Starting phenix.real_space_refine on Sat Aug 23 12:57:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c96_7434/08_2025/6c96_7434.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c96_7434/08_2025/6c96_7434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c96_7434/08_2025/6c96_7434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c96_7434/08_2025/6c96_7434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c96_7434/08_2025/6c96_7434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c96_7434/08_2025/6c96_7434.map" } resolution = 3.4 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 S 76 5.16 5 Na 2 4.78 5 C 7960 2.51 5 N 1978 2.21 5 O 2074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 12090 Number of models: 1 Model: "" Number of chains: 6 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: "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: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' NA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.27, per 1000 atoms: 0.27 Number of scatterers: 12090 At special positions: 0 Unit cell: (131.61, 105.93, 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 Na 2 11.00 O 2074 8.00 N 1978 7.00 C 7960 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 A 600 " " NAG D 1 " - " ASN B 600 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 551.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 70 helices and 4 sheets defined 75.0% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 66 through 84 removed outlier: 3.784A pdb=" N GLY A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 4.007A pdb=" N LEU A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 123 removed outlier: 3.510A pdb=" N TYR A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 removed outlier: 3.812A pdb=" N GLU A 127 " --> pdb=" O SER A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 137 through 163 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 171 through 195 removed outlier: 3.772A pdb=" N MET A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 206 through 212 removed outlier: 4.028A pdb=" N LEU A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.548A pdb=" N SER A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 256 removed outlier: 4.351A pdb=" N ILE A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.965A pdb=" N THR A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.617A pdb=" N MET A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 4.010A pdb=" N ARG A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.917A pdb=" N PHE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 350 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 376 through 387 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 441 through 466 removed outlier: 3.883A pdb=" N GLN A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 450 " --> pdb=" O TYR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 499 removed outlier: 3.625A pdb=" N VAL A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 507 through 527 removed outlier: 3.673A pdb=" N PHE A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.801A pdb=" N PHE A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 550 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 564 removed outlier: 3.645A pdb=" N ARG A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 588 Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.533A pdb=" N ASN A 617 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 618' Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.790A pdb=" N ASN A 629 " --> pdb=" O TYR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 removed outlier: 3.762A pdb=" N VAL A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 removed outlier: 4.460A pdb=" N ILE A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 698 removed outlier: 4.137A pdb=" N PHE A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 removed outlier: 3.675A pdb=" N LEU A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 752 removed outlier: 3.826A pdb=" N VAL A 738 " --> pdb=" O THR A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 774 Processing helix chain 'A' and resid 777 through 791 Processing helix chain 'B' and resid 67 through 84 removed outlier: 3.784A pdb=" N GLY B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 removed outlier: 4.007A pdb=" N LEU B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.508A pdb=" N TYR B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 removed outlier: 3.811A pdb=" N GLU B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 127' Processing helix chain 'B' and resid 137 through 163 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 171 through 195 removed outlier: 3.772A pdb=" N MET B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 206 through 212 removed outlier: 4.029A pdb=" N LEU B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 229 removed outlier: 3.548A pdb=" N SER B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 256 removed outlier: 4.352A pdb=" N ILE B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.964A pdb=" N THR B 279 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 294 removed outlier: 3.616A pdb=" N MET B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 4.010A pdb=" N ARG B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 309 removed outlier: 3.917A pdb=" N PHE B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 350 Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'B' and resid 376 through 387 Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 441 through 466 removed outlier: 3.884A pdb=" N GLN B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 499 removed outlier: 3.625A pdb=" N VAL B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 505 Processing helix chain 'B' and resid 507 through 527 removed outlier: 3.673A pdb=" N PHE B 511 " --> pdb=" O GLY B 507 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 550 removed outlier: 3.803A pdb=" N PHE B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 550 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 removed outlier: 3.645A pdb=" N ARG B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 588 Processing helix chain 'B' and resid 614 through 618 removed outlier: 3.532A pdb=" N ASN B 617 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 614 through 618' Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.790A pdb=" N ASN B 629 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 removed outlier: 3.762A pdb=" N VAL B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 659 removed outlier: 4.461A pdb=" N ILE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 698 removed outlier: 4.137A pdb=" N PHE B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 732 removed outlier: 3.675A pdb=" N LEU B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 752 removed outlier: 3.826A pdb=" N VAL B 738 " --> pdb=" O THR B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 774 Processing helix chain 'B' and resid 777 through 791 Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA2, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA4, first strand: chain 'B' and resid 610 through 613 773 hydrogen bonds defined for protein. 2241 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: 1.64 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3562 1.34 - 1.45: 2387 1.45 - 1.57: 6317 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 12402 Sorted by residual: bond pdb=" CB ASN A 222 " pdb=" CG ASN A 222 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.19e+00 bond pdb=" CB ASN B 222 " pdb=" CG ASN B 222 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.09e+00 bond pdb=" CG1 ILE A 236 " pdb=" CD1 ILE A 236 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.14e+00 bond pdb=" CG1 ILE B 236 " pdb=" CD1 ILE B 236 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.09e+00 bond pdb=" C1 NAG A1003 " pdb=" O5 NAG A1003 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 ... (remaining 12397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 15753 1.95 - 3.89: 867 3.89 - 5.84: 116 5.84 - 7.78: 37 7.78 - 9.73: 19 Bond angle restraints: 16792 Sorted by residual: angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 112.83 107.38 5.45 9.90e-01 1.02e+00 3.04e+01 angle pdb=" N VAL B 201 " pdb=" CA VAL B 201 " pdb=" C VAL B 201 " ideal model delta sigma weight residual 112.83 107.39 5.44 9.90e-01 1.02e+00 3.02e+01 angle pdb=" CA THR B 619 " pdb=" CB THR B 619 " pdb=" CG2 THR B 619 " ideal model delta sigma weight residual 110.50 117.76 -7.26 1.70e+00 3.46e-01 1.82e+01 angle pdb=" CA THR A 619 " pdb=" CB THR A 619 " pdb=" CG2 THR A 619 " ideal model delta sigma weight residual 110.50 117.73 -7.23 1.70e+00 3.46e-01 1.81e+01 angle pdb=" CA ARG B 355 " pdb=" CB ARG B 355 " pdb=" CG ARG B 355 " ideal model delta sigma weight residual 114.10 121.91 -7.81 2.00e+00 2.50e-01 1.52e+01 ... (remaining 16787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 6862 15.13 - 30.25: 396 30.25 - 45.38: 102 45.38 - 60.51: 6 60.51 - 75.63: 4 Dihedral angle restraints: 7370 sinusoidal: 3066 harmonic: 4304 Sorted by residual: dihedral pdb=" CA THR B 645 " pdb=" C THR B 645 " pdb=" N VAL B 646 " pdb=" CA VAL B 646 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA THR A 645 " pdb=" C THR A 645 " pdb=" N VAL A 646 " pdb=" CA VAL A 646 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+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 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 7367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1172 0.050 - 0.101: 541 0.101 - 0.151: 150 0.151 - 0.201: 25 0.201 - 0.251: 10 Chirality restraints: 1898 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.32e+00 chirality pdb=" CA THR A 619 " pdb=" N THR A 619 " pdb=" C THR A 619 " pdb=" CB THR A 619 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA THR B 619 " pdb=" N THR B 619 " pdb=" C THR B 619 " pdb=" CB THR B 619 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1895 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 355 " 0.043 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A 356 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 355 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO B 356 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 356 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 356 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 128 " -0.042 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 129 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.036 5.00e-02 4.00e+02 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3381 2.80 - 3.33: 11053 3.33 - 3.85: 18816 3.85 - 4.38: 21201 4.38 - 4.90: 36317 Nonbonded interactions: 90768 Sorted by model distance: nonbonded pdb=" OE1 GLU B 623 " pdb=" OH TYR B 627 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU A 623 " pdb=" OH TYR A 627 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 480 " pdb=" O ALA A 519 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR B 480 " pdb=" O ALA B 519 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP A 326 " pdb=" NH1 ARG B 699 " model vdw 2.318 3.120 ... (remaining 90763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 66 through 1003) selection = chain 'B' } 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: 0.820 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.880 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.010 0.090 12408 Z= 0.398 Angle : 1.051 9.725 16810 Z= 0.564 Chirality : 0.061 0.251 1898 Planarity : 0.007 0.063 2066 Dihedral : 10.434 75.633 4582 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.30 % Allowed : 3.04 % Favored : 96.66 % 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 aren not related in a simple way. whole: -4.38 (0.17), residues: 1438 helix: -2.62 (0.11), residues: 1042 sheet: -2.73 (0.66), residues: 40 loop : -3.09 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 666 TYR 0.043 0.004 TYR A 110 PHE 0.028 0.003 PHE B 638 TRP 0.024 0.003 TRP A 508 HIS 0.010 0.002 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00953 (12402) covalent geometry : angle 1.04977 (16792) hydrogen bonds : bond 0.18483 ( 773) hydrogen bonds : angle 7.27473 ( 2241) link_BETA1-4 : bond 0.00287 ( 2) link_BETA1-4 : angle 1.90561 ( 6) link_NAG-ASN : bond 0.00541 ( 4) link_NAG-ASN : angle 1.97530 ( 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 317 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 313 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8257 (t0) cc_final: 0.7954 (t0) REVERT: A 111 MET cc_start: 0.8333 (tpp) cc_final: 0.8026 (tpp) REVERT: A 153 VAL cc_start: 0.9232 (t) cc_final: 0.9008 (t) REVERT: A 347 TYR cc_start: 0.8665 (t80) cc_final: 0.7821 (t80) REVERT: A 399 ASP cc_start: 0.7753 (m-30) cc_final: 0.7523 (m-30) REVERT: A 440 ASN cc_start: 0.8353 (t0) cc_final: 0.7703 (m110) REVERT: A 458 TRP cc_start: 0.8268 (t-100) cc_final: 0.7886 (t-100) REVERT: A 515 VAL cc_start: 0.9056 (t) cc_final: 0.8804 (m) REVERT: B 106 ASN cc_start: 0.8087 (t0) cc_final: 0.7669 (t0) REVERT: B 123 LEU cc_start: 0.8933 (tt) cc_final: 0.8672 (tt) REVERT: B 144 LEU cc_start: 0.8948 (mt) cc_final: 0.8640 (mt) REVERT: B 150 MET cc_start: 0.8133 (tpt) cc_final: 0.7850 (tpp) REVERT: B 224 ARG cc_start: 0.7999 (ptm-80) cc_final: 0.7761 (ptp-170) REVERT: B 226 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8742 (mt) REVERT: B 347 TYR cc_start: 0.8852 (t80) cc_final: 0.8580 (t80) REVERT: B 440 ASN cc_start: 0.8186 (t0) cc_final: 0.7476 (m110) REVERT: B 458 TRP cc_start: 0.8305 (t-100) cc_final: 0.7952 (t-100) REVERT: B 726 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8317 (tp30) outliers start: 4 outliers final: 0 residues processed: 315 average time/residue: 0.1108 time to fit residues: 50.2354 Evaluate side-chains 181 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 222 ASN A 314 ASN A 388 ASN A 509 ASN A 591 ASN A 636 ASN A 785 HIS B 222 ASN B 314 ASN B 388 ASN B 509 ASN B 636 ASN B 785 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096983 restraints weight = 22859.248| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.64 r_work: 0.3082 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12408 Z= 0.149 Angle : 0.647 9.200 16810 Z= 0.338 Chirality : 0.041 0.208 1898 Planarity : 0.005 0.045 2066 Dihedral : 5.174 51.171 1728 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.60 % Allowed : 11.25 % Favored : 87.16 % 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 aren not related in a simple way. whole: -1.64 (0.21), residues: 1438 helix: -0.42 (0.15), residues: 1082 sheet: -1.83 (0.58), residues: 60 loop : -3.00 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 417 TYR 0.022 0.002 TYR B 487 PHE 0.021 0.001 PHE A 89 TRP 0.021 0.001 TRP A 650 HIS 0.009 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00297 (12402) covalent geometry : angle 0.64474 (16792) hydrogen bonds : bond 0.06546 ( 773) hydrogen bonds : angle 4.50275 ( 2241) link_BETA1-4 : bond 0.00416 ( 2) link_BETA1-4 : angle 1.70115 ( 6) link_NAG-ASN : bond 0.00312 ( 4) link_NAG-ASN : angle 1.68005 ( 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 257 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7836 (ttm) cc_final: 0.7547 (ttt) REVERT: A 111 MET cc_start: 0.8628 (tpp) cc_final: 0.8423 (tpp) REVERT: A 175 MET cc_start: 0.8799 (mmt) cc_final: 0.8494 (mmt) REVERT: A 226 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8758 (pt) REVERT: A 238 LEU cc_start: 0.8722 (tp) cc_final: 0.8484 (mm) REVERT: A 347 TYR cc_start: 0.8575 (t80) cc_final: 0.7896 (t80) REVERT: A 399 ASP cc_start: 0.8150 (m-30) cc_final: 0.7698 (p0) REVERT: A 405 GLU cc_start: 0.8567 (pm20) cc_final: 0.8306 (mp0) REVERT: A 440 ASN cc_start: 0.8318 (t0) cc_final: 0.7489 (m110) REVERT: A 458 TRP cc_start: 0.8186 (t-100) cc_final: 0.7877 (t-100) REVERT: A 588 GLU cc_start: 0.7496 (tp30) cc_final: 0.7180 (tp30) REVERT: B 111 MET cc_start: 0.8918 (tpp) cc_final: 0.8545 (tpp) REVERT: B 113 GLU cc_start: 0.8526 (tt0) cc_final: 0.8128 (mt-10) REVERT: B 144 LEU cc_start: 0.8801 (mt) cc_final: 0.8487 (mt) REVERT: B 150 MET cc_start: 0.8385 (tpt) cc_final: 0.8058 (tpp) REVERT: B 224 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.7996 (ptp-170) REVERT: B 440 ASN cc_start: 0.8124 (t0) cc_final: 0.7209 (m110) REVERT: B 445 GLN cc_start: 0.9025 (mt0) cc_final: 0.8738 (mp10) REVERT: B 458 TRP cc_start: 0.8243 (t-100) cc_final: 0.7824 (t-100) REVERT: B 490 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8031 (pp20) REVERT: B 726 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8466 (tp30) outliers start: 21 outliers final: 10 residues processed: 243 average time/residue: 0.0939 time to fit residues: 35.3368 Evaluate side-chains 200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 0.0000 chunk 85 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096131 restraints weight = 23131.582| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.60 r_work: 0.3072 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12408 Z= 0.138 Angle : 0.592 11.447 16810 Z= 0.305 Chirality : 0.041 0.147 1898 Planarity : 0.004 0.045 2066 Dihedral : 4.653 49.772 1728 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.28 % Allowed : 13.30 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.22), residues: 1438 helix: 0.51 (0.16), residues: 1062 sheet: -1.42 (0.56), residues: 64 loop : -2.59 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 699 TYR 0.013 0.002 TYR A 110 PHE 0.021 0.001 PHE B 483 TRP 0.007 0.001 TRP A 650 HIS 0.008 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00295 (12402) covalent geometry : angle 0.59006 (16792) hydrogen bonds : bond 0.05699 ( 773) hydrogen bonds : angle 4.12249 ( 2241) link_BETA1-4 : bond 0.00316 ( 2) link_BETA1-4 : angle 1.45958 ( 6) link_NAG-ASN : bond 0.00112 ( 4) link_NAG-ASN : angle 1.72320 ( 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 234 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 119 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8638 (tp) REVERT: A 146 LEU cc_start: 0.8546 (mp) cc_final: 0.8278 (mp) REVERT: A 175 MET cc_start: 0.8821 (mmt) cc_final: 0.8432 (mmt) REVERT: A 238 LEU cc_start: 0.8762 (tp) cc_final: 0.8478 (mm) REVERT: A 313 MET cc_start: 0.8624 (tpp) cc_final: 0.8138 (mmt) REVERT: A 347 TYR cc_start: 0.8524 (t80) cc_final: 0.7767 (t80) REVERT: A 399 ASP cc_start: 0.8114 (m-30) cc_final: 0.7715 (p0) REVERT: A 405 GLU cc_start: 0.8601 (pm20) cc_final: 0.8317 (mp0) REVERT: A 440 ASN cc_start: 0.8499 (t0) cc_final: 0.7608 (m110) REVERT: A 458 TRP cc_start: 0.8120 (t-100) cc_final: 0.7893 (t-100) REVERT: A 462 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8646 (tm-30) REVERT: A 493 MET cc_start: 0.8858 (ttm) cc_final: 0.8485 (ttp) REVERT: A 588 GLU cc_start: 0.7848 (tp30) cc_final: 0.7433 (tp30) REVERT: A 748 MET cc_start: 0.4178 (ptp) cc_final: 0.3924 (ptp) REVERT: B 111 MET cc_start: 0.8907 (tpp) cc_final: 0.8629 (tpp) REVERT: B 119 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8678 (tp) REVERT: B 150 MET cc_start: 0.8309 (tpt) cc_final: 0.8051 (tpp) REVERT: B 175 MET cc_start: 0.8531 (mmt) cc_final: 0.8307 (mmt) REVERT: B 224 ARG cc_start: 0.8353 (ptm-80) cc_final: 0.8048 (ptp-170) REVERT: B 226 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8904 (mt) REVERT: B 382 LEU cc_start: 0.8566 (mm) cc_final: 0.8254 (mp) REVERT: B 440 ASN cc_start: 0.8332 (t0) cc_final: 0.7371 (m110) REVERT: B 458 TRP cc_start: 0.8232 (t-100) cc_final: 0.7920 (t-100) REVERT: B 462 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8540 (tm-30) REVERT: B 670 MET cc_start: 0.8832 (mtt) cc_final: 0.8560 (mtt) REVERT: B 719 GLU cc_start: 0.8075 (pm20) cc_final: 0.7757 (pm20) REVERT: B 728 TYR cc_start: 0.5219 (m-80) cc_final: 0.4972 (m-80) outliers start: 30 outliers final: 15 residues processed: 219 average time/residue: 0.0900 time to fit residues: 30.6290 Evaluate side-chains 190 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 344 GLN B 789 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.131352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095026 restraints weight = 23012.545| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.58 r_work: 0.3060 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12408 Z= 0.147 Angle : 0.581 10.739 16810 Z= 0.299 Chirality : 0.041 0.179 1898 Planarity : 0.004 0.038 2066 Dihedral : 4.458 50.517 1728 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.66 % Allowed : 14.67 % Favored : 82.67 % 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 aren not related in a simple way. whole: 0.16 (0.23), residues: 1438 helix: 0.93 (0.16), residues: 1066 sheet: -1.44 (0.59), residues: 64 loop : -2.36 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 699 TYR 0.013 0.002 TYR B 310 PHE 0.021 0.001 PHE B 227 TRP 0.005 0.001 TRP A 508 HIS 0.008 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00326 (12402) covalent geometry : angle 0.57908 (16792) hydrogen bonds : bond 0.05467 ( 773) hydrogen bonds : angle 3.95835 ( 2241) link_BETA1-4 : bond 0.00250 ( 2) link_BETA1-4 : angle 1.41004 ( 6) link_NAG-ASN : bond 0.00077 ( 4) link_NAG-ASN : angle 1.68371 ( 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 217 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8157 (t0) cc_final: 0.7803 (t0) REVERT: A 111 MET cc_start: 0.8944 (tpp) cc_final: 0.8676 (tpp) REVERT: A 175 MET cc_start: 0.8821 (mmt) cc_final: 0.8495 (mmt) REVERT: A 238 LEU cc_start: 0.8723 (tp) cc_final: 0.8508 (mm) REVERT: A 313 MET cc_start: 0.8641 (tpp) cc_final: 0.8250 (mmt) REVERT: A 399 ASP cc_start: 0.8121 (m-30) cc_final: 0.7739 (p0) REVERT: A 405 GLU cc_start: 0.8597 (pm20) cc_final: 0.8306 (mp0) REVERT: A 440 ASN cc_start: 0.8486 (t0) cc_final: 0.7638 (m110) REVERT: A 448 MET cc_start: 0.8959 (tpt) cc_final: 0.8744 (tpt) REVERT: A 462 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 493 MET cc_start: 0.8834 (ttm) cc_final: 0.8468 (ttp) REVERT: A 588 GLU cc_start: 0.7896 (tp30) cc_final: 0.7502 (tp30) REVERT: A 748 MET cc_start: 0.4031 (ptp) cc_final: 0.3791 (ptp) REVERT: B 111 MET cc_start: 0.8887 (tpp) cc_final: 0.8646 (tpp) REVERT: B 119 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8705 (tp) REVERT: B 150 MET cc_start: 0.8339 (tpt) cc_final: 0.8112 (tpp) REVERT: B 175 MET cc_start: 0.8601 (mmt) cc_final: 0.8303 (mmt) REVERT: B 224 ARG cc_start: 0.8306 (ptm-80) cc_final: 0.8056 (ptp-170) REVERT: B 382 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8265 (mp) REVERT: B 440 ASN cc_start: 0.8251 (t0) cc_final: 0.7320 (m110) REVERT: B 458 TRP cc_start: 0.8230 (t-100) cc_final: 0.7965 (t-100) REVERT: B 462 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8526 (tm-30) REVERT: B 465 MET cc_start: 0.8905 (tpp) cc_final: 0.8694 (tpp) REVERT: B 719 GLU cc_start: 0.8126 (pm20) cc_final: 0.7787 (pm20) outliers start: 35 outliers final: 22 residues processed: 201 average time/residue: 0.0908 time to fit residues: 28.6111 Evaluate side-chains 195 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 647 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096031 restraints weight = 23143.528| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.58 r_work: 0.3077 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12408 Z= 0.126 Angle : 0.551 10.138 16810 Z= 0.284 Chirality : 0.039 0.164 1898 Planarity : 0.004 0.039 2066 Dihedral : 4.122 18.499 1726 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.43 % Allowed : 15.12 % Favored : 82.45 % 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 aren not related in a simple way. whole: 0.54 (0.23), residues: 1438 helix: 1.22 (0.16), residues: 1068 sheet: -1.30 (0.60), residues: 64 loop : -2.27 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 699 TYR 0.013 0.001 TYR B 487 PHE 0.015 0.001 PHE B 447 TRP 0.006 0.001 TRP A 458 HIS 0.007 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00272 (12402) covalent geometry : angle 0.54929 (16792) hydrogen bonds : bond 0.05053 ( 773) hydrogen bonds : angle 3.77232 ( 2241) link_BETA1-4 : bond 0.00322 ( 2) link_BETA1-4 : angle 1.36396 ( 6) link_NAG-ASN : bond 0.00109 ( 4) link_NAG-ASN : angle 1.56835 ( 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 216 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7940 (ttm) cc_final: 0.7579 (ttt) REVERT: A 111 MET cc_start: 0.8878 (tpp) cc_final: 0.8624 (tpp) REVERT: A 313 MET cc_start: 0.8575 (tpp) cc_final: 0.8208 (mmt) REVERT: A 399 ASP cc_start: 0.8111 (m-30) cc_final: 0.7694 (p0) REVERT: A 405 GLU cc_start: 0.8597 (pm20) cc_final: 0.8311 (mp0) REVERT: A 440 ASN cc_start: 0.8383 (t0) cc_final: 0.7579 (m110) REVERT: A 462 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 493 MET cc_start: 0.8798 (ttm) cc_final: 0.8465 (ttp) REVERT: A 588 GLU cc_start: 0.7890 (tp30) cc_final: 0.7513 (tp30) REVERT: A 670 MET cc_start: 0.8739 (mtt) cc_final: 0.8493 (mtt) REVERT: B 119 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8682 (tp) REVERT: B 175 MET cc_start: 0.8552 (mmt) cc_final: 0.8285 (mmt) REVERT: B 224 ARG cc_start: 0.8363 (ptm-80) cc_final: 0.8087 (ptp-170) REVERT: B 382 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8233 (mp) REVERT: B 440 ASN cc_start: 0.8253 (t0) cc_final: 0.7386 (m110) REVERT: B 458 TRP cc_start: 0.8207 (t-100) cc_final: 0.8004 (t-100) REVERT: B 462 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 490 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8019 (pp20) REVERT: B 670 MET cc_start: 0.8775 (mtt) cc_final: 0.8453 (mtt) REVERT: B 680 MET cc_start: 0.7689 (mmm) cc_final: 0.7486 (mmm) REVERT: B 719 GLU cc_start: 0.8138 (pm20) cc_final: 0.7794 (pm20) outliers start: 32 outliers final: 16 residues processed: 204 average time/residue: 0.0933 time to fit residues: 29.5226 Evaluate side-chains 182 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.128645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091847 restraints weight = 23276.441| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.56 r_work: 0.3009 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12408 Z= 0.212 Angle : 0.621 12.381 16810 Z= 0.320 Chirality : 0.043 0.203 1898 Planarity : 0.004 0.036 2066 Dihedral : 4.190 19.875 1726 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.89 % Allowed : 14.44 % Favored : 82.67 % 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 aren not related in a simple way. whole: 0.55 (0.23), residues: 1438 helix: 1.18 (0.16), residues: 1080 sheet: -1.21 (0.60), residues: 64 loop : -2.25 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 567 TYR 0.018 0.002 TYR B 310 PHE 0.024 0.002 PHE B 227 TRP 0.007 0.001 TRP A 458 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00501 (12402) covalent geometry : angle 0.61881 (16792) hydrogen bonds : bond 0.05728 ( 773) hydrogen bonds : angle 3.95269 ( 2241) link_BETA1-4 : bond 0.00289 ( 2) link_BETA1-4 : angle 1.45290 ( 6) link_NAG-ASN : bond 0.00086 ( 4) link_NAG-ASN : angle 1.76566 ( 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 208 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 TYR cc_start: 0.8396 (t80) cc_final: 0.8177 (t80) REVERT: A 399 ASP cc_start: 0.8112 (m-30) cc_final: 0.7695 (p0) REVERT: A 440 ASN cc_start: 0.8365 (t0) cc_final: 0.7553 (m110) REVERT: A 462 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8508 (tm-30) REVERT: A 493 MET cc_start: 0.8886 (ttm) cc_final: 0.8528 (ttp) REVERT: B 175 MET cc_start: 0.8671 (mmt) cc_final: 0.8398 (mmt) REVERT: B 224 ARG cc_start: 0.8454 (ptm-80) cc_final: 0.8152 (ptp-170) REVERT: B 310 TYR cc_start: 0.8346 (t80) cc_final: 0.7999 (t80) REVERT: B 382 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8232 (mp) REVERT: B 440 ASN cc_start: 0.8270 (t0) cc_final: 0.7386 (m110) REVERT: B 458 TRP cc_start: 0.8235 (t-100) cc_final: 0.8015 (t-100) REVERT: B 462 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 490 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8037 (pp20) REVERT: B 719 GLU cc_start: 0.8166 (pm20) cc_final: 0.7799 (pm20) REVERT: B 728 TYR cc_start: 0.5394 (m-80) cc_final: 0.5145 (m-80) outliers start: 38 outliers final: 28 residues processed: 193 average time/residue: 0.0917 time to fit residues: 27.3759 Evaluate side-chains 190 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.0030 chunk 123 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095946 restraints weight = 23027.591| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.54 r_work: 0.3071 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12408 Z= 0.120 Angle : 0.565 12.559 16810 Z= 0.284 Chirality : 0.039 0.165 1898 Planarity : 0.004 0.036 2066 Dihedral : 4.040 19.881 1726 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.98 % Allowed : 15.81 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.23), residues: 1438 helix: 1.41 (0.16), residues: 1076 sheet: -1.10 (0.60), residues: 64 loop : -2.24 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 221 TYR 0.011 0.001 TYR A 487 PHE 0.012 0.001 PHE B 447 TRP 0.007 0.001 TRP A 650 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00246 (12402) covalent geometry : angle 0.56351 (16792) hydrogen bonds : bond 0.04929 ( 773) hydrogen bonds : angle 3.66310 ( 2241) link_BETA1-4 : bond 0.00246 ( 2) link_BETA1-4 : angle 1.32177 ( 6) link_NAG-ASN : bond 0.00171 ( 4) link_NAG-ASN : angle 1.49518 ( 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 206 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8893 (tpp) cc_final: 0.8650 (tpp) REVERT: A 127 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7328 (mp0) REVERT: A 224 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7792 (ttm-80) REVERT: A 310 TYR cc_start: 0.8370 (t80) cc_final: 0.8102 (t80) REVERT: A 313 MET cc_start: 0.8570 (tpp) cc_final: 0.8105 (mmt) REVERT: A 399 ASP cc_start: 0.8080 (m-30) cc_final: 0.7689 (p0) REVERT: A 405 GLU cc_start: 0.8461 (pm20) cc_final: 0.8206 (mp0) REVERT: A 440 ASN cc_start: 0.8357 (t0) cc_final: 0.7592 (m110) REVERT: A 462 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 493 MET cc_start: 0.8797 (ttm) cc_final: 0.8500 (ttp) REVERT: A 728 TYR cc_start: 0.5287 (m-80) cc_final: 0.4896 (m-80) REVERT: B 175 MET cc_start: 0.8503 (mmt) cc_final: 0.8283 (mmt) REVERT: B 224 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.8021 (ttm-80) REVERT: B 310 TYR cc_start: 0.8361 (t80) cc_final: 0.7938 (t80) REVERT: B 382 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8241 (mp) REVERT: B 440 ASN cc_start: 0.8257 (t0) cc_final: 0.7400 (m110) REVERT: B 462 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8545 (tm-30) REVERT: B 490 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8007 (pp20) REVERT: B 670 MET cc_start: 0.8788 (mtt) cc_final: 0.8503 (mtt) REVERT: B 680 MET cc_start: 0.7581 (mmm) cc_final: 0.7351 (mmm) REVERT: B 719 GLU cc_start: 0.8122 (pm20) cc_final: 0.7753 (pm20) REVERT: B 728 TYR cc_start: 0.5405 (m-80) cc_final: 0.5127 (m-80) outliers start: 26 outliers final: 19 residues processed: 199 average time/residue: 0.0990 time to fit residues: 30.0453 Evaluate side-chains 182 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097255 restraints weight = 22946.482| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.60 r_work: 0.3066 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12408 Z= 0.122 Angle : 0.559 12.142 16810 Z= 0.282 Chirality : 0.039 0.180 1898 Planarity : 0.003 0.035 2066 Dihedral : 3.980 19.171 1726 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.36 % Allowed : 15.88 % Favored : 81.76 % 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 aren not related in a simple way. whole: 0.92 (0.23), residues: 1438 helix: 1.47 (0.16), residues: 1078 sheet: -1.07 (0.59), residues: 64 loop : -2.19 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 221 TYR 0.010 0.001 TYR A 487 PHE 0.012 0.001 PHE B 447 TRP 0.006 0.001 TRP A 458 HIS 0.014 0.001 HIS A 785 Details of bonding type rmsd covalent geometry : bond 0.00261 (12402) covalent geometry : angle 0.55730 (16792) hydrogen bonds : bond 0.04788 ( 773) hydrogen bonds : angle 3.61380 ( 2241) link_BETA1-4 : bond 0.00271 ( 2) link_BETA1-4 : angle 1.35877 ( 6) link_NAG-ASN : bond 0.00113 ( 4) link_NAG-ASN : angle 1.48403 ( 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 195 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8886 (tpp) cc_final: 0.8657 (tpp) REVERT: A 127 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7331 (mp0) REVERT: A 224 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7757 (ttm-80) REVERT: A 310 TYR cc_start: 0.8376 (t80) cc_final: 0.8068 (t80) REVERT: A 313 MET cc_start: 0.8603 (tpp) cc_final: 0.8221 (mmt) REVERT: A 359 ILE cc_start: 0.8626 (mt) cc_final: 0.8426 (mm) REVERT: A 399 ASP cc_start: 0.8103 (m-30) cc_final: 0.7712 (p0) REVERT: A 405 GLU cc_start: 0.8491 (pm20) cc_final: 0.8137 (mp0) REVERT: A 440 ASN cc_start: 0.8419 (t0) cc_final: 0.7650 (m110) REVERT: A 462 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 490 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: A 493 MET cc_start: 0.8859 (ttm) cc_final: 0.8529 (ttp) REVERT: B 224 ARG cc_start: 0.8347 (ptm-80) cc_final: 0.7985 (ttm-80) REVERT: B 310 TYR cc_start: 0.8324 (t80) cc_final: 0.7976 (t80) REVERT: B 382 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 440 ASN cc_start: 0.8302 (t0) cc_final: 0.7434 (m110) REVERT: B 462 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8567 (tm-30) REVERT: B 490 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8011 (pp20) REVERT: B 680 MET cc_start: 0.7336 (mmm) cc_final: 0.7066 (mmm) REVERT: B 719 GLU cc_start: 0.8101 (pm20) cc_final: 0.7798 (pm20) outliers start: 31 outliers final: 19 residues processed: 185 average time/residue: 0.0976 time to fit residues: 27.9253 Evaluate side-chains 183 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN B 792 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094161 restraints weight = 23112.873| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.54 r_work: 0.3048 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12408 Z= 0.151 Angle : 0.594 11.929 16810 Z= 0.298 Chirality : 0.041 0.193 1898 Planarity : 0.003 0.035 2066 Dihedral : 3.973 18.562 1726 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.20 % Allowed : 16.64 % Favored : 81.16 % 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 aren not related in a simple way. whole: 0.91 (0.23), residues: 1438 helix: 1.46 (0.16), residues: 1076 sheet: -1.00 (0.60), residues: 64 loop : -2.20 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 567 TYR 0.012 0.001 TYR B 310 PHE 0.014 0.001 PHE B 447 TRP 0.006 0.001 TRP A 458 HIS 0.012 0.001 HIS A 785 Details of bonding type rmsd covalent geometry : bond 0.00350 (12402) covalent geometry : angle 0.59254 (16792) hydrogen bonds : bond 0.05012 ( 773) hydrogen bonds : angle 3.72050 ( 2241) link_BETA1-4 : bond 0.00226 ( 2) link_BETA1-4 : angle 1.34017 ( 6) link_NAG-ASN : bond 0.00024 ( 4) link_NAG-ASN : angle 1.52008 ( 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 194 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8867 (tpp) cc_final: 0.8664 (tpp) REVERT: A 127 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7244 (mp0) REVERT: A 310 TYR cc_start: 0.8414 (t80) cc_final: 0.8111 (t80) REVERT: A 313 MET cc_start: 0.8649 (tpp) cc_final: 0.8270 (mmt) REVERT: A 349 LEU cc_start: 0.8031 (tp) cc_final: 0.7797 (tp) REVERT: A 399 ASP cc_start: 0.8104 (m-30) cc_final: 0.7723 (p0) REVERT: A 405 GLU cc_start: 0.8479 (pm20) cc_final: 0.8130 (mp0) REVERT: A 440 ASN cc_start: 0.8407 (t0) cc_final: 0.7591 (m110) REVERT: A 462 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8572 (tm-30) REVERT: A 493 MET cc_start: 0.8837 (ttm) cc_final: 0.8505 (ttp) REVERT: B 224 ARG cc_start: 0.8392 (ptm-80) cc_final: 0.8135 (ptp-170) REVERT: B 382 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 440 ASN cc_start: 0.8363 (t0) cc_final: 0.7485 (m110) REVERT: B 462 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8539 (tm-30) REVERT: B 490 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7962 (mm-30) REVERT: B 680 MET cc_start: 0.7427 (mmm) cc_final: 0.7153 (mmm) REVERT: B 719 GLU cc_start: 0.8132 (pm20) cc_final: 0.7791 (pm20) outliers start: 29 outliers final: 21 residues processed: 186 average time/residue: 0.0953 time to fit residues: 27.5169 Evaluate side-chains 181 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 59 optimal weight: 5.9990 chunk 113 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.133306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098427 restraints weight = 23078.817| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.62 r_work: 0.3097 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12408 Z= 0.117 Angle : 0.575 12.324 16810 Z= 0.285 Chirality : 0.039 0.176 1898 Planarity : 0.003 0.034 2066 Dihedral : 3.919 19.593 1726 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.67 % Allowed : 17.33 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.23), residues: 1438 helix: 1.50 (0.16), residues: 1076 sheet: -0.96 (0.60), residues: 64 loop : -2.17 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 221 TYR 0.009 0.001 TYR A 310 PHE 0.012 0.001 PHE B 447 TRP 0.011 0.001 TRP A 650 HIS 0.009 0.001 HIS A 785 Details of bonding type rmsd covalent geometry : bond 0.00240 (12402) covalent geometry : angle 0.57388 (16792) hydrogen bonds : bond 0.04518 ( 773) hydrogen bonds : angle 3.60392 ( 2241) link_BETA1-4 : bond 0.00444 ( 2) link_BETA1-4 : angle 1.28879 ( 6) link_NAG-ASN : bond 0.00164 ( 4) link_NAG-ASN : angle 1.34212 ( 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 205 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7924 (ttm) cc_final: 0.7608 (ttt) REVERT: A 127 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7238 (mp0) REVERT: A 175 MET cc_start: 0.8493 (mmt) cc_final: 0.8133 (mmt) REVERT: A 224 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7652 (ttm-80) REVERT: A 234 MET cc_start: 0.8406 (mmm) cc_final: 0.8131 (mmm) REVERT: A 310 TYR cc_start: 0.8367 (t80) cc_final: 0.8065 (t80) REVERT: A 313 MET cc_start: 0.8523 (tpp) cc_final: 0.8090 (mmt) REVERT: A 349 LEU cc_start: 0.7890 (tp) cc_final: 0.7675 (tp) REVERT: A 405 GLU cc_start: 0.8523 (pm20) cc_final: 0.8112 (mp0) REVERT: A 440 ASN cc_start: 0.8485 (t0) cc_final: 0.7725 (m110) REVERT: A 462 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8604 (tm-30) REVERT: A 719 GLU cc_start: 0.8049 (mp0) cc_final: 0.7674 (pm20) REVERT: B 224 ARG cc_start: 0.8369 (ptm-80) cc_final: 0.8087 (ptp-170) REVERT: B 234 MET cc_start: 0.8423 (mmm) cc_final: 0.8132 (mmm) REVERT: B 310 TYR cc_start: 0.8427 (t80) cc_final: 0.8109 (t80) REVERT: B 382 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8303 (mp) REVERT: B 440 ASN cc_start: 0.8379 (t0) cc_final: 0.7510 (m110) REVERT: B 462 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8563 (tm-30) REVERT: B 680 MET cc_start: 0.7400 (mmm) cc_final: 0.7140 (mmm) REVERT: B 719 GLU cc_start: 0.8166 (pm20) cc_final: 0.7819 (pm20) outliers start: 22 outliers final: 20 residues processed: 197 average time/residue: 0.0938 time to fit residues: 28.5204 Evaluate side-chains 191 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093968 restraints weight = 23046.156| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.77 r_work: 0.3004 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12408 Z= 0.200 Angle : 0.646 14.146 16810 Z= 0.321 Chirality : 0.043 0.196 1898 Planarity : 0.004 0.034 2066 Dihedral : 3.961 18.773 1726 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.98 % Allowed : 17.17 % Favored : 80.85 % 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 aren not related in a simple way. whole: 0.90 (0.23), residues: 1438 helix: 1.41 (0.16), residues: 1076 sheet: -0.93 (0.60), residues: 64 loop : -2.04 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 220 TYR 0.019 0.002 TYR B 625 PHE 0.014 0.001 PHE B 447 TRP 0.008 0.001 TRP A 650 HIS 0.011 0.001 HIS A 785 Details of bonding type rmsd covalent geometry : bond 0.00478 (12402) covalent geometry : angle 0.64410 (16792) hydrogen bonds : bond 0.05246 ( 773) hydrogen bonds : angle 3.82339 ( 2241) link_BETA1-4 : bond 0.00691 ( 2) link_BETA1-4 : angle 1.55342 ( 6) link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 1.60686 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.13 seconds wall clock time: 48 minutes 54.69 seconds (2934.69 seconds total)