Starting phenix.real_space_refine on Wed Jul 30 08:58:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c96_7434/07_2025/6c96_7434.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c96_7434/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6c96_7434/07_2025/6c96_7434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c96_7434/07_2025/6c96_7434.map" model { file = "/net/cci-nas-00/data/ceres_data/6c96_7434/07_2025/6c96_7434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c96_7434/07_2025/6c96_7434.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.25, per 1000 atoms: 0.60 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: 2.77 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.21 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: 3.33 Time building geometry restraints manager: 3.30 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 795 or resid 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: 1.010 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.190 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.003 TRP A 508 HIS 0.010 0.002 HIS B 141 PHE 0.028 0.003 PHE B 638 TYR 0.043 0.004 TYR A 110 ARG 0.011 0.001 ARG B 666 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 4) link_NAG-ASN : angle 1.97530 ( 12) link_BETA1-4 : bond 0.00287 ( 2) link_BETA1-4 : angle 1.90561 ( 6) hydrogen bonds : bond 0.18483 ( 773) hydrogen bonds : angle 7.27473 ( 2241) covalent geometry : bond 0.00953 (12402) covalent geometry : angle 1.04977 (16792) *********************** 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 : 1.341 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: 0.7521 (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: 0.8318 (tp30) outliers start: 4 outliers final: 0 residues processed: 315 average time/residue: 0.2499 time to fit residues: 111.9818 Evaluate side-chains 180 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 121 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.133060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096937 restraints weight = 22668.936| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.63 r_work: 0.3085 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12408 Z= 0.148 Angle : 0.649 9.879 16810 Z= 0.339 Chirality : 0.041 0.176 1898 Planarity : 0.005 0.045 2066 Dihedral : 5.219 51.090 1728 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.60 % Allowed : 11.17 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.21), residues: 1438 helix: -0.42 (0.15), residues: 1082 sheet: -1.82 (0.59), residues: 60 loop : -3.02 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 650 HIS 0.009 0.001 HIS A 141 PHE 0.019 0.001 PHE A 89 TYR 0.022 0.002 TYR B 487 ARG 0.007 0.001 ARG A 699 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 4) link_NAG-ASN : angle 1.66882 ( 12) link_BETA1-4 : bond 0.00203 ( 2) link_BETA1-4 : angle 1.63532 ( 6) hydrogen bonds : bond 0.06606 ( 773) hydrogen bonds : angle 4.52687 ( 2241) covalent geometry : bond 0.00289 (12402) covalent geometry : angle 0.64740 (16792) *********************** 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 252 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7855 (ttm) cc_final: 0.7562 (ttt) REVERT: A 111 MET cc_start: 0.8678 (tpp) cc_final: 0.8441 (tpp) REVERT: A 146 LEU cc_start: 0.8694 (mm) cc_final: 0.8469 (mp) REVERT: A 175 MET cc_start: 0.8801 (mmt) cc_final: 0.8501 (mmt) REVERT: A 238 LEU cc_start: 0.8724 (tp) cc_final: 0.8491 (mm) REVERT: A 347 TYR cc_start: 0.8583 (t80) cc_final: 0.7898 (t80) REVERT: A 399 ASP cc_start: 0.8047 (m-30) cc_final: 0.7643 (p0) REVERT: A 405 GLU cc_start: 0.8556 (pm20) cc_final: 0.8300 (mp0) REVERT: A 440 ASN cc_start: 0.8317 (t0) cc_final: 0.7490 (m110) REVERT: A 458 TRP cc_start: 0.8167 (t-100) cc_final: 0.7850 (t-100) REVERT: A 588 GLU cc_start: 0.7466 (tp30) cc_final: 0.7148 (tp30) REVERT: B 111 MET cc_start: 0.8924 (tpp) cc_final: 0.8555 (tpp) REVERT: B 113 GLU cc_start: 0.8531 (tt0) cc_final: 0.8081 (mt-10) REVERT: B 144 LEU cc_start: 0.8853 (mt) cc_final: 0.8547 (mt) REVERT: B 150 MET cc_start: 0.8380 (tpt) cc_final: 0.8040 (tpp) REVERT: B 224 ARG cc_start: 0.8273 (ptm-80) cc_final: 0.8001 (ptp-170) REVERT: B 226 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8661 (pt) REVERT: B 440 ASN cc_start: 0.8098 (t0) cc_final: 0.7222 (m110) REVERT: B 458 TRP cc_start: 0.8247 (t-100) cc_final: 0.7821 (t-100) REVERT: B 490 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8031 (pp20) REVERT: B 726 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8466 (tp30) outliers start: 21 outliers final: 9 residues processed: 238 average time/residue: 0.1975 time to fit residues: 72.2391 Evaluate side-chains 190 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 133 optimal weight: 0.3980 chunk 125 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.128218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091197 restraints weight = 23320.491| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.59 r_work: 0.2991 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12408 Z= 0.227 Angle : 0.673 11.824 16810 Z= 0.351 Chirality : 0.044 0.176 1898 Planarity : 0.005 0.045 2066 Dihedral : 4.846 50.608 1728 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.72 % Allowed : 12.39 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1438 helix: 0.36 (0.16), residues: 1066 sheet: -1.57 (0.58), residues: 60 loop : -2.53 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 508 HIS 0.008 0.001 HIS B 141 PHE 0.023 0.002 PHE B 483 TYR 0.022 0.002 TYR B 110 ARG 0.005 0.001 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 4) link_NAG-ASN : angle 1.99563 ( 12) link_BETA1-4 : bond 0.00238 ( 2) link_BETA1-4 : angle 1.53814 ( 6) hydrogen bonds : bond 0.06552 ( 773) hydrogen bonds : angle 4.39314 ( 2241) covalent geometry : bond 0.00531 (12402) covalent geometry : angle 0.67067 (16792) *********************** 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 240 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7546 (mt-10) REVERT: A 146 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8361 (mm) REVERT: A 175 MET cc_start: 0.8906 (mmt) cc_final: 0.8533 (mmt) REVERT: A 347 TYR cc_start: 0.8662 (t80) cc_final: 0.7954 (t80) REVERT: A 399 ASP cc_start: 0.8106 (m-30) cc_final: 0.7675 (p0) REVERT: A 440 ASN cc_start: 0.8350 (t0) cc_final: 0.7638 (m110) REVERT: A 448 MET cc_start: 0.8858 (tpt) cc_final: 0.8649 (tpt) REVERT: A 458 TRP cc_start: 0.8229 (t-100) cc_final: 0.7937 (t-100) REVERT: A 462 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8594 (tm-30) REVERT: A 588 GLU cc_start: 0.7854 (tp30) cc_final: 0.7402 (tp30) REVERT: A 728 TYR cc_start: 0.5273 (m-80) cc_final: 0.5073 (m-80) REVERT: A 748 MET cc_start: 0.4069 (ptp) cc_final: 0.3796 (ptp) REVERT: B 146 LEU cc_start: 0.8669 (mm) cc_final: 0.8448 (mm) REVERT: B 150 MET cc_start: 0.8357 (tpt) cc_final: 0.8074 (tpp) REVERT: B 175 MET cc_start: 0.8651 (mmt) cc_final: 0.8396 (mmt) REVERT: B 224 ARG cc_start: 0.8584 (ptm-80) cc_final: 0.8271 (ptp-170) REVERT: B 440 ASN cc_start: 0.8269 (t0) cc_final: 0.7331 (m110) REVERT: B 458 TRP cc_start: 0.8416 (t-100) cc_final: 0.7994 (t-100) REVERT: B 462 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8498 (tm-30) REVERT: B 719 GLU cc_start: 0.8090 (pm20) cc_final: 0.7719 (pm20) REVERT: B 726 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8520 (tp30) outliers start: 49 outliers final: 29 residues processed: 220 average time/residue: 0.2269 time to fit residues: 75.9090 Evaluate side-chains 194 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 146 LEU 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 226 ILE Chi-restraints excluded: chain A residue 322 ASP 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 647 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain B residue 89 PHE 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 202 THR 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 322 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 647 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 344 GLN B 344 GLN B 789 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094944 restraints weight = 22859.653| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.56 r_work: 0.3059 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12408 Z= 0.133 Angle : 0.581 10.867 16810 Z= 0.299 Chirality : 0.040 0.178 1898 Planarity : 0.004 0.037 2066 Dihedral : 4.530 51.015 1728 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.13 % Allowed : 15.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1438 helix: 0.86 (0.16), residues: 1070 sheet: -1.36 (0.59), residues: 64 loop : -2.45 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 650 HIS 0.008 0.001 HIS B 141 PHE 0.012 0.001 PHE B 686 TYR 0.014 0.001 TYR A 487 ARG 0.003 0.000 ARG A 699 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 4) link_NAG-ASN : angle 1.68479 ( 12) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 1.48639 ( 6) hydrogen bonds : bond 0.05492 ( 773) hydrogen bonds : angle 3.97448 ( 2241) covalent geometry : bond 0.00281 (12402) covalent geometry : angle 0.57932 (16792) *********************** 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 214 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8950 (tpp) cc_final: 0.8498 (tpp) REVERT: A 313 MET cc_start: 0.8650 (tpp) cc_final: 0.8161 (mmt) REVERT: A 399 ASP cc_start: 0.8122 (m-30) cc_final: 0.7680 (p0) REVERT: A 405 GLU cc_start: 0.8502 (pm20) cc_final: 0.8170 (mp0) REVERT: A 440 ASN cc_start: 0.8399 (t0) cc_final: 0.7598 (m110) REVERT: A 458 TRP cc_start: 0.8159 (t-100) cc_final: 0.7929 (t-100) REVERT: A 462 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8629 (tm-30) REVERT: A 588 GLU cc_start: 0.7928 (tp30) cc_final: 0.7462 (tp30) REVERT: A 670 MET cc_start: 0.8872 (mtt) cc_final: 0.8642 (mtt) REVERT: A 728 TYR cc_start: 0.5339 (m-80) cc_final: 0.5095 (m-80) REVERT: A 748 MET cc_start: 0.4029 (ptp) cc_final: 0.3776 (ptp) REVERT: B 111 MET cc_start: 0.8928 (tpp) cc_final: 0.8717 (tpp) REVERT: B 146 LEU cc_start: 0.8599 (mm) cc_final: 0.8381 (mm) REVERT: B 150 MET cc_start: 0.8334 (tpt) cc_final: 0.8095 (tpp) REVERT: B 175 MET cc_start: 0.8624 (mmt) cc_final: 0.8339 (mmt) REVERT: B 224 ARG cc_start: 0.8402 (ptm-80) cc_final: 0.8133 (ptp-170) REVERT: B 226 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8922 (pt) REVERT: B 382 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 440 ASN cc_start: 0.8282 (t0) cc_final: 0.7344 (m110) REVERT: B 458 TRP cc_start: 0.8325 (t-100) cc_final: 0.8064 (t-100) REVERT: B 462 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8572 (tm-30) REVERT: B 670 MET cc_start: 0.8881 (mtt) cc_final: 0.8638 (mtt) REVERT: B 719 GLU cc_start: 0.8070 (pm20) cc_final: 0.7706 (pm20) REVERT: B 726 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8515 (tp30) outliers start: 28 outliers final: 14 residues processed: 200 average time/residue: 0.2357 time to fit residues: 73.6736 Evaluate side-chains 187 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 659 SER Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 226 ILE 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 623 GLU Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.132285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097139 restraints weight = 22976.931| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.62 r_work: 0.3079 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12408 Z= 0.121 Angle : 0.553 10.889 16810 Z= 0.283 Chirality : 0.039 0.156 1898 Planarity : 0.004 0.039 2066 Dihedral : 4.322 50.554 1728 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.51 % Allowed : 15.35 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1438 helix: 1.19 (0.16), residues: 1068 sheet: -1.20 (0.60), residues: 64 loop : -2.22 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 650 HIS 0.007 0.001 HIS B 141 PHE 0.024 0.001 PHE B 227 TYR 0.014 0.001 TYR B 310 ARG 0.004 0.000 ARG B 540 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 4) link_NAG-ASN : angle 1.58903 ( 12) link_BETA1-4 : bond 0.00432 ( 2) link_BETA1-4 : angle 1.40586 ( 6) hydrogen bonds : bond 0.04977 ( 773) hydrogen bonds : angle 3.75496 ( 2241) covalent geometry : bond 0.00253 (12402) covalent geometry : angle 0.55064 (16792) *********************** 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 219 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8898 (tpp) cc_final: 0.8618 (tpp) REVERT: A 175 MET cc_start: 0.8706 (mmt) cc_final: 0.8343 (mmt) REVERT: A 313 MET cc_start: 0.8572 (tpp) cc_final: 0.8185 (mmt) REVERT: A 399 ASP cc_start: 0.8094 (m-30) cc_final: 0.7692 (p0) REVERT: A 405 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: A 440 ASN cc_start: 0.8381 (t0) cc_final: 0.7575 (m110) REVERT: A 448 MET cc_start: 0.8918 (tpt) cc_final: 0.8649 (mmt) REVERT: A 458 TRP cc_start: 0.8024 (t-100) cc_final: 0.7744 (t60) REVERT: A 462 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8661 (tm-30) REVERT: A 588 GLU cc_start: 0.7953 (tp30) cc_final: 0.7694 (tp30) REVERT: A 670 MET cc_start: 0.8829 (mtt) cc_final: 0.8517 (mtt) REVERT: A 680 MET cc_start: 0.7554 (mmm) cc_final: 0.7277 (mmm) REVERT: A 728 TYR cc_start: 0.5401 (m-80) cc_final: 0.5100 (m-80) REVERT: B 146 LEU cc_start: 0.8603 (mm) cc_final: 0.8375 (mm) REVERT: B 158 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8772 (mmm) REVERT: B 175 MET cc_start: 0.8572 (mmt) cc_final: 0.8322 (mmt) REVERT: B 202 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8703 (p) REVERT: B 224 ARG cc_start: 0.8417 (ptm-80) cc_final: 0.8109 (ptp-170) REVERT: B 226 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8719 (mt) REVERT: B 382 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 440 ASN cc_start: 0.8270 (t0) cc_final: 0.7370 (m110) REVERT: B 458 TRP cc_start: 0.8218 (t-100) cc_final: 0.8008 (t-100) REVERT: B 462 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8547 (tm-30) REVERT: B 670 MET cc_start: 0.8812 (mtt) cc_final: 0.8518 (mtt) REVERT: B 680 MET cc_start: 0.7705 (mmm) cc_final: 0.7501 (mmm) REVERT: B 719 GLU cc_start: 0.8113 (pm20) cc_final: 0.7779 (pm20) REVERT: B 726 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8478 (tp30) outliers start: 33 outliers final: 17 residues processed: 205 average time/residue: 0.2185 time to fit residues: 67.7884 Evaluate side-chains 190 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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 266 THR Chi-restraints excluded: chain A residue 405 GLU 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 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 158 MET 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 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 Chi-restraints excluded: chain B residue 623 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 118 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 B 792 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096039 restraints weight = 23286.384| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.57 r_work: 0.3081 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3885 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= 0.123 Angle : 0.544 10.240 16810 Z= 0.279 Chirality : 0.039 0.174 1898 Planarity : 0.003 0.036 2066 Dihedral : 4.240 50.686 1728 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.36 % Allowed : 15.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1438 helix: 1.32 (0.16), residues: 1078 sheet: -1.09 (0.60), residues: 64 loop : -2.14 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 650 HIS 0.007 0.001 HIS B 141 PHE 0.014 0.001 PHE B 447 TYR 0.014 0.001 TYR A 487 ARG 0.003 0.000 ARG B 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 4) link_NAG-ASN : angle 1.53630 ( 12) link_BETA1-4 : bond 0.00421 ( 2) link_BETA1-4 : angle 1.37087 ( 6) hydrogen bonds : bond 0.04865 ( 773) hydrogen bonds : angle 3.68030 ( 2241) covalent geometry : bond 0.00267 (12402) covalent geometry : angle 0.54230 (16792) *********************** 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 206 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8858 (tpp) cc_final: 0.8599 (tpp) REVERT: A 310 TYR cc_start: 0.8341 (t80) cc_final: 0.7996 (t80) REVERT: A 313 MET cc_start: 0.8567 (tpp) cc_final: 0.8190 (mmt) REVERT: A 399 ASP cc_start: 0.8106 (m-30) cc_final: 0.7686 (p0) REVERT: A 405 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: A 440 ASN cc_start: 0.8413 (t0) cc_final: 0.7595 (m110) REVERT: A 448 MET cc_start: 0.8969 (tpt) cc_final: 0.8723 (mmt) REVERT: A 458 TRP cc_start: 0.7858 (t-100) cc_final: 0.7624 (t60) REVERT: A 462 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8616 (tm-30) REVERT: A 670 MET cc_start: 0.8837 (mtt) cc_final: 0.8540 (mtt) REVERT: A 680 MET cc_start: 0.7349 (mmm) cc_final: 0.7059 (mmm) REVERT: B 146 LEU cc_start: 0.8582 (mm) cc_final: 0.8363 (mm) REVERT: B 158 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8733 (mmm) REVERT: B 175 MET cc_start: 0.8487 (mmt) cc_final: 0.8252 (mmt) REVERT: B 202 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8775 (p) REVERT: B 224 ARG cc_start: 0.8319 (ptm-80) cc_final: 0.7940 (ttm-80) REVERT: B 382 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8253 (mp) REVERT: B 440 ASN cc_start: 0.8328 (t0) cc_final: 0.7440 (m110) REVERT: B 448 MET cc_start: 0.8725 (mmt) cc_final: 0.8482 (mmt) REVERT: B 462 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8536 (tm-30) REVERT: B 490 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 670 MET cc_start: 0.8785 (mtt) cc_final: 0.8453 (mtt) REVERT: B 680 MET cc_start: 0.7568 (mmm) cc_final: 0.7351 (mmm) REVERT: B 719 GLU cc_start: 0.8157 (pm20) cc_final: 0.7843 (pm20) outliers start: 31 outliers final: 21 residues processed: 193 average time/residue: 0.2126 time to fit residues: 62.4550 Evaluate side-chains 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 297 SER Chi-restraints excluded: chain A residue 405 GLU 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 158 MET 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 Chi-restraints excluded: chain B residue 623 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 11 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 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 A 344 GLN A 789 GLN B 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091844 restraints weight = 22931.921| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.54 r_work: 0.3006 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3881 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= 0.206 Angle : 0.616 13.067 16810 Z= 0.318 Chirality : 0.042 0.205 1898 Planarity : 0.004 0.036 2066 Dihedral : 4.124 19.545 1726 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.12 % Allowed : 14.74 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1438 helix: 1.26 (0.16), residues: 1078 sheet: -1.10 (0.59), residues: 64 loop : -2.17 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 650 HIS 0.007 0.001 HIS B 141 PHE 0.015 0.002 PHE B 447 TYR 0.015 0.002 TYR B 361 ARG 0.005 0.001 ARG B 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 4) link_NAG-ASN : angle 1.72641 ( 12) link_BETA1-4 : bond 0.00263 ( 2) link_BETA1-4 : angle 1.44928 ( 6) hydrogen bonds : bond 0.05653 ( 773) hydrogen bonds : angle 3.92133 ( 2241) covalent geometry : bond 0.00486 (12402) covalent geometry : angle 0.61449 (16792) *********************** 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 209 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7341 (mp0) REVERT: A 175 MET cc_start: 0.8658 (mmt) cc_final: 0.8325 (mmt) REVERT: A 310 TYR cc_start: 0.8408 (t80) cc_final: 0.8176 (t80) REVERT: A 399 ASP cc_start: 0.8121 (m-30) cc_final: 0.7728 (p0) REVERT: A 405 GLU cc_start: 0.8535 (pm20) cc_final: 0.8299 (mp0) REVERT: A 440 ASN cc_start: 0.8384 (t0) cc_final: 0.7558 (m110) REVERT: A 448 MET cc_start: 0.9015 (tpt) cc_final: 0.8772 (mmt) REVERT: A 458 TRP cc_start: 0.7982 (t-100) cc_final: 0.7685 (t60) REVERT: A 462 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8564 (tm-30) REVERT: B 175 MET cc_start: 0.8586 (mmt) cc_final: 0.8330 (mmt) REVERT: B 224 ARG cc_start: 0.8396 (ptm-80) cc_final: 0.8110 (ptp-170) REVERT: B 310 TYR cc_start: 0.8365 (t80) cc_final: 0.8148 (t80) REVERT: B 382 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8288 (mp) REVERT: B 440 ASN cc_start: 0.8302 (t0) cc_final: 0.7414 (m110) REVERT: B 462 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8504 (tm-30) REVERT: B 490 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7871 (mm-30) REVERT: B 719 GLU cc_start: 0.8057 (pm20) cc_final: 0.7663 (pm20) REVERT: B 728 TYR cc_start: 0.5040 (m-80) cc_final: 0.4797 (m-80) outliers start: 41 outliers final: 27 residues processed: 194 average time/residue: 0.2066 time to fit residues: 61.6202 Evaluate side-chains 192 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 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 151 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASN 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 445 GLN Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 623 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 104 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.131886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096799 restraints weight = 23248.975| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.70 r_work: 0.3060 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12408 Z= 0.119 Angle : 0.566 13.089 16810 Z= 0.284 Chirality : 0.039 0.170 1898 Planarity : 0.003 0.035 2066 Dihedral : 3.977 18.419 1726 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.13 % Allowed : 16.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1438 helix: 1.48 (0.16), residues: 1076 sheet: -0.96 (0.60), residues: 64 loop : -2.13 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 650 HIS 0.007 0.001 HIS A 141 PHE 0.014 0.001 PHE B 447 TYR 0.011 0.001 TYR A 487 ARG 0.003 0.000 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 4) link_NAG-ASN : angle 1.47131 ( 12) link_BETA1-4 : bond 0.00391 ( 2) link_BETA1-4 : angle 1.29199 ( 6) hydrogen bonds : bond 0.04872 ( 773) hydrogen bonds : angle 3.63857 ( 2241) covalent geometry : bond 0.00243 (12402) covalent geometry : angle 0.56439 (16792) *********************** 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 210 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8827 (tpp) cc_final: 0.8593 (mmm) REVERT: A 127 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7229 (mp0) REVERT: A 175 MET cc_start: 0.8518 (mmt) cc_final: 0.8168 (mmt) REVERT: A 224 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7746 (ttm-80) REVERT: A 234 MET cc_start: 0.8466 (mmm) cc_final: 0.8176 (mmm) REVERT: A 310 TYR cc_start: 0.8379 (t80) cc_final: 0.8079 (t80) REVERT: A 313 MET cc_start: 0.8534 (tpp) cc_final: 0.8169 (mmt) REVERT: A 399 ASP cc_start: 0.8133 (m-30) cc_final: 0.7722 (p0) REVERT: A 405 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: A 440 ASN cc_start: 0.8382 (t0) cc_final: 0.7575 (m110) REVERT: A 448 MET cc_start: 0.8974 (tpt) cc_final: 0.8714 (mmt) REVERT: A 458 TRP cc_start: 0.7864 (t-100) cc_final: 0.7657 (t60) REVERT: A 462 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8597 (tm-30) REVERT: A 670 MET cc_start: 0.8823 (mtt) cc_final: 0.8533 (mtt) REVERT: A 680 MET cc_start: 0.7352 (mmm) cc_final: 0.7032 (mmm) REVERT: B 127 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7390 (mp0) REVERT: B 146 LEU cc_start: 0.8589 (mm) cc_final: 0.8289 (mm) REVERT: B 202 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8800 (p) REVERT: B 224 ARG cc_start: 0.8391 (ptm-80) cc_final: 0.8116 (ptp-170) REVERT: B 310 TYR cc_start: 0.8339 (t80) cc_final: 0.8068 (t80) REVERT: B 349 LEU cc_start: 0.8215 (tp) cc_final: 0.8001 (tp) REVERT: B 382 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8282 (mp) REVERT: B 440 ASN cc_start: 0.8349 (t0) cc_final: 0.7484 (m110) REVERT: B 462 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8547 (tm-30) REVERT: B 490 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7927 (mm-30) REVERT: B 670 MET cc_start: 0.8801 (mtt) cc_final: 0.8500 (mtt) REVERT: B 680 MET cc_start: 0.7440 (mmm) cc_final: 0.7151 (mmm) REVERT: B 719 GLU cc_start: 0.8085 (pm20) cc_final: 0.7717 (pm20) outliers start: 28 outliers final: 19 residues processed: 198 average time/residue: 0.2224 time to fit residues: 67.3318 Evaluate side-chains 193 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 297 SER Chi-restraints excluded: chain A residue 405 GLU 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 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 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 623 GLU Chi-restraints excluded: chain B residue 792 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.130856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094642 restraints weight = 23189.900| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.54 r_work: 0.3059 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12408 Z= 0.136 Angle : 0.582 13.150 16810 Z= 0.292 Chirality : 0.040 0.154 1898 Planarity : 0.003 0.034 2066 Dihedral : 3.936 18.055 1726 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.28 % Allowed : 16.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.23), residues: 1438 helix: 1.47 (0.16), residues: 1078 sheet: -0.93 (0.60), residues: 64 loop : -2.16 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 650 HIS 0.013 0.001 HIS A 785 PHE 0.014 0.001 PHE B 447 TYR 0.010 0.001 TYR B 361 ARG 0.003 0.000 ARG B 540 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 4) link_NAG-ASN : angle 1.50231 ( 12) link_BETA1-4 : bond 0.00345 ( 2) link_BETA1-4 : angle 1.32952 ( 6) hydrogen bonds : bond 0.04924 ( 773) hydrogen bonds : angle 3.64599 ( 2241) covalent geometry : bond 0.00309 (12402) covalent geometry : angle 0.58056 (16792) *********************** 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 199 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8823 (tpp) cc_final: 0.8606 (mmm) REVERT: A 127 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7233 (mp0) REVERT: A 175 MET cc_start: 0.8546 (mmt) cc_final: 0.8299 (mmt) REVERT: A 234 MET cc_start: 0.8425 (mmm) cc_final: 0.8124 (mmm) REVERT: A 310 TYR cc_start: 0.8398 (t80) cc_final: 0.8100 (t80) REVERT: A 313 MET cc_start: 0.8598 (tpp) cc_final: 0.8276 (mmt) REVERT: A 349 LEU cc_start: 0.8060 (tp) cc_final: 0.7834 (tp) REVERT: A 399 ASP cc_start: 0.8085 (m-30) cc_final: 0.7714 (p0) REVERT: A 405 GLU cc_start: 0.8605 (pm20) cc_final: 0.8301 (mp0) REVERT: A 440 ASN cc_start: 0.8363 (t0) cc_final: 0.7613 (m110) REVERT: A 448 MET cc_start: 0.8992 (tpt) cc_final: 0.8730 (mmt) REVERT: A 462 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8575 (tm-30) REVERT: A 670 MET cc_start: 0.8788 (mtt) cc_final: 0.8451 (mtt) REVERT: A 680 MET cc_start: 0.7358 (mmm) cc_final: 0.7048 (mmm) REVERT: B 127 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7372 (mp0) REVERT: B 202 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8785 (p) REVERT: B 224 ARG cc_start: 0.8395 (ptm-80) cc_final: 0.8093 (ptp-170) REVERT: B 234 MET cc_start: 0.8444 (mmm) cc_final: 0.8139 (mmm) REVERT: B 310 TYR cc_start: 0.8379 (t80) cc_final: 0.8110 (t80) REVERT: B 349 LEU cc_start: 0.8222 (tp) cc_final: 0.8015 (tp) REVERT: B 382 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8269 (mp) REVERT: B 440 ASN cc_start: 0.8388 (t0) cc_final: 0.7581 (m110) REVERT: B 462 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 490 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 670 MET cc_start: 0.8780 (mtt) cc_final: 0.8461 (mtt) REVERT: B 680 MET cc_start: 0.7458 (mmm) cc_final: 0.7175 (mmm) REVERT: B 719 GLU cc_start: 0.8088 (pm20) cc_final: 0.7794 (pm20) outliers start: 30 outliers final: 23 residues processed: 188 average time/residue: 0.2175 time to fit residues: 62.8454 Evaluate side-chains 190 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 792 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.129487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094408 restraints weight = 22866.700| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.78 r_work: 0.3006 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12408 Z= 0.168 Angle : 0.609 12.866 16810 Z= 0.308 Chirality : 0.041 0.162 1898 Planarity : 0.004 0.034 2066 Dihedral : 3.974 18.471 1726 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.20 % Allowed : 17.02 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1438 helix: 1.45 (0.16), residues: 1076 sheet: -0.93 (0.60), residues: 64 loop : -2.16 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 650 HIS 0.012 0.001 HIS A 785 PHE 0.015 0.001 PHE B 447 TYR 0.012 0.002 TYR A 361 ARG 0.003 0.000 ARG B 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 4) link_NAG-ASN : angle 1.55971 ( 12) link_BETA1-4 : bond 0.00277 ( 2) link_BETA1-4 : angle 1.32641 ( 6) hydrogen bonds : bond 0.05213 ( 773) hydrogen bonds : angle 3.76679 ( 2241) covalent geometry : bond 0.00394 (12402) covalent geometry : angle 0.60787 (16792) ********************** 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 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8871 (tpp) cc_final: 0.8579 (tpp) REVERT: A 127 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7275 (mp0) REVERT: A 175 MET cc_start: 0.8565 (mmt) cc_final: 0.8328 (mmt) REVERT: A 234 MET cc_start: 0.8514 (mmm) cc_final: 0.8207 (mmm) REVERT: A 310 TYR cc_start: 0.8473 (t80) cc_final: 0.8181 (t80) REVERT: A 313 MET cc_start: 0.8650 (tpp) cc_final: 0.8378 (mmt) REVERT: A 349 LEU cc_start: 0.8156 (tp) cc_final: 0.7945 (tp) REVERT: A 399 ASP cc_start: 0.8077 (m-30) cc_final: 0.7736 (p0) REVERT: A 440 ASN cc_start: 0.8474 (t0) cc_final: 0.7700 (m110) REVERT: A 462 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8606 (tm-30) REVERT: A 670 MET cc_start: 0.8903 (mtt) cc_final: 0.8615 (mtt) REVERT: A 680 MET cc_start: 0.7489 (mmm) cc_final: 0.7171 (mmm) REVERT: A 728 TYR cc_start: 0.5650 (m-80) cc_final: 0.5360 (m-80) REVERT: B 127 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7319 (mp0) REVERT: B 202 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8672 (p) REVERT: B 224 ARG cc_start: 0.8478 (ptm-80) cc_final: 0.8181 (ptp-170) REVERT: B 310 TYR cc_start: 0.8455 (t80) cc_final: 0.8196 (t80) REVERT: B 382 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8288 (mp) REVERT: B 440 ASN cc_start: 0.8427 (t0) cc_final: 0.7581 (m110) REVERT: B 462 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8516 (tm-30) REVERT: B 490 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 670 MET cc_start: 0.8931 (mtt) cc_final: 0.8661 (mtt) REVERT: B 680 MET cc_start: 0.7537 (mmm) cc_final: 0.7249 (mmm) REVERT: B 719 GLU cc_start: 0.8138 (pm20) cc_final: 0.7791 (pm20) outliers start: 29 outliers final: 23 residues processed: 187 average time/residue: 0.2989 time to fit residues: 87.5601 Evaluate side-chains 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 2.404 ------------------------------------------------------------------------------- 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 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 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 623 GLU Chi-restraints excluded: chain B residue 792 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 chunk 90 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 785 HIS A 789 GLN B 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095634 restraints weight = 22863.030| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.67 r_work: 0.3044 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12408 Z= 0.131 Angle : 0.597 12.951 16810 Z= 0.297 Chirality : 0.040 0.172 1898 Planarity : 0.003 0.034 2066 Dihedral : 3.933 18.228 1726 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.05 % Allowed : 17.25 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.23), residues: 1438 helix: 1.55 (0.16), residues: 1064 sheet: -0.93 (0.60), residues: 64 loop : -2.14 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 650 HIS 0.010 0.001 HIS A 785 PHE 0.014 0.001 PHE B 447 TYR 0.011 0.001 TYR B 728 ARG 0.002 0.000 ARG B 540 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 4) link_NAG-ASN : angle 1.43831 ( 12) link_BETA1-4 : bond 0.00387 ( 2) link_BETA1-4 : angle 1.29947 ( 6) hydrogen bonds : bond 0.04925 ( 773) hydrogen bonds : angle 3.65076 ( 2241) covalent geometry : bond 0.00291 (12402) covalent geometry : angle 0.59603 (16792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6133.37 seconds wall clock time: 109 minutes 48.99 seconds (6588.99 seconds total)