Starting phenix.real_space_refine on Thu Aug 6 09:59:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rnj_54094/08_2026/9rnj_54094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rnj_54094/08_2026/9rnj_54094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rnj_54094/08_2026/9rnj_54094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rnj_54094/08_2026/9rnj_54094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rnj_54094/08_2026/9rnj_54094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rnj_54094/08_2026/9rnj_54094.map" } resolution = 3.86 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= -0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 124 5.16 5 Cl 2 4.86 5 Na 4 4.78 5 C 9100 2.51 5 N 2386 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14148 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7013 Classifications: {'peptide': 904} Link IDs: {'PTRANS': 34, 'TRANS': 869} Chain breaks: 2 Chain: "A" Number of atoms: 7013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7013 Classifications: {'peptide': 904} Link IDs: {'PTRANS': 34, 'TRANS': 869} Chain breaks: 2 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {' CL': 1, ' NA': 2, 'ATP': 1, 'JUX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {' CL': 1, ' NA': 2, 'ATP': 1, 'JUX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.90, per 1000 atoms: 0.20 Number of scatterers: 14148 At special positions: 0 Unit cell: (97.3104, 119.381, 149.477, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 124 16.00 P 6 15.00 Na 4 11.00 O 2526 8.00 N 2386 7.00 C 9100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 331 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 632.2 milliseconds 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 59.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.500A pdb=" N LEU B 61 " --> pdb=" O MET B 57 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 131 through 155 removed outlier: 3.557A pdb=" N MET B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 173 through 206 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 222 through 247 removed outlier: 4.042A pdb=" N VAL B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 278 removed outlier: 3.699A pdb=" N TYR B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 322 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 354 through 358 removed outlier: 4.217A pdb=" N LEU B 358 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 408 Processing helix chain 'B' and resid 409 through 412 removed outlier: 3.514A pdb=" N THR B 412 " --> pdb=" O PRO B 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 through 412' Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.852A pdb=" N ARG B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 457 Proline residue: B 432 - end of helix Processing helix chain 'B' and resid 458 through 464 removed outlier: 3.704A pdb=" N ASP B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 removed outlier: 4.039A pdb=" N ALA B 480 " --> pdb=" O GLY B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 517 removed outlier: 4.115A pdb=" N ILE B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) Proline residue: B 507 - end of helix removed outlier: 3.511A pdb=" N GLY B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 527 removed outlier: 3.675A pdb=" N GLN B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL B 524 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 527 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.555A pdb=" N LEU B 540 " --> pdb=" O TRP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 583 removed outlier: 4.689A pdb=" N CYS B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLN B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 612 Processing helix chain 'B' and resid 614 through 634 Processing helix chain 'B' and resid 643 through 660 removed outlier: 4.081A pdb=" N GLY B 647 " --> pdb=" O ASP B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 699 removed outlier: 4.141A pdb=" N LEU B 692 " --> pdb=" O HIS B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 702 No H-bonds generated for 'chain 'B' and resid 700 through 702' Processing helix chain 'B' and resid 714 through 736 Proline residue: B 720 - end of helix Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 778 through 782 removed outlier: 3.785A pdb=" N LYS B 782 " --> pdb=" O TRP B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 801 removed outlier: 3.840A pdb=" N PHE B 791 " --> pdb=" O THR B 787 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 792 " --> pdb=" O TRP B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 848 Proline residue: B 842 - end of helix Processing helix chain 'B' and resid 867 through 882 Processing helix chain 'B' and resid 1046 through 1065 Processing helix chain 'B' and resid 1080 through 1082 No H-bonds generated for 'chain 'B' and resid 1080 through 1082' Processing helix chain 'B' and resid 1083 through 1095 Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.501A pdb=" N LEU A 61 " --> pdb=" O MET A 57 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.550A pdb=" N LEU A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 131 through 155 removed outlier: 3.551A pdb=" N MET A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 173 through 206 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 222 through 247 removed outlier: 4.004A pdb=" N VAL A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 278 removed outlier: 3.843A pdb=" N TYR A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 354 through 358 removed outlier: 4.158A pdb=" N LEU A 358 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 409 through 412 removed outlier: 3.505A pdb=" N THR A 412 " --> pdb=" O PRO A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 412' Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.825A pdb=" N ARG A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 457 Proline residue: A 432 - end of helix Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.648A pdb=" N ASP A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 removed outlier: 4.022A pdb=" N ALA A 480 " --> pdb=" O GLY A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 517 removed outlier: 4.105A pdb=" N ILE A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 3.534A pdb=" N GLY A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 527 removed outlier: 3.516A pdb=" N LEU A 522 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL A 524 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS A 527 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 4.051A pdb=" N LEU A 540 " --> pdb=" O TRP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 583 removed outlier: 4.684A pdb=" N CYS A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 612 Processing helix chain 'A' and resid 614 through 634 Processing helix chain 'A' and resid 643 through 660 removed outlier: 4.065A pdb=" N GLY A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 699 removed outlier: 4.158A pdb=" N LEU A 692 " --> pdb=" O HIS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 714 through 736 removed outlier: 3.519A pdb=" N HIS A 719 " --> pdb=" O PHE A 715 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 778 through 782 removed outlier: 3.821A pdb=" N LYS A 782 " --> pdb=" O TRP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 801 removed outlier: 3.838A pdb=" N PHE A 791 " --> pdb=" O THR A 787 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 792 " --> pdb=" O TRP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 848 Proline residue: A 842 - end of helix Processing helix chain 'A' and resid 867 through 882 Processing helix chain 'A' and resid 1046 through 1065 Processing helix chain 'A' and resid 1080 through 1082 No H-bonds generated for 'chain 'A' and resid 1080 through 1082' Processing helix chain 'A' and resid 1083 through 1095 Processing sheet with id=AA1, first strand: chain 'B' and resid 285 through 289 removed outlier: 3.622A pdb=" N ILE B 286 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 741 through 742 removed outlier: 6.257A pdb=" N VAL B 676 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY B 774 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B1101 " --> pdb=" O LYS B 809 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B1070 " --> pdb=" O MET B1102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B1104 " --> pdb=" O VAL B1070 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU B1072 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 861 " --> pdb=" O TRP B 830 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR B 860 " --> pdb=" O GLU B 889 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 891 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 289 removed outlier: 3.620A pdb=" N ILE A 286 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 741 through 742 removed outlier: 6.417A pdb=" N VAL A 676 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY A 774 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A1101 " --> pdb=" O LYS A 809 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A1070 " --> pdb=" O MET A1102 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A1104 " --> pdb=" O VAL A1070 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU A1072 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A 861 " --> pdb=" O TRP A 830 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 858 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL A 891 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR A 860 " --> pdb=" O VAL A 891 " (cutoff:3.500A) 755 hydrogen bonds defined for protein. 2214 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: 2.40 Time building geometry restraints manager: 1.58 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: 4457 1.34 - 1.46: 2176 1.46 - 1.58: 7619 1.58 - 1.69: 10 1.69 - 1.81: 202 Bond restraints: 14464 Sorted by residual: bond pdb=" N JUX B1201 " pdb=" CA JUX B1201 " ideal model delta sigma weight residual 1.443 1.504 -0.061 2.00e-02 2.50e+03 9.20e+00 bond pdb=" N JUX A1201 " pdb=" CA JUX A1201 " ideal model delta sigma weight residual 1.443 1.504 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" N JUX A1201 " pdb=" C5 JUX A1201 " ideal model delta sigma weight residual 1.393 1.437 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" N JUX B1201 " pdb=" C5 JUX B1201 " ideal model delta sigma weight residual 1.393 1.437 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" N JUX A1201 " pdb=" C1 JUX A1201 " ideal model delta sigma weight residual 1.371 1.413 -0.042 2.00e-02 2.50e+03 4.37e+00 ... (remaining 14459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 19141 1.47 - 2.94: 393 2.94 - 4.41: 69 4.41 - 5.88: 34 5.88 - 7.36: 5 Bond angle restraints: 19642 Sorted by residual: angle pdb=" C TRP A 536 " pdb=" N ALA A 537 " pdb=" CA ALA A 537 " ideal model delta sigma weight residual 120.82 126.07 -5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C ARG A 592 " pdb=" CA ARG A 592 " pdb=" CB ARG A 592 " ideal model delta sigma weight residual 115.89 111.38 4.51 1.32e+00 5.74e-01 1.17e+01 angle pdb=" C ARG B 592 " pdb=" CA ARG B 592 " pdb=" CB ARG B 592 " ideal model delta sigma weight residual 115.89 111.45 4.44 1.32e+00 5.74e-01 1.13e+01 angle pdb=" C THR A 535 " pdb=" N TRP A 536 " pdb=" CA TRP A 536 " ideal model delta sigma weight residual 120.44 124.68 -4.24 1.30e+00 5.92e-01 1.07e+01 angle pdb=" N GLY A 663 " pdb=" CA GLY A 663 " pdb=" C GLY A 663 " ideal model delta sigma weight residual 112.34 118.90 -6.56 2.04e+00 2.40e-01 1.03e+01 ... (remaining 19637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.69: 8397 28.69 - 57.37: 135 57.37 - 86.06: 6 86.06 - 114.74: 0 114.74 - 143.43: 2 Dihedral angle restraints: 8540 sinusoidal: 3382 harmonic: 5158 Sorted by residual: dihedral pdb=" CA ILE A 612 " pdb=" C ILE A 612 " pdb=" N CYS A 613 " pdb=" CA CYS A 613 " ideal model delta harmonic sigma weight residual 180.00 147.70 32.30 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA ILE B 612 " pdb=" C ILE B 612 " pdb=" N CYS B 613 " pdb=" CA CYS B 613 " ideal model delta harmonic sigma weight residual 180.00 148.73 31.27 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA GLY A 663 " pdb=" C GLY A 663 " pdb=" N PRO A 664 " pdb=" CA PRO A 664 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 8537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1429 0.028 - 0.056: 491 0.056 - 0.084: 198 0.084 - 0.112: 108 0.112 - 0.140: 20 Chirality restraints: 2246 Sorted by residual: chirality pdb=" CA THR A 383 " pdb=" N THR A 383 " pdb=" C THR A 383 " pdb=" CB THR A 383 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA THR B 383 " pdb=" N THR B 383 " pdb=" C THR B 383 " pdb=" CB THR B 383 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA HIS B 719 " pdb=" N HIS B 719 " pdb=" C HIS B 719 " pdb=" CB HIS B 719 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 2243 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N JUX A1201 " -0.045 2.00e-02 2.50e+03 8.31e-02 1.04e+02 pdb=" CA JUX A1201 " -0.074 2.00e-02 2.50e+03 pdb=" OH JUX A1201 " -0.094 2.00e-02 2.50e+03 pdb=" C1 JUX A1201 " -0.009 2.00e-02 2.50e+03 pdb=" C5 JUX A1201 " 0.116 2.00e-02 2.50e+03 pdb=" C9 JUX A1201 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N JUX B1201 " 0.045 2.00e-02 2.50e+03 8.27e-02 1.03e+02 pdb=" CA JUX B1201 " 0.074 2.00e-02 2.50e+03 pdb=" OH JUX B1201 " 0.094 2.00e-02 2.50e+03 pdb=" C1 JUX B1201 " 0.010 2.00e-02 2.50e+03 pdb=" C5 JUX B1201 " -0.116 2.00e-02 2.50e+03 pdb=" C9 JUX B1201 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 576 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C CYS B 576 " -0.046 2.00e-02 2.50e+03 pdb=" O CYS B 576 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 577 " 0.016 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4766 2.85 - 3.37: 14650 3.37 - 3.88: 23422 3.88 - 4.39: 26024 4.39 - 4.90: 45269 Nonbonded interactions: 114131 Sorted by model distance: nonbonded pdb=" OG1 THR B 412 " pdb="NA NA B1205 " model vdw 2.344 2.470 nonbonded pdb=" OG1 THR A 412 " pdb="NA NA A1205 " model vdw 2.349 2.470 nonbonded pdb=" OH TYR B 195 " pdb="NA NA B1205 " model vdw 2.356 2.470 nonbonded pdb=" OH TYR A 195 " pdb="NA NA A1205 " model vdw 2.367 2.470 nonbonded pdb=" OH JUX A1201 " pdb=" N2 JUX A1201 " model vdw 2.539 3.120 ... (remaining 114126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.360 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5758 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 : 0.002 0.061 14466 Z= 0.130 Angle : 0.549 7.356 19646 Z= 0.301 Chirality : 0.038 0.140 2246 Planarity : 0.005 0.083 2450 Dihedral : 10.559 143.431 5234 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 3.75 % Allowed : 5.73 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1796 helix: 1.99 (0.17), residues: 930 sheet: -0.66 (0.53), residues: 102 loop : -2.17 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.007 0.001 TYR A 399 PHE 0.012 0.001 PHE B 492 TRP 0.012 0.001 TRP A 596 HIS 0.003 0.000 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (14464) covalent geometry : angle 0.54869 / 0.30 (19642) SS BOND : bond 0.00022 / 0.01 ( 2) SS BOND : angle 0.22923 / 0.12 ( 4) hydrogen bonds : bond 0.12273 / 7.88 ( 755) hydrogen bonds : angle 5.18270 / 3.76 ( 2214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 523 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 GLU cc_start: 0.8190 (pt0) cc_final: 0.7834 (mp0) REVERT: B 164 SER cc_start: 0.6554 (m) cc_final: 0.6157 (t) REVERT: B 203 LEU cc_start: 0.9409 (tt) cc_final: 0.9129 (pp) REVERT: B 251 TYR cc_start: 0.7905 (m-10) cc_final: 0.7458 (m-80) REVERT: B 255 PHE cc_start: 0.8489 (m-10) cc_final: 0.8097 (m-80) REVERT: B 260 LEU cc_start: 0.9170 (mt) cc_final: 0.8662 (mt) REVERT: B 560 ILE cc_start: 0.9125 (mt) cc_final: 0.8210 (mp) REVERT: B 570 MET cc_start: 0.9025 (ttp) cc_final: 0.8688 (ttm) REVERT: B 616 TYR cc_start: 0.6440 (t80) cc_final: 0.6064 (m-10) REVERT: B 688 HIS cc_start: 0.5732 (m170) cc_final: 0.4936 (p-80) REVERT: B 723 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8071 (mp10) REVERT: B 817 ASN cc_start: 0.6663 (m-40) cc_final: 0.5751 (t0) REVERT: B 833 HIS cc_start: 0.8285 (t-170) cc_final: 0.7999 (t-170) REVERT: B 854 CYS cc_start: 0.6803 (m) cc_final: 0.5911 (m) REVERT: B 856 MET cc_start: 0.6513 (ttt) cc_final: 0.5336 (ttm) REVERT: B 1071 LEU cc_start: 0.8584 (mp) cc_final: 0.7522 (mp) REVERT: B 1084 ASP cc_start: 0.8194 (m-30) cc_final: 0.7344 (p0) REVERT: B 1093 VAL cc_start: 0.8637 (t) cc_final: 0.8386 (p) REVERT: A 137 PHE cc_start: 0.7758 (t80) cc_final: 0.7466 (t80) REVERT: A 211 MET cc_start: 0.6713 (mmt) cc_final: 0.6143 (mmp) REVERT: A 246 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5328 (t80) REVERT: A 415 MET cc_start: 0.7462 (tpp) cc_final: 0.6555 (tpp) REVERT: A 418 SER cc_start: 0.7608 (m) cc_final: 0.6796 (p) REVERT: A 629 TYR cc_start: 0.8310 (t80) cc_final: 0.7699 (t80) REVERT: A 692 LEU cc_start: 0.9227 (mt) cc_final: 0.8887 (tp) REVERT: A 702 LYS cc_start: 0.7274 (mtmm) cc_final: 0.6859 (mmmt) REVERT: A 796 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7624 (mmt180) REVERT: A 803 LEU cc_start: 0.7534 (mt) cc_final: 0.7133 (tt) REVERT: A 834 ASP cc_start: 0.6703 (m-30) cc_final: 0.6484 (m-30) REVERT: A 840 LEU cc_start: 0.7880 (tp) cc_final: 0.7368 (tp) outliers start: 57 outliers final: 9 residues processed: 555 average time/residue: 0.1071 time to fit residues: 86.8423 Evaluate side-chains 354 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 344 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 894 HIS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 8.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 ASN B1086 ASN A 586 ASN A 688 HIS ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN A 810 ASN A 881 HIS ** A1057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.146605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.129379 restraints weight = 50641.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.132170 restraints weight = 34609.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.134070 restraints weight = 25869.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.135403 restraints weight = 20641.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.136351 restraints weight = 17341.328| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14466 Z= 0.181 Angle : 0.753 11.376 19646 Z= 0.378 Chirality : 0.044 0.200 2246 Planarity : 0.005 0.052 2450 Dihedral : 9.019 143.534 2066 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.24 % Favored : 90.70 % Rotamer: Outliers : 4.74 % Allowed : 14.69 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.13 (0.20), residues: 1796 helix: 1.57 (0.17), residues: 934 sheet: -1.10 (0.45), residues: 126 loop : -2.20 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1049 TYR 0.045 0.002 TYR B 271 PHE 0.041 0.002 PHE B 564 TRP 0.021 0.002 TRP B 779 HIS 0.007 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (14464) covalent geometry : angle 0.75278 / 0.38 (19642) SS BOND : bond 0.00161 / 0.08 ( 2) SS BOND : angle 0.73922 / 0.42 ( 4) hydrogen bonds : bond 0.04399 / 2.92 ( 755) hydrogen bonds : angle 4.61208 / 3.35 ( 2214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 369 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.8054 (mmm) cc_final: 0.7688 (mmm) REVERT: B 203 LEU cc_start: 0.9404 (tt) cc_final: 0.9021 (pp) REVERT: B 254 LYS cc_start: 0.8555 (mttt) cc_final: 0.8351 (ptpt) REVERT: B 260 LEU cc_start: 0.8627 (mt) cc_final: 0.8315 (mt) REVERT: B 563 MET cc_start: 0.7888 (tpp) cc_final: 0.7631 (tpp) REVERT: B 570 MET cc_start: 0.8801 (ttp) cc_final: 0.8239 (ttm) REVERT: B 603 MET cc_start: 0.9024 (mtm) cc_final: 0.8530 (mtt) REVERT: B 1084 ASP cc_start: 0.7867 (m-30) cc_final: 0.7544 (p0) REVERT: A 150 MET cc_start: 0.7926 (mmm) cc_final: 0.7686 (mmm) REVERT: A 167 MET cc_start: 0.7896 (mtp) cc_final: 0.7622 (mtp) REVERT: A 211 MET cc_start: 0.6816 (mmt) cc_final: 0.6509 (mmp) REVERT: A 246 PHE cc_start: 0.5558 (OUTLIER) cc_final: 0.4988 (t80) REVERT: A 567 MET cc_start: 0.8391 (mtm) cc_final: 0.7827 (ptp) REVERT: A 570 MET cc_start: 0.8068 (tmm) cc_final: 0.7846 (tmm) REVERT: A 629 TYR cc_start: 0.7893 (t80) cc_final: 0.7381 (t80) REVERT: A 803 LEU cc_start: 0.7324 (mt) cc_final: 0.7001 (tt) REVERT: A 834 ASP cc_start: 0.7095 (m-30) cc_final: 0.6698 (m-30) REVERT: A 1088 MET cc_start: 0.7485 (tpt) cc_final: 0.7283 (tpp) outliers start: 72 outliers final: 42 residues processed: 410 average time/residue: 0.1038 time to fit residues: 64.3222 Evaluate side-chains 352 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 309 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 1 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 HIS ** A1057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.136216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.118625 restraints weight = 53717.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.121234 restraints weight = 36169.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.123052 restraints weight = 26805.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.124324 restraints weight = 21328.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.125233 restraints weight = 17951.295| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14466 Z= 0.246 Angle : 0.808 10.959 19646 Z= 0.419 Chirality : 0.047 0.225 2246 Planarity : 0.005 0.054 2450 Dihedral : 9.761 144.039 2063 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.91 % Favored : 91.04 % Rotamer: Outliers : 5.99 % Allowed : 17.72 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.71 (0.19), residues: 1796 helix: 0.95 (0.16), residues: 948 sheet: -1.47 (0.44), residues: 130 loop : -2.29 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 730 TYR 0.028 0.002 TYR B 271 PHE 0.032 0.003 PHE B 564 TRP 0.037 0.002 TRP A 122 HIS 0.010 0.002 HIS A1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.25 (14464) covalent geometry : angle 0.80765 / 0.42 (19642) SS BOND : bond 0.00214 / 0.11 ( 2) SS BOND : angle 0.45227 / 0.25 ( 4) hydrogen bonds : bond 0.04821 / 3.25 ( 755) hydrogen bonds : angle 4.85048 / 3.52 ( 2214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 331 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ASN cc_start: 0.6421 (m-40) cc_final: 0.5768 (p0) REVERT: B 130 MET cc_start: 0.8313 (mmm) cc_final: 0.7857 (mmm) REVERT: B 254 LYS cc_start: 0.8689 (mttt) cc_final: 0.8309 (mttt) REVERT: B 260 LEU cc_start: 0.8747 (mt) cc_final: 0.8411 (mt) REVERT: B 563 MET cc_start: 0.7929 (tpp) cc_final: 0.7671 (tpp) REVERT: B 570 MET cc_start: 0.8868 (ttp) cc_final: 0.8660 (ttm) REVERT: B 610 MET cc_start: 0.7752 (mtt) cc_final: 0.7172 (mtt) REVERT: B 796 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7997 (mtm180) REVERT: B 843 PHE cc_start: 0.7161 (t80) cc_final: 0.6112 (t80) REVERT: B 844 LEU cc_start: 0.8939 (mt) cc_final: 0.8673 (mp) REVERT: B 847 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7801 (m-70) REVERT: B 1050 MET cc_start: 0.7996 (mtt) cc_final: 0.7778 (mtt) REVERT: A 52 MET cc_start: 0.3995 (mpp) cc_final: 0.3661 (mpp) REVERT: A 144 MET cc_start: 0.6772 (ptp) cc_final: 0.6560 (ptt) REVERT: A 149 SER cc_start: 0.7634 (m) cc_final: 0.7300 (p) REVERT: A 211 MET cc_start: 0.6800 (mmt) cc_final: 0.6551 (mmp) REVERT: A 246 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.5261 (t80) REVERT: A 387 MET cc_start: 0.7223 (pmm) cc_final: 0.6849 (pmm) REVERT: A 629 TYR cc_start: 0.8121 (t80) cc_final: 0.7812 (t80) REVERT: A 739 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5957 (pttp) REVERT: A 834 ASP cc_start: 0.7524 (m-30) cc_final: 0.7086 (m-30) REVERT: A 845 LEU cc_start: 0.8452 (mt) cc_final: 0.8240 (mt) REVERT: A 871 MET cc_start: 0.8860 (mmp) cc_final: 0.8620 (mmp) REVERT: A 1088 MET cc_start: 0.7826 (tpt) cc_final: 0.7361 (tpp) outliers start: 91 outliers final: 56 residues processed: 379 average time/residue: 0.0971 time to fit residues: 56.2798 Evaluate side-chains 352 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 817 ASN Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 HIS Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 0.0770 chunk 100 optimal weight: 1.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN B 291 ASN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 ASN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.139531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.122061 restraints weight = 53113.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.124864 restraints weight = 34473.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.126797 restraints weight = 24995.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.128132 restraints weight = 19523.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.129122 restraints weight = 16183.855| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14466 Z= 0.151 Angle : 0.740 10.215 19646 Z= 0.370 Chirality : 0.044 0.236 2246 Planarity : 0.005 0.054 2450 Dihedral : 9.436 142.013 2060 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.41 % Favored : 90.53 % Rotamer: Outliers : 4.48 % Allowed : 21.01 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.56 (0.20), residues: 1796 helix: 1.10 (0.17), residues: 950 sheet: -1.09 (0.45), residues: 122 loop : -2.34 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 780 TYR 0.047 0.002 TYR B 271 PHE 0.034 0.002 PHE B 408 TRP 0.039 0.003 TRP A 851 HIS 0.012 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (14464) covalent geometry : angle 0.74049 / 0.37 (19642) SS BOND : bond 0.00062 / 0.03 ( 2) SS BOND : angle 0.24192 / 0.13 ( 4) hydrogen bonds : bond 0.04272 / 2.84 ( 755) hydrogen bonds : angle 4.61339 / 3.36 ( 2214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 333 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ASN cc_start: 0.6326 (m-40) cc_final: 0.5691 (p0) REVERT: B 130 MET cc_start: 0.8194 (mmm) cc_final: 0.7743 (mmm) REVERT: B 150 MET cc_start: 0.6929 (mmm) cc_final: 0.6671 (mmm) REVERT: B 203 LEU cc_start: 0.9545 (tp) cc_final: 0.9061 (pp) REVERT: B 254 LYS cc_start: 0.8592 (mttt) cc_final: 0.8217 (mttt) REVERT: B 260 LEU cc_start: 0.8791 (mt) cc_final: 0.8401 (mt) REVERT: B 374 MET cc_start: -0.0051 (ttt) cc_final: -0.0359 (ptm) REVERT: B 563 MET cc_start: 0.7925 (tpp) cc_final: 0.7700 (tpp) REVERT: B 566 LEU cc_start: 0.8494 (mm) cc_final: 0.8190 (mm) REVERT: B 796 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.8025 (mtm180) REVERT: B 843 PHE cc_start: 0.6992 (t80) cc_final: 0.6232 (t80) REVERT: B 847 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7996 (m-70) REVERT: B 1050 MET cc_start: 0.8072 (mtt) cc_final: 0.7760 (mtt) REVERT: B 1088 MET cc_start: 0.7783 (tpp) cc_final: 0.7309 (tpp) REVERT: A 52 MET cc_start: 0.3644 (mpp) cc_final: 0.3365 (mpp) REVERT: A 149 SER cc_start: 0.7593 (m) cc_final: 0.7227 (p) REVERT: A 211 MET cc_start: 0.6844 (mmt) cc_final: 0.6583 (mmp) REVERT: A 246 PHE cc_start: 0.5618 (OUTLIER) cc_final: 0.5180 (t80) REVERT: A 387 MET cc_start: 0.7351 (pmm) cc_final: 0.7021 (pmm) REVERT: A 460 VAL cc_start: 0.6454 (OUTLIER) cc_final: 0.6194 (p) REVERT: A 482 PRO cc_start: 0.6335 (Cg_endo) cc_final: 0.6129 (Cg_exo) REVERT: A 629 TYR cc_start: 0.8140 (t80) cc_final: 0.7769 (t80) REVERT: A 658 LEU cc_start: 0.6878 (mt) cc_final: 0.6660 (mt) REVERT: A 834 ASP cc_start: 0.7410 (m-30) cc_final: 0.7028 (m-30) REVERT: A 851 TRP cc_start: 0.7393 (m100) cc_final: 0.7152 (m100) REVERT: A 871 MET cc_start: 0.8797 (mmp) cc_final: 0.8590 (mmp) REVERT: A 1088 MET cc_start: 0.8033 (tpt) cc_final: 0.7011 (tpt) REVERT: A 1092 GLU cc_start: 0.7889 (pt0) cc_final: 0.6015 (pm20) outliers start: 68 outliers final: 41 residues processed: 367 average time/residue: 0.0928 time to fit residues: 52.8410 Evaluate side-chains 341 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 297 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 HIS ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 ASN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.137122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.119639 restraints weight = 53456.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.122318 restraints weight = 35387.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.124170 restraints weight = 25998.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.125484 restraints weight = 20565.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.126381 restraints weight = 17157.062| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14466 Z= 0.157 Angle : 0.740 10.392 19646 Z= 0.372 Chirality : 0.045 0.242 2246 Planarity : 0.005 0.055 2450 Dihedral : 9.397 142.014 2059 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.24 % Favored : 90.70 % Rotamer: Outliers : 5.40 % Allowed : 22.20 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.65 (0.20), residues: 1796 helix: 1.06 (0.16), residues: 948 sheet: -1.17 (0.45), residues: 122 loop : -2.41 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1105 TYR 0.018 0.001 TYR B 233 PHE 0.035 0.002 PHE A 466 TRP 0.057 0.002 TRP A 122 HIS 0.014 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (14464) covalent geometry : angle 0.74010 / 0.37 (19642) SS BOND : bond 0.00086 / 0.05 ( 2) SS BOND : angle 0.27758 / 0.14 ( 4) hydrogen bonds : bond 0.04319 / 2.87 ( 755) hydrogen bonds : angle 4.64694 / 3.37 ( 2214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 314 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.8236 (mmm) cc_final: 0.7786 (mmm) REVERT: B 203 LEU cc_start: 0.9471 (tp) cc_final: 0.9021 (pp) REVERT: B 230 MET cc_start: 0.5390 (mtt) cc_final: 0.5154 (tpp) REVERT: B 254 LYS cc_start: 0.8573 (mttt) cc_final: 0.8202 (mttt) REVERT: B 260 LEU cc_start: 0.8668 (mt) cc_final: 0.8314 (mt) REVERT: B 395 ASP cc_start: 0.5381 (OUTLIER) cc_final: 0.5147 (m-30) REVERT: B 479 LEU cc_start: 0.8259 (mt) cc_final: 0.7505 (tp) REVERT: B 843 PHE cc_start: 0.7027 (t80) cc_final: 0.6481 (t80) REVERT: B 1050 MET cc_start: 0.7985 (mtt) cc_final: 0.7686 (mtt) REVERT: B 1088 MET cc_start: 0.7854 (tpp) cc_final: 0.7459 (tpp) REVERT: A 52 MET cc_start: 0.4105 (mpp) cc_final: 0.3884 (mpp) REVERT: A 142 CYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7944 (p) REVERT: A 149 SER cc_start: 0.7721 (m) cc_final: 0.7401 (p) REVERT: A 211 MET cc_start: 0.6623 (mmt) cc_final: 0.6413 (mmp) REVERT: A 246 PHE cc_start: 0.5533 (OUTLIER) cc_final: 0.5126 (t80) REVERT: A 284 PHE cc_start: 0.4987 (t80) cc_final: 0.4599 (t80) REVERT: A 387 MET cc_start: 0.7242 (pmm) cc_final: 0.6840 (pmm) REVERT: A 479 LEU cc_start: 0.8148 (mt) cc_final: 0.7397 (tp) REVERT: A 603 MET cc_start: 0.7693 (mtm) cc_final: 0.7448 (mtm) REVERT: A 629 TYR cc_start: 0.8019 (t80) cc_final: 0.7751 (t80) REVERT: A 834 ASP cc_start: 0.7562 (m-30) cc_final: 0.7281 (m-30) REVERT: A 871 MET cc_start: 0.8917 (mmp) cc_final: 0.8668 (mmp) REVERT: A 893 MET cc_start: 0.8140 (mpp) cc_final: 0.7845 (pmm) REVERT: A 1088 MET cc_start: 0.7947 (tpt) cc_final: 0.7311 (tpt) REVERT: A 1092 GLU cc_start: 0.7877 (pt0) cc_final: 0.6779 (pm20) outliers start: 82 outliers final: 53 residues processed: 357 average time/residue: 0.0973 time to fit residues: 53.9120 Evaluate side-chains 348 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN A 291 ASN A 723 GLN ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.135183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.117702 restraints weight = 54314.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.120300 restraints weight = 35744.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.122168 restraints weight = 26099.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.123459 restraints weight = 20573.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.124341 restraints weight = 17169.032| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14466 Z= 0.169 Angle : 0.754 11.133 19646 Z= 0.380 Chirality : 0.045 0.197 2246 Planarity : 0.005 0.054 2450 Dihedral : 9.391 142.069 2057 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.30 % Favored : 90.65 % Rotamer: Outliers : 5.67 % Allowed : 22.53 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.72 (0.19), residues: 1796 helix: 0.97 (0.16), residues: 960 sheet: -1.14 (0.45), residues: 122 loop : -2.48 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1055 TYR 0.017 0.002 TYR B 271 PHE 0.026 0.002 PHE A 466 TRP 0.035 0.002 TRP A 122 HIS 0.008 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (14464) covalent geometry : angle 0.75391 / 0.38 (19642) SS BOND : bond 0.00107 / 0.06 ( 2) SS BOND : angle 0.29409 / 0.16 ( 4) hydrogen bonds : bond 0.04432 / 2.96 ( 755) hydrogen bonds : angle 4.71385 / 3.41 ( 2214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 306 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.8251 (mmm) cc_final: 0.7841 (mmm) REVERT: B 203 LEU cc_start: 0.9443 (tp) cc_final: 0.9024 (pp) REVERT: B 230 MET cc_start: 0.5535 (mtt) cc_final: 0.5180 (tpp) REVERT: B 254 LYS cc_start: 0.8554 (mttt) cc_final: 0.8202 (mttt) REVERT: B 260 LEU cc_start: 0.8653 (mt) cc_final: 0.8298 (mt) REVERT: B 479 LEU cc_start: 0.8230 (mt) cc_final: 0.7589 (tp) REVERT: B 563 MET cc_start: 0.7741 (tpp) cc_final: 0.7461 (tpp) REVERT: B 570 MET cc_start: 0.7755 (tpp) cc_final: 0.7049 (tpp) REVERT: B 603 MET cc_start: 0.9332 (mmm) cc_final: 0.8954 (mmm) REVERT: B 610 MET cc_start: 0.7803 (mtt) cc_final: 0.7422 (mtt) REVERT: B 847 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.8095 (m-70) REVERT: B 1050 MET cc_start: 0.8016 (mtt) cc_final: 0.7686 (mtt) REVERT: B 1088 MET cc_start: 0.7866 (tpp) cc_final: 0.7464 (tpp) REVERT: A 52 MET cc_start: 0.4288 (mpp) cc_final: 0.3953 (mpp) REVERT: A 149 SER cc_start: 0.7796 (m) cc_final: 0.7487 (p) REVERT: A 150 MET cc_start: 0.8745 (mmm) cc_final: 0.8488 (tpp) REVERT: A 246 PHE cc_start: 0.5925 (OUTLIER) cc_final: 0.5614 (t80) REVERT: A 284 PHE cc_start: 0.5046 (t80) cc_final: 0.4659 (t80) REVERT: A 387 MET cc_start: 0.7277 (pmm) cc_final: 0.6932 (pmm) REVERT: A 479 LEU cc_start: 0.8289 (mt) cc_final: 0.7608 (tt) REVERT: A 481 TRP cc_start: 0.5671 (t60) cc_final: 0.5368 (t60) REVERT: A 746 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.6233 (mm) REVERT: A 834 ASP cc_start: 0.7709 (m-30) cc_final: 0.7288 (m-30) REVERT: A 871 MET cc_start: 0.8910 (mmp) cc_final: 0.8704 (mmp) REVERT: A 1088 MET cc_start: 0.7732 (tpt) cc_final: 0.7481 (tpt) REVERT: A 1092 GLU cc_start: 0.7685 (pt0) cc_final: 0.7164 (pm20) outliers start: 86 outliers final: 62 residues processed: 358 average time/residue: 0.1044 time to fit residues: 57.8295 Evaluate side-chains 351 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 286 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 797 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 119 optimal weight: 0.0000 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 291 ASN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 ASN A 110 ASN A 229 ASN ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 ASN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.138498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.121173 restraints weight = 53488.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.123701 restraints weight = 35475.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.125488 restraints weight = 26171.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.126780 restraints weight = 20907.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.127720 restraints weight = 17556.130| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14466 Z= 0.141 Angle : 0.763 15.615 19646 Z= 0.375 Chirality : 0.044 0.186 2246 Planarity : 0.005 0.055 2450 Dihedral : 9.139 141.782 2057 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.19 % Favored : 90.76 % Rotamer: Outliers : 4.22 % Allowed : 24.24 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.65 (0.20), residues: 1796 helix: 1.07 (0.16), residues: 948 sheet: -1.14 (0.45), residues: 126 loop : -2.45 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1049 TYR 0.031 0.002 TYR B 233 PHE 0.034 0.002 PHE A 591 TRP 0.024 0.002 TRP A 122 HIS 0.005 0.001 HIS B 894 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (14464) covalent geometry : angle 0.76317 / 0.37 (19642) SS BOND : bond 0.00047 / 0.02 ( 2) SS BOND : angle 0.27942 / 0.15 ( 4) hydrogen bonds : bond 0.04204 / 2.76 ( 755) hydrogen bonds : angle 4.59744 / 3.36 ( 2214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 321 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.8157 (mmm) cc_final: 0.7676 (mmm) REVERT: B 150 MET cc_start: 0.7238 (mmt) cc_final: 0.6713 (mmm) REVERT: B 203 LEU cc_start: 0.9491 (tp) cc_final: 0.9061 (pp) REVERT: B 230 MET cc_start: 0.5549 (mtt) cc_final: 0.5207 (tpp) REVERT: B 254 LYS cc_start: 0.8588 (mttt) cc_final: 0.8209 (mttt) REVERT: B 260 LEU cc_start: 0.8656 (mt) cc_final: 0.8264 (mt) REVERT: B 479 LEU cc_start: 0.8272 (mt) cc_final: 0.7734 (tp) REVERT: B 563 MET cc_start: 0.7921 (tpp) cc_final: 0.7637 (tpp) REVERT: B 570 MET cc_start: 0.7968 (tpp) cc_final: 0.7231 (tpp) REVERT: B 603 MET cc_start: 0.9473 (mmm) cc_final: 0.9088 (mmm) REVERT: B 610 MET cc_start: 0.8053 (mtt) cc_final: 0.7506 (mtt) REVERT: B 759 GLN cc_start: 0.7662 (mt0) cc_final: 0.6597 (tm-30) REVERT: B 847 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7969 (m-70) REVERT: B 1049 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7813 (mtm-85) REVERT: B 1050 MET cc_start: 0.7996 (mtt) cc_final: 0.7638 (mtt) REVERT: B 1088 MET cc_start: 0.8050 (tpp) cc_final: 0.7702 (tpp) REVERT: B 1102 MET cc_start: 0.5887 (ppp) cc_final: 0.5345 (pmm) REVERT: A 52 MET cc_start: 0.4288 (mpp) cc_final: 0.3920 (mpp) REVERT: A 149 SER cc_start: 0.7669 (m) cc_final: 0.7363 (p) REVERT: A 246 PHE cc_start: 0.5981 (OUTLIER) cc_final: 0.5679 (t80) REVERT: A 387 MET cc_start: 0.7097 (pmm) cc_final: 0.6802 (pmm) REVERT: A 479 LEU cc_start: 0.8311 (mt) cc_final: 0.7739 (tt) REVERT: A 809 LYS cc_start: 0.7851 (tppt) cc_final: 0.7463 (tppt) REVERT: A 834 ASP cc_start: 0.7551 (m-30) cc_final: 0.7262 (m-30) outliers start: 64 outliers final: 51 residues processed: 357 average time/residue: 0.1013 time to fit residues: 56.3804 Evaluate side-chains 342 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 797 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 178 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B1073 ASN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.137922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.120594 restraints weight = 53401.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.123171 restraints weight = 35192.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.124982 restraints weight = 25875.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.126253 restraints weight = 20550.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.127032 restraints weight = 17277.128| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14466 Z= 0.146 Angle : 0.785 14.433 19646 Z= 0.385 Chirality : 0.045 0.292 2246 Planarity : 0.005 0.055 2450 Dihedral : 9.089 141.924 2057 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.02 % Favored : 90.92 % Rotamer: Outliers : 4.28 % Allowed : 25.16 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.72 (0.20), residues: 1796 helix: 1.03 (0.16), residues: 948 sheet: -1.35 (0.43), residues: 128 loop : -2.46 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1055 TYR 0.063 0.002 TYR B 233 PHE 0.051 0.002 PHE B 564 TRP 0.025 0.002 TRP B 615 HIS 0.008 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (14464) covalent geometry : angle 0.78480 / 0.38 (19642) SS BOND : bond 0.00064 / 0.03 ( 2) SS BOND : angle 0.27476 / 0.14 ( 4) hydrogen bonds : bond 0.04240 / 2.81 ( 755) hydrogen bonds : angle 4.62666 / 3.37 ( 2214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 301 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.8164 (mmm) cc_final: 0.7676 (mmm) REVERT: B 203 LEU cc_start: 0.9485 (tp) cc_final: 0.9082 (pp) REVERT: B 254 LYS cc_start: 0.8584 (mttt) cc_final: 0.8206 (mttt) REVERT: B 260 LEU cc_start: 0.8622 (mt) cc_final: 0.8239 (mt) REVERT: B 479 LEU cc_start: 0.8244 (mt) cc_final: 0.7666 (tp) REVERT: B 563 MET cc_start: 0.7825 (tpp) cc_final: 0.7563 (tpp) REVERT: B 570 MET cc_start: 0.7904 (tpp) cc_final: 0.7568 (tpp) REVERT: B 603 MET cc_start: 0.9467 (mmm) cc_final: 0.9125 (mmp) REVERT: B 610 MET cc_start: 0.8037 (mtt) cc_final: 0.7517 (mtt) REVERT: B 847 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7919 (m-70) REVERT: B 1049 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7846 (mtm-85) REVERT: B 1050 MET cc_start: 0.8002 (mtt) cc_final: 0.7645 (mtt) REVERT: B 1088 MET cc_start: 0.8031 (tpp) cc_final: 0.7707 (tpp) REVERT: B 1102 MET cc_start: 0.5899 (ppp) cc_final: 0.5453 (pmm) REVERT: A 52 MET cc_start: 0.4146 (mpp) cc_final: 0.3803 (mpp) REVERT: A 149 SER cc_start: 0.7661 (m) cc_final: 0.7424 (p) REVERT: A 246 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.5529 (t80) REVERT: A 387 MET cc_start: 0.7041 (pmm) cc_final: 0.6758 (pmm) REVERT: A 415 MET cc_start: 0.6135 (tpp) cc_final: 0.5914 (mmt) REVERT: A 479 LEU cc_start: 0.8311 (mt) cc_final: 0.7699 (tp) REVERT: A 481 TRP cc_start: 0.5659 (t60) cc_final: 0.5337 (t60) REVERT: A 809 LYS cc_start: 0.7876 (tppt) cc_final: 0.7436 (tppt) REVERT: A 834 ASP cc_start: 0.7594 (m-30) cc_final: 0.7306 (m-30) outliers start: 65 outliers final: 53 residues processed: 339 average time/residue: 0.0986 time to fit residues: 52.0237 Evaluate side-chains 344 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 289 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 176 optimal weight: 0.0570 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.134733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.117386 restraints weight = 54287.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.119915 restraints weight = 35481.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.121681 restraints weight = 26125.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.122872 restraints weight = 20829.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.123675 restraints weight = 17583.831| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14466 Z= 0.170 Angle : 0.800 13.701 19646 Z= 0.400 Chirality : 0.046 0.260 2246 Planarity : 0.005 0.055 2450 Dihedral : 9.329 142.073 2057 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.52 % Favored : 90.42 % Rotamer: Outliers : 3.89 % Allowed : 25.10 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.80 (0.20), residues: 1796 helix: 0.96 (0.16), residues: 958 sheet: -1.49 (0.43), residues: 132 loop : -2.52 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 820 TYR 0.054 0.002 TYR B 233 PHE 0.048 0.002 PHE B 564 TRP 0.034 0.002 TRP A 307 HIS 0.007 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (14464) covalent geometry : angle 0.80007 / 0.40 (19642) SS BOND : bond 0.00112 / 0.06 ( 2) SS BOND : angle 0.30047 / 0.16 ( 4) hydrogen bonds : bond 0.04430 / 2.95 ( 755) hydrogen bonds : angle 4.73894 / 3.45 ( 2214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 294 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.8231 (mmm) cc_final: 0.7760 (mmm) REVERT: B 226 MET cc_start: 0.6223 (tmm) cc_final: 0.5893 (tmm) REVERT: B 254 LYS cc_start: 0.8630 (mttt) cc_final: 0.8247 (mttt) REVERT: B 260 LEU cc_start: 0.8719 (mt) cc_final: 0.8328 (mt) REVERT: B 475 VAL cc_start: 0.8716 (t) cc_final: 0.8371 (p) REVERT: B 479 LEU cc_start: 0.8346 (mt) cc_final: 0.7739 (tp) REVERT: B 563 MET cc_start: 0.7772 (tpp) cc_final: 0.7516 (tpp) REVERT: B 570 MET cc_start: 0.8017 (tpp) cc_final: 0.7590 (tpp) REVERT: B 603 MET cc_start: 0.9492 (mmm) cc_final: 0.9173 (mmp) REVERT: B 610 MET cc_start: 0.8123 (mtt) cc_final: 0.7559 (mtt) REVERT: B 759 GLN cc_start: 0.7727 (mt0) cc_final: 0.6699 (tm-30) REVERT: B 796 ARG cc_start: 0.8238 (mtt90) cc_final: 0.7983 (mtt90) REVERT: B 847 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8017 (m-70) REVERT: B 1049 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7943 (mtm-85) REVERT: B 1050 MET cc_start: 0.8139 (mtt) cc_final: 0.7797 (mtt) REVERT: B 1088 MET cc_start: 0.8059 (tpp) cc_final: 0.7680 (tpp) REVERT: B 1102 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5677 (pmm) REVERT: A 52 MET cc_start: 0.4290 (mpp) cc_final: 0.3885 (mpp) REVERT: A 57 MET cc_start: 0.1965 (tpt) cc_final: 0.1163 (tpp) REVERT: A 387 MET cc_start: 0.7150 (pmm) cc_final: 0.6862 (pmm) REVERT: A 479 LEU cc_start: 0.8515 (mt) cc_final: 0.7940 (tp) REVERT: A 834 ASP cc_start: 0.7757 (m-30) cc_final: 0.7457 (m-30) REVERT: A 1088 MET cc_start: 0.7588 (tpt) cc_final: 0.7329 (tpt) outliers start: 59 outliers final: 56 residues processed: 329 average time/residue: 0.1011 time to fit residues: 51.2423 Evaluate side-chains 341 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 1102 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN B 291 ASN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 HIS B 870 GLN B1073 ASN ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.136714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.119650 restraints weight = 53703.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.122167 restraints weight = 35545.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.123959 restraints weight = 26193.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.125140 restraints weight = 20750.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.125925 restraints weight = 17550.024| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14466 Z= 0.147 Angle : 0.814 14.050 19646 Z= 0.400 Chirality : 0.046 0.259 2246 Planarity : 0.005 0.063 2450 Dihedral : 9.124 142.344 2055 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.47 % Favored : 90.48 % Rotamer: Outliers : 3.56 % Allowed : 26.61 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.86 (0.19), residues: 1796 helix: 0.89 (0.16), residues: 946 sheet: -1.32 (0.44), residues: 128 loop : -2.50 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1049 TYR 0.042 0.002 TYR B 233 PHE 0.049 0.002 PHE B 564 TRP 0.033 0.002 TRP A 307 HIS 0.007 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14464) covalent geometry : angle 0.81374 / 0.40 (19642) SS BOND : bond 0.00044 / 0.02 ( 2) SS BOND : angle 0.27166 / 0.14 ( 4) hydrogen bonds : bond 0.04341 / 2.88 ( 755) hydrogen bonds : angle 4.71817 / 3.45 ( 2214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 TYR cc_start: 0.7824 (t80) cc_final: 0.7496 (t80) REVERT: B 254 LYS cc_start: 0.8530 (mttt) cc_final: 0.8177 (mttt) REVERT: B 260 LEU cc_start: 0.8549 (mt) cc_final: 0.8215 (mt) REVERT: B 475 VAL cc_start: 0.8610 (t) cc_final: 0.8332 (p) REVERT: B 479 LEU cc_start: 0.8273 (mt) cc_final: 0.7757 (tp) REVERT: B 563 MET cc_start: 0.7619 (tpp) cc_final: 0.7353 (tpp) REVERT: B 610 MET cc_start: 0.7951 (mtt) cc_final: 0.7658 (mtt) REVERT: B 629 TYR cc_start: 0.7642 (t80) cc_final: 0.7396 (t80) REVERT: B 759 GLN cc_start: 0.7493 (mt0) cc_final: 0.6660 (tm-30) REVERT: B 796 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7492 (mtm180) REVERT: B 830 TRP cc_start: 0.7394 (t-100) cc_final: 0.6985 (t-100) REVERT: B 847 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.7807 (m-70) REVERT: B 1049 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7774 (mtm-85) REVERT: B 1050 MET cc_start: 0.7926 (mtt) cc_final: 0.7602 (mtt) REVERT: B 1088 MET cc_start: 0.7955 (tpp) cc_final: 0.7669 (tpp) REVERT: B 1102 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5419 (pmm) REVERT: A 52 MET cc_start: 0.4005 (mpp) cc_final: 0.3703 (mpp) REVERT: A 57 MET cc_start: 0.1635 (tpt) cc_final: 0.1265 (tpp) REVERT: A 142 CYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7741 (p) REVERT: A 387 MET cc_start: 0.7035 (pmm) cc_final: 0.6762 (pmm) REVERT: A 479 LEU cc_start: 0.8358 (mt) cc_final: 0.7840 (tp) REVERT: A 481 TRP cc_start: 0.5656 (t60) cc_final: 0.5146 (t60) REVERT: A 658 LEU cc_start: 0.6971 (mt) cc_final: 0.6765 (mt) REVERT: A 833 HIS cc_start: 0.7671 (t70) cc_final: 0.7197 (t-90) REVERT: A 1088 MET cc_start: 0.7539 (tpt) cc_final: 0.7214 (tpt) outliers start: 54 outliers final: 48 residues processed: 331 average time/residue: 0.0964 time to fit residues: 49.8979 Evaluate side-chains 343 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1102 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 HIS Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** 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 = 0.4559 r_free = 0.4559 target = 0.135801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.118786 restraints weight = 54572.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.121335 restraints weight = 35696.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.123131 restraints weight = 26068.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.124359 restraints weight = 20571.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.125158 restraints weight = 17224.179| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.6993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.321 14466 Z= 0.278 Angle : 1.136 59.146 19646 Z= 0.648 Chirality : 0.051 0.604 2246 Planarity : 0.005 0.066 2450 Dihedral : 9.152 142.337 2055 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.41 % Favored : 90.53 % Rotamer: Outliers : 3.75 % Allowed : 26.61 % Favored : 69.63 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.87 (0.19), residues: 1796 helix: 0.87 (0.16), residues: 946 sheet: -1.31 (0.44), residues: 128 loop : -2.50 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1081 TYR 0.041 0.002 TYR B 233 PHE 0.048 0.002 PHE B 564 TRP 0.045 0.003 TRP B 788 HIS 0.021 0.002 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.28 (14464) covalent geometry : angle 1.13614 / 0.65 (19642) SS BOND : bond 0.00055 / 0.03 ( 2) SS BOND : angle 0.25917 / 0.13 ( 4) hydrogen bonds : bond 0.04354 / 2.89 ( 755) hydrogen bonds : angle 4.74457 / 3.48 ( 2214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.30 seconds wall clock time: 44 minutes 16.65 seconds (2656.65 seconds total)