Starting phenix.real_space_refine on Fri Sep 11 23:09:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6c96_7434/09_2026/6c96_7434.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c96_7434/09_2026/6c96_7434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c96_7434/09_2026/6c96_7434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c96_7434/09_2026/6c96_7434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c96_7434/09_2026/6c96_7434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c96_7434/09_2026/6c96_7434.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6c96_7434/09_2026/6c96_7434.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6c96_7434/09_2026/6c96_7434.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 76 5.16 5 Na 2 4.78 5 C 7960 2.51 5 N 1978 2.21 5 O 2074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12090 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 6002 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 20, 'TRANS': 702} Chain breaks: 1 Chain: "B" Number of atoms: 6002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 6002 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 20, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 1 Time building chain proxies: 2.61, per 1000 atoms: 0.22 Number of scatterers: 12090 At special positions: 0 Unit cell: (131.61, 105.93, 120.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 Na 2 11.00 O 2074 8.00 N 1978 7.00 C 7960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1003 " - " ASN A 612 " " NAG B1003 " - " ASN B 612 " " NAG C 1 " - " ASN A 600 " " NAG D 1 " - " ASN B 600 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 470.7 milliseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 4 sheets defined 75.0% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 66 through 84 removed outlier: 3.784A pdb=" N GLY A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 4.007A pdb=" N LEU A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 123 removed outlier: 3.510A pdb=" N TYR A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 removed outlier: 3.812A pdb=" N GLU A 127 " --> pdb=" O SER A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 137 through 163 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 171 through 195 removed outlier: 3.772A pdb=" N MET A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 206 through 212 removed outlier: 4.028A pdb=" N LEU A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.548A pdb=" N SER A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 256 removed outlier: 4.351A pdb=" N ILE A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.965A pdb=" N THR A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.617A pdb=" N MET A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 4.010A pdb=" N ARG A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.917A pdb=" N PHE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 350 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 376 through 387 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 441 through 466 removed outlier: 3.883A pdb=" N GLN A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 450 " --> pdb=" O TYR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 499 removed outlier: 3.625A pdb=" N VAL A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 507 through 527 removed outlier: 3.673A pdb=" N PHE A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.801A pdb=" N PHE A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 550 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 564 removed outlier: 3.645A pdb=" N ARG A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 588 Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.533A pdb=" N ASN A 617 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 618' Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.790A pdb=" N ASN A 629 " --> pdb=" O TYR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 removed outlier: 3.762A pdb=" N VAL A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 removed outlier: 4.460A pdb=" N ILE A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 698 removed outlier: 4.137A pdb=" N PHE A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 removed outlier: 3.675A pdb=" N LEU A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 752 removed outlier: 3.826A pdb=" N VAL A 738 " --> pdb=" O THR A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 774 Processing helix chain 'A' and resid 777 through 791 Processing helix chain 'B' and resid 67 through 84 removed outlier: 3.784A pdb=" N GLY B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 removed outlier: 4.007A pdb=" N LEU B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.508A pdb=" N TYR B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 removed outlier: 3.811A pdb=" N GLU B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 127' Processing helix chain 'B' and resid 137 through 163 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 171 through 195 removed outlier: 3.772A pdb=" N MET B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 206 through 212 removed outlier: 4.029A pdb=" N LEU B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 229 removed outlier: 3.548A pdb=" N SER B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 256 removed outlier: 4.352A pdb=" N ILE B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.964A pdb=" N THR B 279 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 294 removed outlier: 3.616A pdb=" N MET B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 4.010A pdb=" N ARG B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 309 removed outlier: 3.917A pdb=" N PHE B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 350 Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'B' and resid 376 through 387 Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 441 through 466 removed outlier: 3.884A pdb=" N GLN B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 499 removed outlier: 3.625A pdb=" N VAL B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 505 Processing helix chain 'B' and resid 507 through 527 removed outlier: 3.673A pdb=" N PHE B 511 " --> pdb=" O GLY B 507 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 550 removed outlier: 3.803A pdb=" N PHE B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 550 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 removed outlier: 3.645A pdb=" N ARG B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 588 Processing helix chain 'B' and resid 614 through 618 removed outlier: 3.532A pdb=" N ASN B 617 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 614 through 618' Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.790A pdb=" N ASN B 629 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 removed outlier: 3.762A pdb=" N VAL B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 659 removed outlier: 4.461A pdb=" N ILE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 698 removed outlier: 4.137A pdb=" N PHE B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 732 removed outlier: 3.675A pdb=" N LEU B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 752 removed outlier: 3.826A pdb=" N VAL B 738 " --> pdb=" O THR B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 774 Processing helix chain 'B' and resid 777 through 791 Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA2, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA4, first strand: chain 'B' and resid 610 through 613 773 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.18 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: 6746 15.13 - 30.25: 390 30.25 - 45.38: 98 45.38 - 60.51: 6 60.51 - 75.63: 4 Dihedral angle restraints: 7244 sinusoidal: 2940 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 7241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1172 0.050 - 0.101: 541 0.101 - 0.151: 150 0.151 - 0.201: 25 0.201 - 0.251: 10 Chirality restraints: 1898 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.32e+00 chirality pdb=" CA THR A 619 " pdb=" N THR A 619 " pdb=" C THR A 619 " pdb=" CB THR A 619 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA THR B 619 " pdb=" N THR B 619 " pdb=" C THR B 619 " pdb=" CB THR B 619 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1895 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 355 " 0.043 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A 356 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 355 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO B 356 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 356 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 356 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 128 " -0.042 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 129 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.036 5.00e-02 4.00e+02 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3381 2.80 - 3.33: 11053 3.33 - 3.85: 18816 3.85 - 4.38: 21201 4.38 - 4.90: 36317 Nonbonded interactions: 90768 Sorted by model distance: nonbonded pdb=" OE1 GLU B 623 " pdb=" OH TYR B 627 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU A 623 " pdb=" OH TYR A 627 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 480 " pdb=" O ALA A 519 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR B 480 " pdb=" O ALA B 519 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP A 326 " pdb=" NH1 ARG B 699 " model vdw 2.318 3.120 ... (remaining 90763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 66 through 1003) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.240 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 10.478 75.633 4456 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.30 % Allowed : 3.04 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.38 (0.17), residues: 1438 helix: -2.62 (0.11), residues: 1042 sheet: -2.73 (0.66), residues: 40 loop : -3.09 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 666 TYR 0.043 0.004 TYR A 110 PHE 0.028 0.003 PHE B 638 TRP 0.024 0.003 TRP A 508 HIS 0.010 0.002 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00953 / 0.40 (12402) covalent geometry : angle 1.04977 / 0.56 (16792) hydrogen bonds : bond 0.18483 / 12.05 ( 773) hydrogen bonds : angle 7.27473 / 5.16 ( 2241) link_BETA1-4 : bond 0.00287 / 0.14 ( 2) link_BETA1-4 : angle 1.90561 / 1.38 ( 6) link_NAG-ASN : bond 0.00541 / 0.28 ( 4) link_NAG-ASN : angle 1.97530 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 313 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8257 (t0) cc_final: 0.7954 (t0) REVERT: A 111 MET cc_start: 0.8333 (tpp) cc_final: 0.8026 (tpp) REVERT: A 153 VAL cc_start: 0.9232 (t) cc_final: 0.9008 (t) REVERT: A 347 TYR cc_start: 0.8665 (t80) cc_final: 0.7821 (t80) REVERT: A 399 ASP cc_start: 0.7753 (m-30) cc_final: 0.7523 (m-30) REVERT: A 440 ASN cc_start: 0.8353 (t0) cc_final: 0.7703 (m110) REVERT: A 458 TRP cc_start: 0.8268 (t-100) cc_final: 0.7886 (t-100) REVERT: A 515 VAL cc_start: 0.9056 (t) cc_final: 0.8804 (m) REVERT: B 106 ASN cc_start: 0.8087 (t0) cc_final: 0.7669 (t0) REVERT: B 123 LEU cc_start: 0.8933 (tt) cc_final: 0.8672 (tt) REVERT: B 144 LEU cc_start: 0.8948 (mt) cc_final: 0.8640 (mt) REVERT: B 150 MET cc_start: 0.8133 (tpt) cc_final: 0.7850 (tpp) REVERT: B 224 ARG cc_start: 0.7999 (ptm-80) cc_final: 0.7761 (ptp-170) REVERT: B 226 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8742 (mt) REVERT: B 347 TYR cc_start: 0.8852 (t80) cc_final: 0.8580 (t80) REVERT: B 440 ASN cc_start: 0.8186 (t0) cc_final: 0.7476 (m110) REVERT: B 458 TRP cc_start: 0.8305 (t-100) cc_final: 0.7952 (t-100) REVERT: B 726 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8317 (tp30) outliers start: 4 outliers final: 0 residues processed: 315 average time/residue: 0.1016 time to fit residues: 46.4839 Evaluate side-chains 181 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3749 r_free = 0.3749 target = 0.132757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096684 restraints weight = 22878.928| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.63 r_work: 0.3078 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12408 Z= 0.151 Angle : 0.653 8.345 16810 Z= 0.341 Chirality : 0.041 0.227 1898 Planarity : 0.005 0.046 2066 Dihedral : 5.229 50.911 1602 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.60 % Allowed : 11.09 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1438 helix: -0.43 (0.15), residues: 1082 sheet: -1.87 (0.58), residues: 60 loop : -3.00 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 699 TYR 0.022 0.002 TYR B 487 PHE 0.019 0.001 PHE A 89 TRP 0.020 0.001 TRP A 650 HIS 0.009 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (12402) covalent geometry : angle 0.65089 / 0.34 (16792) hydrogen bonds : bond 0.06658 / 4.33 ( 773) hydrogen bonds : angle 4.54383 / 3.25 ( 2241) link_BETA1-4 : bond 0.00233 / 0.12 ( 2) link_BETA1-4 : angle 1.50806 / 1.07 ( 6) link_NAG-ASN : bond 0.00271 / 0.13 ( 4) link_NAG-ASN : angle 1.59352 / 1.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8675 (tpp) cc_final: 0.8434 (tpp) REVERT: A 175 MET cc_start: 0.8802 (mmt) cc_final: 0.8502 (mmt) REVERT: A 238 LEU cc_start: 0.8731 (tp) cc_final: 0.8505 (mm) REVERT: A 347 TYR cc_start: 0.8584 (t80) cc_final: 0.7894 (t80) REVERT: A 399 ASP cc_start: 0.8050 (m-30) cc_final: 0.7637 (p0) REVERT: A 405 GLU cc_start: 0.8548 (pm20) cc_final: 0.8295 (mp0) REVERT: A 440 ASN cc_start: 0.8332 (t0) cc_final: 0.7495 (m110) REVERT: A 458 TRP cc_start: 0.8171 (t-100) cc_final: 0.7844 (t-100) REVERT: A 588 GLU cc_start: 0.7482 (tp30) cc_final: 0.7160 (tp30) REVERT: B 111 MET cc_start: 0.8935 (tpp) cc_final: 0.8527 (tpp) REVERT: B 113 GLU cc_start: 0.8518 (tt0) cc_final: 0.8061 (mt-10) REVERT: B 144 LEU cc_start: 0.8852 (mt) cc_final: 0.8542 (mt) REVERT: B 150 MET cc_start: 0.8385 (tpt) cc_final: 0.8041 (tpp) REVERT: B 224 ARG cc_start: 0.8281 (ptm-80) cc_final: 0.8010 (ptp-170) REVERT: B 226 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8685 (pt) REVERT: B 440 ASN cc_start: 0.8106 (t0) cc_final: 0.7226 (m110) REVERT: B 458 TRP cc_start: 0.8256 (t-100) cc_final: 0.7819 (t-100) REVERT: B 490 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8033 (pp20) REVERT: B 726 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8464 (tp30) outliers start: 21 outliers final: 10 residues processed: 240 average time/residue: 0.0778 time to fit residues: 29.1225 Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 47 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 108 optimal weight: 0.0070 chunk 85 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3771 r_free = 0.3771 target = 0.134351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098346 restraints weight = 23128.580| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.61 r_work: 0.3109 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12408 Z= 0.126 Angle : 0.571 10.662 16810 Z= 0.295 Chirality : 0.040 0.142 1898 Planarity : 0.004 0.046 2066 Dihedral : 4.716 49.157 1602 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.20 % Allowed : 13.37 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.22), residues: 1438 helix: 0.54 (0.16), residues: 1062 sheet: -1.55 (0.56), residues: 64 loop : -2.63 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 699 TYR 0.014 0.001 TYR A 310 PHE 0.021 0.001 PHE B 483 TRP 0.010 0.001 TRP A 650 HIS 0.008 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (12402) covalent geometry : angle 0.56929 / 0.29 (16792) hydrogen bonds : bond 0.05425 / 3.54 ( 773) hydrogen bonds : angle 4.04884 / 2.89 ( 2241) link_BETA1-4 : bond 0.00273 / 0.13 ( 2) link_BETA1-4 : angle 1.14971 / 0.89 ( 6) link_NAG-ASN : bond 0.00122 / 0.06 ( 4) link_NAG-ASN : angle 1.58146 / 1.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 119 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8625 (tp) REVERT: A 155 GLU cc_start: 0.8368 (tt0) cc_final: 0.8085 (tt0) REVERT: A 175 MET cc_start: 0.8772 (mmt) cc_final: 0.8378 (mmt) REVERT: A 238 LEU cc_start: 0.8675 (tp) cc_final: 0.8378 (mm) REVERT: A 313 MET cc_start: 0.8571 (tpp) cc_final: 0.8069 (mmt) REVERT: A 347 TYR cc_start: 0.8472 (t80) cc_final: 0.7750 (t80) REVERT: A 375 MET cc_start: 0.8387 (ttm) cc_final: 0.8173 (ttp) REVERT: A 399 ASP cc_start: 0.8156 (m-30) cc_final: 0.7728 (p0) REVERT: A 405 GLU cc_start: 0.8638 (pm20) cc_final: 0.8321 (mp0) REVERT: A 440 ASN cc_start: 0.8474 (t0) cc_final: 0.7544 (m110) REVERT: A 458 TRP cc_start: 0.8024 (t-100) cc_final: 0.7823 (t-100) REVERT: A 462 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8639 (tm-30) REVERT: A 588 GLU cc_start: 0.7790 (tp30) cc_final: 0.7413 (tp30) REVERT: A 670 MET cc_start: 0.8819 (mtt) cc_final: 0.8561 (mtt) REVERT: A 748 MET cc_start: 0.4163 (ptp) cc_final: 0.3898 (ptp) REVERT: B 111 MET cc_start: 0.8883 (tpp) cc_final: 0.8601 (tpp) REVERT: B 119 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8665 (tp) REVERT: B 150 MET cc_start: 0.8240 (tpt) cc_final: 0.7987 (tpp) REVERT: B 224 ARG cc_start: 0.8311 (ptm-80) cc_final: 0.7986 (ptp-170) REVERT: B 440 ASN cc_start: 0.8295 (t0) cc_final: 0.7409 (m110) REVERT: B 458 TRP cc_start: 0.8234 (t-100) cc_final: 0.7931 (t-100) REVERT: B 462 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8537 (tm-30) REVERT: B 670 MET cc_start: 0.8725 (mtt) cc_final: 0.8413 (mtt) REVERT: B 719 GLU cc_start: 0.8091 (pm20) cc_final: 0.7703 (pm20) REVERT: B 726 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8438 (tp30) REVERT: B 728 TYR cc_start: 0.5219 (m-80) cc_final: 0.4963 (m-80) outliers start: 29 outliers final: 13 residues processed: 224 average time/residue: 0.0812 time to fit residues: 28.3109 Evaluate side-chains 185 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3763 r_free = 0.3763 target = 0.133520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097240 restraints weight = 23043.475| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.62 r_work: 0.3096 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12408 Z= 0.127 Angle : 0.571 10.648 16810 Z= 0.290 Chirality : 0.040 0.195 1898 Planarity : 0.004 0.039 2066 Dihedral : 4.334 19.156 1600 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.98 % Allowed : 14.97 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.23), residues: 1438 helix: 0.92 (0.16), residues: 1064 sheet: -1.68 (0.56), residues: 68 loop : -2.40 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 699 TYR 0.012 0.001 TYR A 487 PHE 0.021 0.001 PHE B 227 TRP 0.005 0.001 TRP B 162 HIS 0.007 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (12402) covalent geometry : angle 0.56913 / 0.29 (16792) hydrogen bonds : bond 0.05161 / 3.37 ( 773) hydrogen bonds : angle 3.87925 / 2.77 ( 2241) link_BETA1-4 : bond 0.00416 / 0.21 ( 2) link_BETA1-4 : angle 1.10992 / 0.87 ( 6) link_NAG-ASN : bond 0.00093 / 0.05 ( 4) link_NAG-ASN : angle 1.53405 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8953 (tpp) cc_final: 0.8501 (tpp) REVERT: A 113 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7666 (mt-10) REVERT: A 155 GLU cc_start: 0.8464 (tt0) cc_final: 0.8239 (tt0) REVERT: A 238 LEU cc_start: 0.8715 (tp) cc_final: 0.8382 (mm) REVERT: A 313 MET cc_start: 0.8590 (tpp) cc_final: 0.8161 (mmt) REVERT: A 399 ASP cc_start: 0.8149 (m-30) cc_final: 0.7745 (p0) REVERT: A 405 GLU cc_start: 0.8642 (pm20) cc_final: 0.8332 (mp0) REVERT: A 440 ASN cc_start: 0.8519 (t0) cc_final: 0.7658 (m110) REVERT: A 458 TRP cc_start: 0.7981 (t-100) cc_final: 0.7677 (t60) REVERT: A 462 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 588 GLU cc_start: 0.7881 (tp30) cc_final: 0.7522 (tp30) REVERT: A 670 MET cc_start: 0.8774 (mtt) cc_final: 0.8546 (mtt) REVERT: A 728 TYR cc_start: 0.5222 (m-80) cc_final: 0.4840 (m-80) REVERT: B 111 MET cc_start: 0.8859 (tpp) cc_final: 0.8616 (tpp) REVERT: B 119 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8651 (tp) REVERT: B 150 MET cc_start: 0.8251 (tpt) cc_final: 0.8022 (tpp) REVERT: B 175 MET cc_start: 0.8599 (mmt) cc_final: 0.8290 (mmt) REVERT: B 224 ARG cc_start: 0.8310 (ptm-80) cc_final: 0.7997 (ptp-170) REVERT: B 226 ILE cc_start: 0.8932 (pp) cc_final: 0.8715 (pt) REVERT: B 382 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8275 (mp) REVERT: B 440 ASN cc_start: 0.8248 (t0) cc_final: 0.7379 (m110) REVERT: B 458 TRP cc_start: 0.8154 (t-100) cc_final: 0.7917 (t-100) REVERT: B 462 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8519 (tm-30) REVERT: B 465 MET cc_start: 0.8889 (tpp) cc_final: 0.8685 (tpp) REVERT: B 490 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7995 (pp20) REVERT: B 719 GLU cc_start: 0.8122 (pm20) cc_final: 0.7787 (pm20) outliers start: 26 outliers final: 13 residues processed: 200 average time/residue: 0.0833 time to fit residues: 25.8520 Evaluate side-chains 183 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 235 ASP 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 119 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098567 restraints weight = 23168.178| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.82 r_work: 0.3085 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3709 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= 0.125 Angle : 0.553 10.275 16810 Z= 0.283 Chirality : 0.039 0.197 1898 Planarity : 0.004 0.040 2066 Dihedral : 4.224 18.437 1600 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.75 % Allowed : 15.50 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1438 helix: 1.18 (0.16), residues: 1066 sheet: -1.36 (0.61), residues: 64 loop : -2.31 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 540 TYR 0.011 0.001 TYR B 310 PHE 0.013 0.001 PHE A 447 TRP 0.005 0.001 TRP B 478 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (12402) covalent geometry : angle 0.55111 / 0.28 (16792) hydrogen bonds : bond 0.04956 / 3.24 ( 773) hydrogen bonds : angle 3.74363 / 2.67 ( 2241) link_BETA1-4 : bond 0.00375 / 0.19 ( 2) link_BETA1-4 : angle 1.10621 / 0.89 ( 6) link_NAG-ASN : bond 0.00072 / 0.04 ( 4) link_NAG-ASN : angle 1.49177 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7481 (mt-10) REVERT: A 155 GLU cc_start: 0.8548 (tt0) cc_final: 0.8102 (tt0) REVERT: A 175 MET cc_start: 0.8706 (mmt) cc_final: 0.8219 (mmt) REVERT: A 238 LEU cc_start: 0.8737 (tp) cc_final: 0.8406 (mm) REVERT: A 313 MET cc_start: 0.8599 (tpp) cc_final: 0.8271 (mmt) REVERT: A 405 GLU cc_start: 0.8683 (pm20) cc_final: 0.8351 (mp0) REVERT: A 440 ASN cc_start: 0.8433 (t0) cc_final: 0.7557 (m110) REVERT: A 458 TRP cc_start: 0.7970 (t-100) cc_final: 0.7680 (t60) REVERT: A 462 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8638 (tm-30) REVERT: A 588 GLU cc_start: 0.7996 (tp30) cc_final: 0.7614 (tp30) REVERT: A 670 MET cc_start: 0.8745 (mtt) cc_final: 0.8466 (mtt) REVERT: B 111 MET cc_start: 0.8910 (tpp) cc_final: 0.8710 (tpp) REVERT: B 146 LEU cc_start: 0.8539 (mm) cc_final: 0.8308 (mm) REVERT: B 150 MET cc_start: 0.8248 (tpt) cc_final: 0.8021 (tpp) REVERT: B 175 MET cc_start: 0.8522 (mmt) cc_final: 0.8255 (mmt) REVERT: B 224 ARG cc_start: 0.8359 (ptm-80) cc_final: 0.8040 (ptp-170) REVERT: B 382 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 440 ASN cc_start: 0.8256 (t0) cc_final: 0.7381 (m110) REVERT: B 462 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8564 (tm-30) REVERT: B 490 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7993 (pp20) REVERT: B 719 GLU cc_start: 0.8174 (pm20) cc_final: 0.7827 (pm20) REVERT: B 728 TYR cc_start: 0.5206 (m-80) cc_final: 0.4985 (m-80) outliers start: 23 outliers final: 15 residues processed: 199 average time/residue: 0.0823 time to fit residues: 25.5809 Evaluate side-chains 180 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 235 ASP 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 659 SER 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 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 35 optimal weight: 0.0020 chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN B 792 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092810 restraints weight = 23217.367| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.55 r_work: 0.3030 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12408 Z= 0.190 Angle : 0.605 11.233 16810 Z= 0.312 Chirality : 0.042 0.183 1898 Planarity : 0.004 0.037 2066 Dihedral : 4.237 19.511 1600 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.81 % Allowed : 15.20 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1438 helix: 1.20 (0.16), residues: 1082 sheet: -1.27 (0.61), residues: 64 loop : -2.24 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.018 0.002 TYR A 310 PHE 0.024 0.002 PHE B 227 TRP 0.006 0.001 TRP A 650 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (12402) covalent geometry : angle 0.60313 / 0.31 (16792) hydrogen bonds : bond 0.05574 / 3.62 ( 773) hydrogen bonds : angle 3.89044 / 2.77 ( 2241) link_BETA1-4 : bond 0.00349 / 0.17 ( 2) link_BETA1-4 : angle 1.22405 / 1.00 ( 6) link_NAG-ASN : bond 0.00136 / 0.07 ( 4) link_NAG-ASN : angle 1.69333 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8946 (tpp) cc_final: 0.8711 (tpp) REVERT: A 113 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 155 GLU cc_start: 0.8526 (tt0) cc_final: 0.8074 (tt0) REVERT: A 175 MET cc_start: 0.8652 (mmt) cc_final: 0.8259 (mmt) REVERT: A 313 MET cc_start: 0.8692 (tpp) cc_final: 0.8439 (mmt) REVERT: A 405 GLU cc_start: 0.8641 (pm20) cc_final: 0.8425 (mp0) REVERT: A 440 ASN cc_start: 0.8421 (t0) cc_final: 0.7616 (m110) REVERT: A 458 TRP cc_start: 0.8075 (t-100) cc_final: 0.7758 (t60) REVERT: A 462 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8560 (tm-30) REVERT: A 490 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8106 (tm-30) REVERT: A 728 TYR cc_start: 0.5353 (m-80) cc_final: 0.5040 (m-80) REVERT: B 146 LEU cc_start: 0.8583 (mm) cc_final: 0.8365 (mm) REVERT: B 150 MET cc_start: 0.8192 (tpt) cc_final: 0.7974 (tpp) REVERT: B 175 MET cc_start: 0.8572 (mmt) cc_final: 0.8289 (mmt) REVERT: B 224 ARG cc_start: 0.8453 (ptm-80) cc_final: 0.8148 (ptp-170) REVERT: B 382 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8225 (mp) REVERT: B 440 ASN cc_start: 0.8350 (t0) cc_final: 0.7465 (m110) REVERT: B 462 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8527 (tm-30) REVERT: B 490 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8022 (pp20) REVERT: B 719 GLU cc_start: 0.8140 (pm20) cc_final: 0.7784 (pm20) REVERT: B 728 TYR cc_start: 0.5326 (m-80) cc_final: 0.5105 (m-80) outliers start: 37 outliers final: 27 residues processed: 190 average time/residue: 0.0804 time to fit residues: 24.0359 Evaluate side-chains 189 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL 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 235 ASP 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 472 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 235 ASP 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 472 THR 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 559 ASP Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 677 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.133164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097930 restraints weight = 23053.031| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.77 r_work: 0.3075 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4017 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= 0.116 Angle : 0.553 10.854 16810 Z= 0.279 Chirality : 0.039 0.208 1898 Planarity : 0.004 0.037 2066 Dihedral : 4.099 18.239 1600 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.05 % Allowed : 16.19 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1438 helix: 1.47 (0.16), residues: 1078 sheet: -1.19 (0.60), residues: 64 loop : -2.24 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 699 TYR 0.010 0.001 TYR B 487 PHE 0.012 0.001 PHE A 447 TRP 0.007 0.001 TRP A 650 HIS 0.008 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (12402) covalent geometry : angle 0.55195 / 0.28 (16792) hydrogen bonds : bond 0.04757 / 3.11 ( 773) hydrogen bonds : angle 3.60711 / 2.57 ( 2241) link_BETA1-4 : bond 0.00363 / 0.18 ( 2) link_BETA1-4 : angle 1.18276 / 0.96 ( 6) link_NAG-ASN : bond 0.00155 / 0.08 ( 4) link_NAG-ASN : angle 1.40352 / 1.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 155 GLU cc_start: 0.8531 (tt0) cc_final: 0.8037 (tt0) REVERT: A 175 MET cc_start: 0.8556 (mmt) cc_final: 0.8176 (mmt) REVERT: A 313 MET cc_start: 0.8582 (tpp) cc_final: 0.8291 (mmt) REVERT: A 349 LEU cc_start: 0.7964 (tp) cc_final: 0.7725 (tp) REVERT: A 405 GLU cc_start: 0.8690 (pm20) cc_final: 0.8427 (mp0) REVERT: A 440 ASN cc_start: 0.8432 (t0) cc_final: 0.7625 (m110) REVERT: A 458 TRP cc_start: 0.7793 (t-100) cc_final: 0.7567 (t-100) REVERT: A 462 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8604 (tm-30) REVERT: A 490 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8046 (tm-30) REVERT: A 670 MET cc_start: 0.8775 (mtt) cc_final: 0.8524 (mtt) REVERT: B 224 ARG cc_start: 0.8341 (ptm-80) cc_final: 0.8042 (ptp-170) REVERT: B 382 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8221 (mp) REVERT: B 440 ASN cc_start: 0.8333 (t0) cc_final: 0.7464 (m110) REVERT: B 462 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8555 (tm-30) REVERT: B 490 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8002 (pp20) REVERT: B 719 GLU cc_start: 0.8157 (pm20) cc_final: 0.7786 (pm20) REVERT: B 728 TYR cc_start: 0.5264 (m-80) cc_final: 0.5025 (m-80) outliers start: 27 outliers final: 20 residues processed: 198 average time/residue: 0.0812 time to fit residues: 25.4529 Evaluate side-chains 185 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 266 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 202 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 564 LEU Chi-restraints excluded: chain B residue 677 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.0170 chunk 16 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098636 restraints weight = 22916.459| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.69 r_work: 0.3088 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12408 Z= 0.118 Angle : 0.580 13.742 16810 Z= 0.285 Chirality : 0.039 0.223 1898 Planarity : 0.003 0.035 2066 Dihedral : 4.023 17.625 1600 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.43 % Allowed : 15.88 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.23), residues: 1438 helix: 1.53 (0.16), residues: 1076 sheet: -1.13 (0.60), residues: 64 loop : -2.11 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 699 TYR 0.009 0.001 TYR B 487 PHE 0.012 0.001 PHE B 447 TRP 0.006 0.001 TRP A 650 HIS 0.008 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (12402) covalent geometry : angle 0.57900 / 0.28 (16792) hydrogen bonds : bond 0.04581 / 3.00 ( 773) hydrogen bonds : angle 3.57982 / 2.54 ( 2241) link_BETA1-4 : bond 0.00392 / 0.19 ( 2) link_BETA1-4 : angle 1.12901 / 0.91 ( 6) link_NAG-ASN : bond 0.00102 / 0.05 ( 4) link_NAG-ASN : angle 1.37734 / 1.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7362 (mt-10) REVERT: A 127 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7388 (mp0) REVERT: A 155 GLU cc_start: 0.8523 (tt0) cc_final: 0.8037 (tt0) REVERT: A 235 ASP cc_start: 0.7958 (p0) cc_final: 0.7616 (m-30) REVERT: A 310 TYR cc_start: 0.8322 (t80) cc_final: 0.7802 (t80) REVERT: A 313 MET cc_start: 0.8493 (tpp) cc_final: 0.8278 (mmt) REVERT: A 349 LEU cc_start: 0.7964 (tp) cc_final: 0.7740 (tp) REVERT: A 405 GLU cc_start: 0.8671 (pm20) cc_final: 0.8415 (mp0) REVERT: A 440 ASN cc_start: 0.8445 (t0) cc_final: 0.7681 (m110) REVERT: A 448 MET cc_start: 0.8954 (tpt) cc_final: 0.8753 (mmt) REVERT: A 462 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8604 (tm-30) REVERT: A 490 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7724 (mm-30) REVERT: A 670 MET cc_start: 0.8681 (mtt) cc_final: 0.8444 (mtt) REVERT: A 728 TYR cc_start: 0.5304 (m-80) cc_final: 0.5040 (m-80) REVERT: B 155 GLU cc_start: 0.7984 (tt0) cc_final: 0.7432 (tt0) REVERT: B 224 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.8052 (ptp-170) REVERT: B 382 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8264 (mp) REVERT: B 440 ASN cc_start: 0.8273 (t0) cc_final: 0.7448 (m110) REVERT: B 462 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8538 (tm-30) REVERT: B 490 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8000 (pp20) REVERT: B 588 GLU cc_start: 0.7999 (tp30) cc_final: 0.7727 (tp30) REVERT: B 719 GLU cc_start: 0.8133 (pm20) cc_final: 0.7753 (pm20) REVERT: B 728 TYR cc_start: 0.5222 (m-80) cc_final: 0.4981 (m-80) outliers start: 32 outliers final: 24 residues processed: 194 average time/residue: 0.0844 time to fit residues: 25.5666 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 : 0.487 ------------------------------------------------------------------------------- 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 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 584 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 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 564 LEU Chi-restraints excluded: chain B residue 677 MET 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 44 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 106 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096965 restraints weight = 23009.941| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.74 r_work: 0.3050 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12408 Z= 0.140 Angle : 0.595 13.442 16810 Z= 0.296 Chirality : 0.040 0.160 1898 Planarity : 0.003 0.035 2066 Dihedral : 3.996 17.785 1600 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.05 % Allowed : 16.19 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1438 helix: 1.52 (0.16), residues: 1076 sheet: -1.12 (0.60), residues: 64 loop : -2.00 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 699 TYR 0.013 0.001 TYR A 310 PHE 0.027 0.001 PHE B 227 TRP 0.005 0.001 TRP A 650 HIS 0.014 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12402) covalent geometry : angle 0.59361 / 0.30 (16792) hydrogen bonds : bond 0.04813 / 3.15 ( 773) hydrogen bonds : angle 3.62398 / 2.58 ( 2241) link_BETA1-4 : bond 0.00331 / 0.17 ( 2) link_BETA1-4 : angle 1.16892 / 0.94 ( 6) link_NAG-ASN : bond 0.00044 / 0.02 ( 4) link_NAG-ASN : angle 1.42040 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7324 (mp0) REVERT: A 155 GLU cc_start: 0.8567 (tt0) cc_final: 0.8103 (tt0) REVERT: A 175 MET cc_start: 0.8525 (mmt) cc_final: 0.8197 (mmt) REVERT: A 235 ASP cc_start: 0.8036 (p0) cc_final: 0.7638 (m-30) REVERT: A 310 TYR cc_start: 0.8342 (t80) cc_final: 0.7982 (t80) REVERT: A 313 MET cc_start: 0.8576 (tpp) cc_final: 0.8374 (mmt) REVERT: A 405 GLU cc_start: 0.8695 (pm20) cc_final: 0.8447 (mp0) REVERT: A 440 ASN cc_start: 0.8436 (t0) cc_final: 0.7668 (m110) REVERT: A 462 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8610 (tm-30) REVERT: A 490 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 670 MET cc_start: 0.8728 (mtt) cc_final: 0.8495 (mtt) REVERT: B 224 ARG cc_start: 0.8399 (ptm-80) cc_final: 0.8104 (ptp-170) REVERT: B 349 LEU cc_start: 0.8201 (tp) cc_final: 0.7995 (tp) REVERT: B 382 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8263 (mp) REVERT: B 440 ASN cc_start: 0.8368 (t0) cc_final: 0.7488 (m110) REVERT: B 462 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 719 GLU cc_start: 0.8137 (pm20) cc_final: 0.7872 (pm20) REVERT: B 728 TYR cc_start: 0.5265 (m-80) cc_final: 0.5045 (m-80) REVERT: B 748 MET cc_start: 0.3115 (mtm) cc_final: 0.2787 (mtm) outliers start: 27 outliers final: 25 residues processed: 186 average time/residue: 0.0814 time to fit residues: 24.0605 Evaluate side-chains 189 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR 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 584 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 270 SER 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 564 LEU Chi-restraints excluded: chain B residue 677 MET 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 63 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 128 optimal weight: 0.0010 chunk 88 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099383 restraints weight = 23080.915| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.71 r_work: 0.3098 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12408 Z= 0.115 Angle : 0.587 13.559 16810 Z= 0.286 Chirality : 0.039 0.177 1898 Planarity : 0.003 0.035 2066 Dihedral : 3.955 16.952 1600 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.90 % Allowed : 16.49 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.23), residues: 1438 helix: 1.61 (0.16), residues: 1076 sheet: -1.04 (0.60), residues: 64 loop : -2.10 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 699 TYR 0.009 0.001 TYR B 310 PHE 0.014 0.001 PHE A 447 TRP 0.008 0.001 TRP A 650 HIS 0.011 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (12402) covalent geometry : angle 0.58636 / 0.29 (16792) hydrogen bonds : bond 0.04399 / 2.90 ( 773) hydrogen bonds : angle 3.53286 / 2.51 ( 2241) link_BETA1-4 : bond 0.00506 / 0.26 ( 2) link_BETA1-4 : angle 1.14170 / 0.93 ( 6) link_NAG-ASN : bond 0.00112 / 0.06 ( 4) link_NAG-ASN : angle 1.24602 / 0.98 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7258 (mp0) REVERT: A 175 MET cc_start: 0.8438 (mmt) cc_final: 0.8184 (mmt) REVERT: A 192 LEU cc_start: 0.9057 (tt) cc_final: 0.8850 (tt) REVERT: A 235 ASP cc_start: 0.7986 (p0) cc_final: 0.7563 (m-30) REVERT: A 310 TYR cc_start: 0.8252 (t80) cc_final: 0.8026 (t80) REVERT: A 313 MET cc_start: 0.8435 (tpp) cc_final: 0.8190 (mmt) REVERT: A 349 LEU cc_start: 0.7831 (tp) cc_final: 0.7601 (tp) REVERT: A 405 GLU cc_start: 0.8693 (pm20) cc_final: 0.8441 (mp0) REVERT: A 440 ASN cc_start: 0.8511 (t0) cc_final: 0.7779 (m110) REVERT: A 462 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8625 (tm-30) REVERT: A 719 GLU cc_start: 0.8138 (mp0) cc_final: 0.7770 (pm20) REVERT: B 127 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7359 (mp0) REVERT: B 175 MET cc_start: 0.8425 (mmt) cc_final: 0.8179 (mmp) REVERT: B 224 ARG cc_start: 0.8357 (ptm-80) cc_final: 0.8077 (ptp-170) REVERT: B 382 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8274 (mp) REVERT: B 440 ASN cc_start: 0.8364 (t0) cc_final: 0.7518 (m110) REVERT: B 462 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 490 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7978 (pp20) REVERT: B 719 GLU cc_start: 0.8045 (pm20) cc_final: 0.7788 (pm20) REVERT: B 748 MET cc_start: 0.2984 (mtm) cc_final: 0.2691 (mtm) outliers start: 25 outliers final: 24 residues processed: 198 average time/residue: 0.0784 time to fit residues: 24.4498 Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR 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 584 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 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 564 LEU Chi-restraints excluded: chain B residue 677 MET 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 72 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091671 restraints weight = 22999.281| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.69 r_work: 0.2980 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12408 Z= 0.250 Angle : 0.709 13.361 16810 Z= 0.355 Chirality : 0.045 0.170 1898 Planarity : 0.004 0.035 2066 Dihedral : 4.182 19.810 1600 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.28 % Allowed : 16.79 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1438 helix: 1.31 (0.16), residues: 1078 sheet: -1.10 (0.60), residues: 64 loop : -2.09 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 546 TYR 0.024 0.002 TYR A 310 PHE 0.028 0.002 PHE B 227 TRP 0.016 0.001 TRP A 650 HIS 0.015 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (12402) covalent geometry : angle 0.70733 / 0.35 (16792) hydrogen bonds : bond 0.05891 / 3.82 ( 773) hydrogen bonds : angle 3.98344 / 2.83 ( 2241) link_BETA1-4 : bond 0.00161 / 0.08 ( 2) link_BETA1-4 : angle 1.37159 / 1.13 ( 6) link_NAG-ASN : bond 0.00210 / 0.10 ( 4) link_NAG-ASN : angle 1.73893 / 1.38 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2415.86 seconds wall clock time: 42 minutes 14.34 seconds (2534.34 seconds total)