRO A 129 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1454 0.064 - 0.128: 390 0.128 - 0.192: 58 0.192 - 0.256: 8 0.256 - 0.320: 2 Chirality restraints: 1912 Sorted by residual: chirality pdb=" C5 EUJ B1000 " pdb=" C4 EUJ B1000 " pdb=" C6 EUJ B1000 " pdb=" O5 EUJ B1000 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C5 EUJ A1000 " pdb=" C4 EUJ A1000 " pdb=" C6 EUJ A1000 " pdb=" O5 EUJ A1000 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA PHE B 283 " pdb=" N PHE B 283 " pdb=" C PHE B 283 " pdb=" CB PHE B 283 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1909 not shown) Planarity restraints: 2074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 782 " 0.025 2.00e-02 2.50e+03 2.18e-02 9.46e+00 pdb=" CG TYR B 782 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 782 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 782 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 782 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 782 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 782 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 782 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 782 " -0.025 2.00e-02 2.50e+03 2.17e-02 9.38e+00 pdb=" CG TYR A 782 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 782 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 782 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 782 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 782 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 782 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 782 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 531 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO A 532 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " -0.039 5.00e-02 4.00e+02 ... (remaining 2071 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3963 2.84 - 3.36: 10993 3.36 - 3.87: 18880 3.87 - 4.39: 20979 4.39 - 4.90: 36896 Nonbonded interactions: 91711 Sorted by model distance: nonbonded pdb=" OG1 THR B 138 " pdb=" OE1 GLN B 195 " model vdw 2.331 3.040 nonbonded pdb=" OG1 THR A 138 " pdb=" OE1 GLN A 195 " model vdw 2.331 3.040 nonbonded pdb=" OG SER B 352 " pdb=" O PRO B 356 " model vdw 2.340 3.040 nonbonded pdb=" OG SER A 352 " pdb=" O PRO A 356 " model vdw 2.340 3.040 nonbonded pdb=" OE1 GLU B 623 " pdb=" OH TYR B 627 " model vdw 2.344 3.040 ... (remaining 91706 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.410 Find NCS groups from input model: 0.210 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:1.120 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 0.091 12502 Z= 0.388 Angle : 1.120 12.770 16940 Z= 0.578 Chirality : 0.059 0.320 1912 Planarity : 0.008 0.069 2070 Dihedral : 10.843 75.390 4592 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.16), residues: 1438 helix: -2.65 (0.10), residues: 1050 sheet: -2.07 (0.59), residues: 64 loop : -3.07 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 173 TYR 0.052 0.004 TYR B 782 PHE 0.030 0.003 PHE A 518 TRP 0.019 0.002 TRP B 162 HIS 0.015 0.002 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00938 / 0.39 (12496) covalent geometry : angle 1.11752 / 0.58 (16922) hydrogen bonds : bond 0.19318 / 13.02 ( 776) hydrogen bonds : angle 7.47480 / 5.34 ( 2244) link_BETA1-4 : bond 0.00620 / 0.32 ( 2) link_BETA1-4 : angle 1.38285 / 0.83 ( 6) link_NAG-ASN : bond 0.00526 / 0.26 ( 4) link_NAG-ASN : angle 2.92650 / 2.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.460 Fit side-chains REVERT: B 111 MET cc_start: 0.8542 (tpp) cc_final: 0.8280 (mmt) REVERT: B 175 MET cc_start: 0.7847 (mmm) cc_final: 0.7637 (mmm) REVERT: B 394 LEU cc_start: 0.8015 (mt) cc_final: 0.7506 (mp) REVERT: B 398 LYS cc_start: 0.8894 (mttt) cc_final: 0.8652 (ttpp) REVERT: B 433 LYS cc_start: 0.7632 (mttt) cc_final: 0.7411 (mttp) REVERT: B 559 ASP cc_start: 0.7311 (m-30) cc_final: 0.7001 (m-30) REVERT: B 561 MET cc_start: 0.8107 (ttp) cc_final: 0.7900 (ttm) REVERT: B 680 MET cc_start: 0.8007 (tpt) cc_final: 0.7762 (mmm) REVERT: A 379 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7601 (mt-10) REVERT: A 438 LEU cc_start: 0.7947 (mt) cc_final: 0.7639 (mt) REVERT: A 521 LEU cc_start: 0.7895 (tp) cc_final: 0.7648 (mm) REVERT: A 568 MET cc_start: 0.8091 (mtp) cc_final: 0.7777 (mtp) REVERT: A 587 MET cc_start: 0.8818 (mtm) cc_final: 0.8612 (mtm) REVERT: A 756 MET cc_start: 0.7969 (ttt) cc_final: 0.7741 (ttm) REVERT: A 773 MET cc_start: 0.8963 (mtt) cc_final: 0.8756 (mtt) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1102 time to fit residues: 46.6446 Evaluate side-chains 174 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 ASN B 107 HIS B 171 HIS B 269 ASN B 314 ASN B 363 GLN B 591 ASN B 629 ASN B 785 HIS A 107 HIS ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 269 ASN A 314 ASN A 363 GLN A 591 ASN A 785 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116881 restraints weight = 17431.317| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.11 r_work: 0.3143 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12502 Z= 0.149 Angle : 0.648 10.374 16940 Z= 0.338 Chirality : 0.040 0.148 1912 Planarity : 0.005 0.049 2070 Dihedral : 7.055 54.607 1736 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.52 % Allowed : 8.81 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1438 helix: 0.17 (0.15), residues: 1034 sheet: -2.01 (0.63), residues: 60 loop : -2.60 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 362 TYR 0.017 0.001 TYR B 782 PHE 0.045 0.002 PHE A 429 TRP 0.009 0.001 TRP A 650 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (12496) covalent geometry : angle 0.64641 / 0.34 (16922) hydrogen bonds : bond 0.06355 / 4.13 ( 776) hydrogen bonds : angle 4.35697 / 3.07 ( 2244) link_BETA1-4 : bond 0.00780 / 0.40 ( 2) link_BETA1-4 : angle 1.26737 / 1.04 ( 6) link_NAG-ASN : bond 0.00273 / 0.14 ( 4) link_NAG-ASN : angle 1.72593 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.420 Fit side-chains REVERT: B 96 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7481 (ttp-170) REVERT: B 111 MET cc_start: 0.8659 (tpp) cc_final: 0.8449 (mmt) REVERT: B 199 VAL cc_start: 0.7461 (t) cc_final: 0.7242 (p) REVERT: B 313 MET cc_start: 0.8232 (tpt) cc_final: 0.7945 (tpt) REVERT: B 394 LEU cc_start: 0.8098 (mt) cc_final: 0.7682 (mp) REVERT: B 398 LYS cc_start: 0.9016 (mttt) cc_final: 0.8649 (ttpt) REVERT: B 433 LYS cc_start: 0.7491 (mttt) cc_final: 0.7257 (mttp) REVERT: B 490 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7737 (tt0) REVERT: B 530 MET cc_start: 0.6298 (tpt) cc_final: 0.6042 (tpp) REVERT: A 290 SER cc_start: 0.8935 (m) cc_final: 0.8735 (p) REVERT: A 438 LEU cc_start: 0.8014 (mt) cc_final: 0.7726 (mt) REVERT: A 575 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8444 (tp) REVERT: A 680 MET cc_start: 0.8666 (tpt) cc_final: 0.8361 (tpt) REVERT: A 718 LYS cc_start: 0.7541 (tttt) cc_final: 0.7294 (mmmt) REVERT: A 722 MET cc_start: 0.8208 (mpp) cc_final: 0.7244 (mpp) REVERT: A 780 GLU cc_start: 0.7804 (tt0) cc_final: 0.7535 (mp0) outliers start: 20 outliers final: 12 residues processed: 219 average time/residue: 0.0947 time to fit residues: 30.9491 Evaluate side-chains 173 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 621 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 HIS B 345 HIS A 85 ASN A 141 HIS A 345 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113464 restraints weight = 17521.785| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.03 r_work: 0.3169 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12502 Z= 0.134 Angle : 0.571 8.499 16940 Z= 0.293 Chirality : 0.039 0.147 1912 Planarity : 0.004 0.043 2070 Dihedral : 6.657 59.504 1736 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.20 % Allowed : 10.87 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1438 helix: 1.13 (0.16), residues: 1048 sheet: -1.86 (0.64), residues: 60 loop : -2.56 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 362 TYR 0.016 0.001 TYR B 782 PHE 0.040 0.001 PHE A 429 TRP 0.006 0.001 TRP B 650 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (12496) covalent geometry : angle 0.56891 / 0.29 (16922) hydrogen bonds : bond 0.05486 / 3.57 ( 776) hydrogen bonds : angle 3.86484 / 2.71 ( 2244) link_BETA1-4 : bond 0.00121 / 0.06 ( 2) link_BETA1-4 : angle 0.97949 / 0.75 ( 6) link_NAG-ASN : bond 0.00052 / 0.03 ( 4) link_NAG-ASN : angle 1.65756 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: B 96 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7357 (ptt180) REVERT: B 230 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8632 (mp) REVERT: B 313 MET cc_start: 0.8294 (tpt) cc_final: 0.8032 (tpt) REVERT: B 394 LEU cc_start: 0.8192 (mt) cc_final: 0.7765 (mp) REVERT: B 433 LYS cc_start: 0.7556 (mttt) cc_final: 0.7292 (mttp) REVERT: B 490 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7850 (tt0) REVERT: B 715 GLU cc_start: 0.8099 (pm20) cc_final: 0.7858 (pm20) REVERT: B 718 LYS cc_start: 0.8072 (mttt) cc_final: 0.7584 (mmtt) REVERT: B 756 MET cc_start: 0.7087 (ttt) cc_final: 0.6245 (ttt) REVERT: A 111 MET cc_start: 0.8295 (tpp) cc_final: 0.7716 (mmt) REVERT: A 376 SER cc_start: 0.7886 (m) cc_final: 0.7490 (p) REVERT: A 438 LEU cc_start: 0.8075 (mt) cc_final: 0.7809 (mt) REVERT: A 575 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8536 (tp) REVERT: A 680 MET cc_start: 0.8728 (tpt) cc_final: 0.8289 (mmm) REVERT: A 748 MET cc_start: 0.6500 (mmt) cc_final: 0.6023 (mmt) REVERT: A 775 GLN cc_start: 0.9194 (tt0) cc_final: 0.8993 (tt0) outliers start: 29 outliers final: 11 residues processed: 202 average time/residue: 0.1049 time to fit residues: 31.0605 Evaluate side-chains 169 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 764 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 125 optimal weight: 0.1980 chunk 5 optimal weight: 0.0030 chunk 130 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118014 restraints weight = 17231.292| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.13 r_work: 0.3235 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12502 Z= 0.112 Angle : 0.541 9.715 16940 Z= 0.272 Chirality : 0.038 0.143 1912 Planarity : 0.004 0.044 2070 Dihedral : 6.320 56.540 1736 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.67 % Allowed : 12.01 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.23), residues: 1438 helix: 1.65 (0.16), residues: 1052 sheet: -1.70 (0.62), residues: 64 loop : -2.44 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 362 TYR 0.011 0.001 TYR B 449 PHE 0.027 0.001 PHE A 429 TRP 0.006 0.001 TRP B 664 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (12496) covalent geometry : angle 0.53985 / 0.27 (16922) hydrogen bonds : bond 0.04651 / 3.01 ( 776) hydrogen bonds : angle 3.61995 / 2.54 ( 2244) link_BETA1-4 : bond 0.00356 / 0.18 ( 2) link_BETA1-4 : angle 0.99737 / 0.81 ( 6) link_NAG-ASN : bond 0.00114 / 0.06 ( 4) link_NAG-ASN : angle 1.53496 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.449 Fit side-chains REVERT: B 96 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7418 (ptt180) REVERT: B 379 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7963 (mp0) REVERT: B 394 LEU cc_start: 0.8171 (mt) cc_final: 0.7746 (mp) REVERT: B 399 ASP cc_start: 0.7975 (p0) cc_final: 0.7619 (m-30) REVERT: B 433 LYS cc_start: 0.7414 (mttt) cc_final: 0.7164 (mttp) REVERT: B 490 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7854 (tt0) REVERT: B 530 MET cc_start: 0.6760 (tpt) cc_final: 0.6486 (tpp) REVERT: B 715 GLU cc_start: 0.8088 (pm20) cc_final: 0.7812 (pm20) REVERT: B 748 MET cc_start: 0.6607 (mmm) cc_final: 0.6387 (mmm) REVERT: A 379 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7592 (mp0) REVERT: A 438 LEU cc_start: 0.8098 (mt) cc_final: 0.7808 (mt) REVERT: A 575 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8423 (tp) outliers start: 22 outliers final: 13 residues processed: 185 average time/residue: 0.0971 time to fit residues: 26.9056 Evaluate side-chains 166 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 764 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 ASN B 629 ASN A 85 ASN A 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118326 restraints weight = 17147.543| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.28 r_work: 0.3197 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12502 Z= 0.116 Angle : 0.532 8.971 16940 Z= 0.270 Chirality : 0.038 0.140 1912 Planarity : 0.004 0.043 2070 Dihedral : 6.116 53.277 1736 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.28 % Allowed : 12.31 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.23), residues: 1438 helix: 1.94 (0.16), residues: 1052 sheet: -1.61 (0.60), residues: 64 loop : -2.33 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.011 0.001 TYR B 449 PHE 0.031 0.001 PHE A 429 TRP 0.005 0.001 TRP B 664 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (12496) covalent geometry : angle 0.53006 / 0.27 (16922) hydrogen bonds : bond 0.04645 / 3.01 ( 776) hydrogen bonds : angle 3.56845 / 2.50 ( 2244) link_BETA1-4 : bond 0.00319 / 0.17 ( 2) link_BETA1-4 : angle 0.97600 / 0.77 ( 6) link_NAG-ASN : bond 0.00100 / 0.05 ( 4) link_NAG-ASN : angle 1.49615 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 96 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7442 (ptt180) REVERT: B 212 ASP cc_start: 0.8319 (t0) cc_final: 0.8015 (t0) REVERT: B 362 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7816 (mtt90) REVERT: B 379 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7991 (mp0) REVERT: B 394 LEU cc_start: 0.8224 (mt) cc_final: 0.7819 (mp) REVERT: B 399 ASP cc_start: 0.7902 (p0) cc_final: 0.7464 (m-30) REVERT: B 433 LYS cc_start: 0.7473 (mttt) cc_final: 0.7220 (mttp) REVERT: B 490 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7880 (tt0) REVERT: B 530 MET cc_start: 0.6901 (tpt) cc_final: 0.6638 (tpp) REVERT: B 715 GLU cc_start: 0.8094 (pm20) cc_final: 0.7823 (pm20) REVERT: A 182 VAL cc_start: 0.8754 (t) cc_final: 0.8539 (t) REVERT: A 379 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7657 (mp0) REVERT: A 438 LEU cc_start: 0.8031 (mt) cc_final: 0.7757 (mt) REVERT: A 575 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8460 (tp) outliers start: 30 outliers final: 16 residues processed: 184 average time/residue: 0.0837 time to fit residues: 23.9006 Evaluate side-chains 169 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 764 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.151020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111653 restraints weight = 17378.709| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.12 r_work: 0.2976 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12502 Z= 0.165 Angle : 0.571 7.585 16940 Z= 0.291 Chirality : 0.041 0.177 1912 Planarity : 0.004 0.041 2070 Dihedral : 6.210 57.038 1736 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.43 % Allowed : 12.54 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1438 helix: 1.99 (0.16), residues: 1050 sheet: -1.54 (0.61), residues: 64 loop : -2.28 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 203 TYR 0.014 0.001 TYR A 625 PHE 0.017 0.002 PHE B 247 TRP 0.005 0.001 TRP B 458 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (12496) covalent geometry : angle 0.56922 / 0.29 (16922) hydrogen bonds : bond 0.05598 / 3.64 ( 776) hydrogen bonds : angle 3.73305 / 2.62 ( 2244) link_BETA1-4 : bond 0.00381 / 0.19 ( 2) link_BETA1-4 : angle 1.06501 / 0.85 ( 6) link_NAG-ASN : bond 0.00125 / 0.06 ( 4) link_NAG-ASN : angle 1.59012 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.301 Fit side-chains REVERT: B 96 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7380 (ptt180) REVERT: B 394 LEU cc_start: 0.8127 (mt) cc_final: 0.7912 (mt) REVERT: B 399 ASP cc_start: 0.7928 (p0) cc_final: 0.7589 (m-30) REVERT: B 433 LYS cc_start: 0.7395 (mttt) cc_final: 0.7134 (mttp) REVERT: B 530 MET cc_start: 0.6810 (tpt) cc_final: 0.6578 (tpp) REVERT: B 715 GLU cc_start: 0.8165 (pm20) cc_final: 0.7875 (pm20) REVERT: A 85 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9273 (t0) REVERT: A 182 VAL cc_start: 0.8497 (t) cc_final: 0.8269 (t) REVERT: A 376 SER cc_start: 0.7558 (m) cc_final: 0.7104 (p) REVERT: A 438 LEU cc_start: 0.7992 (mt) cc_final: 0.7718 (mt) REVERT: A 465 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6819 (tpp) REVERT: A 478 TRP cc_start: 0.6667 (m100) cc_final: 0.6433 (m-90) REVERT: A 575 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8328 (tp) outliers start: 32 outliers final: 21 residues processed: 180 average time/residue: 0.0920 time to fit residues: 25.4770 Evaluate side-chains 172 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 764 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114545 restraints weight = 17216.583| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.32 r_work: 0.3185 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12502 Z= 0.112 Angle : 0.527 9.167 16940 Z= 0.266 Chirality : 0.039 0.248 1912 Planarity : 0.004 0.044 2070 Dihedral : 5.963 59.110 1736 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.98 % Allowed : 12.84 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.23), residues: 1438 helix: 2.23 (0.16), residues: 1050 sheet: -1.57 (0.60), residues: 64 loop : -2.26 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.010 0.001 TYR B 449 PHE 0.013 0.001 PHE B 518 TRP 0.006 0.001 TRP B 664 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (12496) covalent geometry : angle 0.52515 / 0.27 (16922) hydrogen bonds : bond 0.04600 / 2.98 ( 776) hydrogen bonds : angle 3.53038 / 2.49 ( 2244) link_BETA1-4 : bond 0.00379 / 0.19 ( 2) link_BETA1-4 : angle 1.01021 / 0.80 ( 6) link_NAG-ASN : bond 0.00118 / 0.06 ( 4) link_NAG-ASN : angle 1.49155 / 1.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.430 Fit side-chains REVERT: B 96 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7417 (ptt180) REVERT: B 376 SER cc_start: 0.8011 (m) cc_final: 0.7801 (p) REVERT: B 394 LEU cc_start: 0.8316 (mt) cc_final: 0.7971 (mt) REVERT: B 399 ASP cc_start: 0.7896 (p0) cc_final: 0.7511 (m-30) REVERT: B 530 MET cc_start: 0.6908 (tpt) cc_final: 0.6658 (tpp) REVERT: B 715 GLU cc_start: 0.8121 (pm20) cc_final: 0.7869 (pm20) REVERT: A 182 VAL cc_start: 0.8621 (t) cc_final: 0.8393 (t) REVERT: A 368 MET cc_start: 0.8739 (mmp) cc_final: 0.8404 (mmm) REVERT: A 376 SER cc_start: 0.7709 (m) cc_final: 0.7310 (p) REVERT: A 438 LEU cc_start: 0.8073 (mt) cc_final: 0.7795 (mt) REVERT: A 458 TRP cc_start: 0.7463 (t-100) cc_final: 0.6987 (t60) REVERT: A 575 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8389 (tp) outliers start: 26 outliers final: 16 residues processed: 182 average time/residue: 0.0917 time to fit residues: 25.4964 Evaluate side-chains 171 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 764 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 128 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 37 optimal weight: 0.0000 chunk 133 optimal weight: 5.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110138 restraints weight = 17142.096| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.26 r_work: 0.3103 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12502 Z= 0.108 Angle : 0.512 7.695 16940 Z= 0.261 Chirality : 0.038 0.146 1912 Planarity : 0.004 0.043 2070 Dihedral : 5.820 59.500 1736 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.82 % Allowed : 13.45 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.23), residues: 1438 helix: 2.34 (0.16), residues: 1050 sheet: -1.49 (0.60), residues: 64 loop : -2.19 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.010 0.001 TYR B 449 PHE 0.022 0.001 PHE B 429 TRP 0.009 0.001 TRP A 420 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (12496) covalent geometry : angle 0.51064 / 0.26 (16922) hydrogen bonds : bond 0.04381 / 2.84 ( 776) hydrogen bonds : angle 3.47263 / 2.45 ( 2244) link_BETA1-4 : bond 0.00414 / 0.21 ( 2) link_BETA1-4 : angle 1.01443 / 0.82 ( 6) link_NAG-ASN : bond 0.00103 / 0.05 ( 4) link_NAG-ASN : angle 1.41579 / 1.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: B 96 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7424 (ptt180) REVERT: B 158 MET cc_start: 0.8372 (mmt) cc_final: 0.8083 (mmm) REVERT: B 376 SER cc_start: 0.7945 (m) cc_final: 0.7701 (p) REVERT: B 394 LEU cc_start: 0.8297 (mt) cc_final: 0.7949 (mt) REVERT: B 399 ASP cc_start: 0.7956 (p0) cc_final: 0.7595 (m-30) REVERT: B 530 MET cc_start: 0.6718 (tpt) cc_final: 0.6440 (tpp) REVERT: B 715 GLU cc_start: 0.8108 (pm20) cc_final: 0.7802 (pm20) REVERT: A 182 VAL cc_start: 0.8548 (t) cc_final: 0.8320 (t) REVERT: A 368 MET cc_start: 0.8704 (mmp) cc_final: 0.8394 (mmm) REVERT: A 376 SER cc_start: 0.7658 (m) cc_final: 0.7251 (p) REVERT: A 438 LEU cc_start: 0.8067 (mt) cc_final: 0.7794 (mt) outliers start: 24 outliers final: 19 residues processed: 179 average time/residue: 0.0860 time to fit residues: 23.9152 Evaluate side-chains 173 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 764 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108870 restraints weight = 17218.826| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.34 r_work: 0.3110 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12502 Z= 0.112 Angle : 0.531 11.572 16940 Z= 0.267 Chirality : 0.039 0.253 1912 Planarity : 0.004 0.043 2070 Dihedral : 5.683 56.993 1736 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.05 % Allowed : 13.60 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.23), residues: 1438 helix: 2.39 (0.16), residues: 1050 sheet: -1.47 (0.59), residues: 64 loop : -2.14 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.017 0.001 TYR B 449 PHE 0.040 0.001 PHE B 429 TRP 0.007 0.001 TRP A 420 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (12496) covalent geometry : angle 0.53006 / 0.27 (16922) hydrogen bonds : bond 0.04406 / 2.86 ( 776) hydrogen bonds : angle 3.47402 / 2.45 ( 2244) link_BETA1-4 : bond 0.00392 / 0.20 ( 2) link_BETA1-4 : angle 0.99906 / 0.81 ( 6) link_NAG-ASN : bond 0.00088 / 0.05 ( 4) link_NAG-ASN : angle 1.38206 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: B 96 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7367 (ptt180) REVERT: B 376 SER cc_start: 0.7934 (m) cc_final: 0.7684 (p) REVERT: B 394 LEU cc_start: 0.8285 (mt) cc_final: 0.8021 (mt) REVERT: B 399 ASP cc_start: 0.7950 (p0) cc_final: 0.7587 (m-30) REVERT: B 490 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7788 (tt0) REVERT: B 530 MET cc_start: 0.6739 (tpt) cc_final: 0.6460 (tpp) REVERT: B 630 ASN cc_start: 0.8740 (m-40) cc_final: 0.8518 (m110) REVERT: B 715 GLU cc_start: 0.8063 (pm20) cc_final: 0.7736 (pm20) REVERT: B 725 LEU cc_start: 0.6392 (mm) cc_final: 0.5632 (tp) REVERT: B 766 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7487 (ptmt) REVERT: A 182 VAL cc_start: 0.8518 (t) cc_final: 0.8282 (t) REVERT: A 368 MET cc_start: 0.8671 (mmp) cc_final: 0.8381 (mmm) REVERT: A 376 SER cc_start: 0.7662 (m) cc_final: 0.7276 (p) REVERT: A 438 LEU cc_start: 0.8061 (mt) cc_final: 0.7784 (mt) outliers start: 27 outliers final: 23 residues processed: 179 average time/residue: 0.0845 time to fit residues: 23.2383 Evaluate side-chains 177 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 764 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 100 optimal weight: 0.0970 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110470 restraints weight = 17304.923| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.04 r_work: 0.3079 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12502 Z= 0.112 Angle : 0.528 10.435 16940 Z= 0.266 Chirality : 0.039 0.308 1912 Planarity : 0.004 0.043 2070 Dihedral : 5.593 53.867 1736 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.82 % Allowed : 13.68 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.23), residues: 1438 helix: 2.42 (0.16), residues: 1050 sheet: -1.42 (0.59), residues: 64 loop : -2.11 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 699 TYR 0.015 0.001 TYR B 449 PHE 0.035 0.001 PHE B 429 TRP 0.006 0.001 TRP A 420 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (12496) covalent geometry : angle 0.52673 / 0.27 (16922) hydrogen bonds : bond 0.04383 / 2.84 ( 776) hydrogen bonds : angle 3.47778 / 2.45 ( 2244) link_BETA1-4 : bond 0.00375 / 0.19 ( 2) link_BETA1-4 : angle 0.99929 / 0.81 ( 6) link_NAG-ASN : bond 0.00084 / 0.04 ( 4) link_NAG-ASN : angle 1.37477 / 1.11 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: B 96 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7470 (ptt180) REVERT: B 394 LEU cc_start: 0.8318 (mt) cc_final: 0.8054 (mt) REVERT: B 399 ASP cc_start: 0.8017 (p0) cc_final: 0.7612 (m-30) REVERT: B 490 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7852 (tt0) REVERT: B 530 MET cc_start: 0.6756 (tpt) cc_final: 0.6471 (tpp) REVERT: B 630 ASN cc_start: 0.8743 (m-40) cc_final: 0.8525 (m110) REVERT: B 715 GLU cc_start: 0.8114 (pm20) cc_final: 0.7743 (pm20) REVERT: B 725 LEU cc_start: 0.6257 (mm) cc_final: 0.5457 (tp) REVERT: B 766 LYS cc_start: 0.8143 (ptpt) cc_final: 0.7553 (ptmt) REVERT: A 182 VAL cc_start: 0.8613 (t) cc_final: 0.8372 (t) REVERT: A 368 MET cc_start: 0.8690 (mmp) cc_final: 0.8426 (mmm) REVERT: A 376 SER cc_start: 0.7753 (m) cc_final: 0.7355 (p) REVERT: A 438 LEU cc_start: 0.8079 (mt) cc_final: 0.7806 (mt) REVERT: A 530 MET cc_start: 0.7783 (mmm) cc_final: 0.7524 (tpp) outliers start: 24 outliers final: 23 residues processed: 175 average time/residue: 0.0841 time to fit residues: 22.6371 Evaluate side-chains 177 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 764 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 764 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 419 HIS A 591 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102941 restraints weight = 17339.934| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.00 r_work: 0.3028 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12502 Z= 0.156 Angle : 0.571 9.180 16940 Z= 0.290 Chirality : 0.041 0.287 1912 Planarity : 0.004 0.041 2070 Dihedral : 5.715 49.838 1736 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.13 % Allowed : 13.30 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.23), residues: 1438 helix: 2.27 (0.16), residues: 1052 sheet: -1.41 (0.58), residues: 64 loop : -2.02 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 699 TYR 0.014 0.001 TYR A 625 PHE 0.036 0.001 PHE B 429 TRP 0.006 0.001 TRP B 458 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (12496) covalent geometry : angle 0.56963 / 0.29 (16922) hydrogen bonds : bond 0.05377 / 3.49 ( 776) hydrogen bonds : angle 3.65403 / 2.57 ( 2244) link_BETA1-4 : bond 0.00373 / 0.18 ( 2) link_BETA1-4 : angle 1.05169 / 0.83 ( 6) link_NAG-ASN : bond 0.00065 / 0.03 ( 4) link_NAG-ASN : angle 1.52083 / 1.24 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3043.66 seconds wall clock time: 52 minutes 43.00 seconds (3163.00 seconds total)