Starting phenix.real_space_refine on Fri Oct 23 07:32:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ofi_70433/10_2026/9ofi_70433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ofi_70433/10_2026/9ofi_70433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ofi_70433/10_2026/9ofi_70433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ofi_70433/10_2026/9ofi_70433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ofi_70433/10_2026/9ofi_70433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ofi_70433/10_2026/9ofi_70433.map" } resolution = 3.41 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= 0.020 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: 6 Type Number sf(0) Gaussians Br 2 7.06 5 P 2 5.49 5 S 61 5.16 5 C 5606 2.51 5 N 1448 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8744 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2168 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 5, 'ARG:plan': 2, 'GLU:plan': 9, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2120 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'ARG:plan': 5, 'GLU:plan': 9, 'GLN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2135 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "D" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2139 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'J86': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'J86': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.15, per 1000 atoms: 0.25 Number of scatterers: 8744 At special positions: 0 Unit cell: (103.837, 132.539, 71.757, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 61 16.00 P 2 15.00 O 1625 8.00 N 1448 7.00 C 5606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 913 " distance=2.03 Simple disulfide: pdb=" SG CYS D 537 " - pdb=" SG CYS D 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 543 " - pdb=" SG CYS D 576 " distance=2.03 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 913 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 902 " - " ASN A 771 " " NAG B1001 " - " ASN B 886 " " NAG C 901 " - " ASN C 471 " " NAG C 902 " - " ASN C 771 " " NAG D1001 " - " ASN D 886 " " NAG E 1 " - " ASN B 549 " " NAG F 1 " - " ASN D 549 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 237.8 milliseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 15 sheets defined 40.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 783 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.614A pdb=" N ASN C 674 " --> pdb=" O PRO C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'B' and resid 550 through 563 Processing helix chain 'B' and resid 578 through 592 Processing helix chain 'B' and resid 614 through 622 Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.926A pdb=" N VAL B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 800 through 810 Processing helix chain 'B' and resid 810 through 819 removed outlier: 4.516A pdb=" N ARG B 819 " --> pdb=" O GLU B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 834 Processing helix chain 'B' and resid 846 through 856 removed outlier: 3.657A pdb=" N TYR B 851 " --> pdb=" O ALA B 847 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 898 Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'D' and resid 550 through 563 removed outlier: 3.640A pdb=" N LEU D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 572 Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 614 through 622 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 782 through 787 removed outlier: 3.694A pdb=" N HIS D 786 " --> pdb=" O ASP D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 810 Processing helix chain 'D' and resid 810 through 818 Processing helix chain 'D' and resid 824 through 834 Processing helix chain 'D' and resid 846 through 856 removed outlier: 3.541A pdb=" N TYR D 851 " --> pdb=" O ALA D 847 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP D 856 " --> pdb=" O GLU D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 897 Processing helix chain 'D' and resid 898 through 908 Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.212A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET A 762 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 528 " --> pdb=" O MET A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 412 removed outlier: 3.595A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA4, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.650A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE A 540 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LEU A 752 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N VAL A 542 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N GLY A 750 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 475 through 478 removed outlier: 6.135A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 401 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 412 removed outlier: 3.569A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AA8, first strand: chain 'C' and resid 534 through 535 removed outlier: 4.105A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.370A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 529 through 530 removed outlier: 6.919A pdb=" N LEU B 542 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE B 599 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU B 544 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 517 " --> pdb=" O ASP B 596 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR B 630 " --> pdb=" O GLY B 874 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY B 874 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE B 632 " --> pdb=" O GLY B 872 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY B 872 " --> pdb=" O PHE B 632 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 655 " --> pdb=" O VAL B 864 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS B 866 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 653 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE B 868 " --> pdb=" O THR B 651 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR B 651 " --> pdb=" O PHE B 868 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N ILE B 870 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N PHE B 649 " --> pdb=" O ILE B 870 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AB3, first strand: chain 'D' and resid 514 through 519 removed outlier: 4.043A pdb=" N ASP D 596 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 517 " --> pdb=" O ASP D 596 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 529 through 530 Processing sheet with id=AB5, first strand: chain 'D' and resid 608 through 609 Processing sheet with id=AB6, first strand: chain 'D' and resid 628 through 633 removed outlier: 4.938A pdb=" N THR D 630 " --> pdb=" O GLY D 874 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY D 874 " --> pdb=" O THR D 630 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE D 632 " --> pdb=" O GLY D 872 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY D 872 " --> pdb=" O PHE D 632 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N GLY D 865 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N VAL D 657 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N ILE D 655 " --> pdb=" O PRO D 867 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA D 869 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 653 " --> pdb=" O ALA D 869 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE D 649 " --> pdb=" O TYR D 873 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 843 " --> pdb=" O GLY D 795 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1756 1.33 - 1.48: 3358 1.48 - 1.63: 3739 1.63 - 1.79: 4 1.79 - 1.94: 94 Bond restraints: 8951 Sorted by residual: bond pdb=" C5 J86 C 903 " pdb=" N3 J86 C 903 " ideal model delta sigma weight residual 1.384 1.503 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C5 J86 A 903 " pdb=" N3 J86 A 903 " ideal model delta sigma weight residual 1.384 1.491 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C4 J86 A 903 " pdb=" N2 J86 A 903 " ideal model delta sigma weight residual 1.383 1.487 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C4 J86 C 903 " pdb=" N2 J86 C 903 " ideal model delta sigma weight residual 1.383 1.482 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C11 J86 C 903 " pdb=" N3 J86 C 903 " ideal model delta sigma weight residual 1.354 1.438 -0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 8946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 12132 3.51 - 7.01: 38 7.01 - 10.52: 4 10.52 - 14.02: 0 14.02 - 17.53: 4 Bond angle restraints: 12178 Sorted by residual: angle pdb=" C2 J86 C 903 " pdb=" C3 J86 C 903 " pdb=" C7 J86 C 903 " ideal model delta sigma weight residual 120.09 102.56 17.53 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C2 J86 A 903 " pdb=" C3 J86 A 903 " pdb=" C7 J86 A 903 " ideal model delta sigma weight residual 120.09 103.55 16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb=" C2 J86 C 903 " pdb=" C3 J86 C 903 " pdb=" C4 J86 C 903 " ideal model delta sigma weight residual 121.16 136.73 -15.57 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C2 J86 A 903 " pdb=" C3 J86 A 903 " pdb=" C4 J86 A 903 " ideal model delta sigma weight residual 121.16 135.68 -14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C THR A 683 " pdb=" N VAL A 684 " pdb=" CA VAL A 684 " ideal model delta sigma weight residual 121.97 116.41 5.56 1.80e+00 3.09e-01 9.53e+00 ... (remaining 12173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 5083 17.08 - 34.17: 285 34.17 - 51.25: 61 51.25 - 68.34: 15 68.34 - 85.42: 2 Dihedral angle restraints: 5446 sinusoidal: 2154 harmonic: 3292 Sorted by residual: dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 575 " pdb=" CB CYS B 575 " ideal model delta sinusoidal sigma weight residual 93.00 135.07 -42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA PHE C 472 " pdb=" C PHE C 472 " pdb=" N THR C 473 " pdb=" CA THR C 473 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA ASN C 491 " pdb=" C ASN C 491 " pdb=" N ASN C 492 " pdb=" CA ASN C 492 " ideal model delta harmonic sigma weight residual -180.00 -164.04 -15.96 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 954 0.036 - 0.072: 307 0.072 - 0.108: 118 0.108 - 0.143: 25 0.143 - 0.179: 3 Chirality restraints: 1407 Sorted by residual: chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 886 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 771 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1404 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 515 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO C 516 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 822 " 0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO B 823 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 823 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 823 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 513 " -0.005 2.00e-02 2.50e+03 1.08e-02 1.17e+00 pdb=" C ILE C 513 " 0.019 2.00e-02 2.50e+03 pdb=" O ILE C 513 " -0.007 2.00e-02 2.50e+03 pdb=" N VAL C 514 " -0.006 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 264 2.70 - 3.25: 8947 3.25 - 3.80: 14300 3.80 - 4.35: 17490 4.35 - 4.90: 29805 Nonbonded interactions: 70806 Sorted by model distance: nonbonded pdb=" O THR C 396 " pdb=" OG1 THR C 473 " model vdw 2.151 3.040 nonbonded pdb=" O THR A 396 " pdb=" OG1 THR A 473 " model vdw 2.189 3.040 nonbonded pdb=" OD2 ASP D 590 " pdb=" OH TYR D 894 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP D 602 " pdb=" OG1 THR D 614 " model vdw 2.222 3.040 nonbonded pdb=" O PRO A 516 " pdb=" N3 J86 A 903 " model vdw 2.249 3.120 ... (remaining 70801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 395 through 441 or (resid 448 and (name N or name CA or na \ me C or name O or name CB )) or resid 449 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 535 or (resid \ 536 and (name N or name CA or name C or name O or name CB )) or resid 537 throug \ h 545 or (resid 663 and (name N or name CA or name C or name O or name CB )) or \ resid 664 through 694 or (resid 695 and (name N or name CA or name C or name O o \ r name CB )) or resid 696 through 764 or (resid 765 and (name N or name CA or na \ me C or name O or name CB )) or resid 766 through 768 or (resid 769 through 770 \ and (name N or name CA or name C or name O or name CB )) or resid 771 through 90 \ 3)) selection = (chain 'C' and (resid 395 through 542 or (resid 543 through 663 and (name N or n \ ame CA or name C or name O or name CB )) or resid 664 through 673 or (resid 674 \ and (name N or name CA or name C or name O or name CB )) or resid 675 through 90 \ 3)) } ncs_group { reference = (chain 'B' and (resid 513 through 550 or (resid 551 through 552 and (name N or n \ ame CA or name C or name O or name CB )) or resid 553 through 563 or (resid 564 \ through 567 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 8 through 797 or (resid 798 through 799 and (name N or name CA or name C or name \ O or name CB )) or resid 800 through 806 or (resid 807 and (name N or name CA o \ r name C or name O or name CB )) or resid 808 through 811 or (resid 812 and (nam \ e N or name CA or name C or name O or name CB )) or resid 813 through 837 or (re \ sid 838 and (name N or name CA or name C or name O or name CB )) or resid 839 th \ rough 857 or (resid 858 and (name N or name CA or name C or name O or name CB )) \ or resid 859 through 865 or (resid 866 and (name N or name CA or name C or name \ O or name CB )) or resid 867 through 892 or (resid 893 and (name N or name CA o \ r name C or name O or name CB )) or resid 894 through 1001)) selection = (chain 'D' and (resid 513 through 546 or (resid 547 through 548 and (name N or n \ ame CA or name C or name O or name CB )) or resid 549 through 555 or (resid 556 \ and (name N or name CA or name C or name O or name CB )) or resid 557 through 58 \ 1 or (resid 582 and (name N or name CA or name C or name O or name CB )) or resi \ d 583 through 584 or (resid 585 and (name N or name CA or name C or name O or na \ me CB )) or resid 586 through 603 or (resid 604 and (name N or name CA or name C \ or name O or name CB )) or resid 605 through 783 or (resid 784 through 785 and \ (name N or name CA or name C or name O or name CB )) or resid 786 through 829 or \ (resid 830 and (name N or name CA or name C or name O or name CB )) or resid 83 \ 1 through 832 or (resid 833 and (name N or name CA or name C or name O or name C \ B )) or resid 834 through 908 or (resid 909 through 911 and (name N or name CA o \ r name C or name O or name CB )) or resid 912 through 1001)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.760 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.005 0.119 8973 Z= 0.220 Angle : 0.653 17.525 12229 Z= 0.293 Chirality : 0.042 0.179 1407 Planarity : 0.003 0.029 1536 Dihedral : 11.381 85.422 3282 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.92 % Allowed : 8.06 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.26), residues: 1110 helix: 1.22 (0.25), residues: 429 sheet: -1.20 (0.43), residues: 156 loop : -0.78 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 397 TYR 0.013 0.001 TYR D 579 PHE 0.017 0.001 PHE C 533 TRP 0.008 0.001 TRP B 907 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 ( 8951) covalent geometry : angle 0.64580 / 0.29 (12178) SS BOND : bond 0.00276 / 0.20 ( 12) SS BOND : angle 0.39418 / 0.26 ( 24) hydrogen bonds : bond 0.16892 / 10.88 ( 367) hydrogen bonds : angle 7.35778 / 5.10 ( 1044) Misc. bond : bond 0.00591 / 0.31 ( 1) link_BETA1-4 : bond 0.00132 / 0.07 ( 2) link_BETA1-4 : angle 2.61873 / 1.38 ( 6) link_NAG-ASN : bond 0.00392 / 0.31 ( 7) link_NAG-ASN : angle 2.13149 / 1.37 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 224 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: A 719 GLN cc_start: 0.7206 (tp40) cc_final: 0.6947 (tp-100) REVERT: A 723 ASP cc_start: 0.7737 (m-30) cc_final: 0.7269 (m-30) REVERT: B 883 LEU cc_start: 0.7183 (pp) cc_final: 0.6431 (tp) REVERT: D 521 ILE cc_start: 0.8245 (mt) cc_final: 0.7902 (mt) REVERT: D 792 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7736 (t80) outliers start: 8 outliers final: 3 residues processed: 231 average time/residue: 0.0917 time to fit residues: 29.4032 Evaluate side-chains 175 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain D residue 792 PHE Chi-restraints excluded: chain D residue 913 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 0.0370 chunk 106 optimal weight: 3.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 ASN C 696 GLN D 786 HIS D 834 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122692 restraints weight = 12332.531| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.35 r_work: 0.3348 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8973 Z= 0.126 Angle : 0.584 7.041 12229 Z= 0.300 Chirality : 0.043 0.186 1407 Planarity : 0.004 0.033 1536 Dihedral : 7.938 88.700 1454 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.99 % Allowed : 13.12 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1110 helix: 1.17 (0.25), residues: 439 sheet: -1.04 (0.42), residues: 167 loop : -0.84 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 793 TYR 0.012 0.001 TYR D 816 PHE 0.021 0.002 PHE D 593 TRP 0.009 0.001 TRP B 907 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8951) covalent geometry : angle 0.57453 / 0.30 (12178) SS BOND : bond 0.00350 / 0.25 ( 12) SS BOND : angle 1.52488 / 1.03 ( 24) hydrogen bonds : bond 0.03806 / 2.41 ( 367) hydrogen bonds : angle 5.90139 / 4.13 ( 1044) Misc. bond : bond 0.00943 / 0.50 ( 1) link_BETA1-4 : bond 0.00293 / 0.15 ( 2) link_BETA1-4 : angle 2.45451 / 1.26 ( 6) link_NAG-ASN : bond 0.00367 / 0.28 ( 7) link_NAG-ASN : angle 1.77355 / 1.21 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 ASP cc_start: 0.8470 (m-30) cc_final: 0.8232 (m-30) REVERT: C 453 GLN cc_start: 0.8488 (mp10) cc_final: 0.8280 (mp10) REVERT: C 540 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8693 (mm) REVERT: C 719 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7196 (tm-30) REVERT: B 883 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.6553 (tp) REVERT: B 893 GLN cc_start: 0.8359 (tt0) cc_final: 0.7998 (tp40) REVERT: D 792 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7834 (t80) REVERT: D 834 ASN cc_start: 0.7165 (m-40) cc_final: 0.6827 (m-40) REVERT: D 873 TYR cc_start: 0.9182 (m-10) cc_final: 0.8912 (m-10) outliers start: 26 outliers final: 12 residues processed: 205 average time/residue: 0.0884 time to fit residues: 25.5409 Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain D residue 792 PHE Chi-restraints excluded: chain D residue 831 TYR Chi-restraints excluded: chain D residue 859 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [50, 25, 15, 94, 46, 104, 80, 83, 72, 31, 84] chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 94 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 ASN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122878 restraints weight = 12264.761| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.35 r_work: 0.3257 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8973 Z= 0.119 Angle : 0.559 7.233 12229 Z= 0.287 Chirality : 0.042 0.160 1407 Planarity : 0.004 0.034 1536 Dihedral : 7.364 85.602 1450 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.99 % Allowed : 14.61 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.26), residues: 1110 helix: 1.17 (0.25), residues: 439 sheet: -1.07 (0.42), residues: 167 loop : -0.86 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 793 TYR 0.017 0.002 TYR D 894 PHE 0.022 0.002 PHE B 593 TRP 0.012 0.001 TRP C 498 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8951) covalent geometry : angle 0.55162 / 0.29 (12178) SS BOND : bond 0.00386 / 0.27 ( 12) SS BOND : angle 0.91932 / 0.61 ( 24) hydrogen bonds : bond 0.03148 / 2.02 ( 367) hydrogen bonds : angle 5.68101 / 3.97 ( 1044) Misc. bond : bond 0.00830 / 0.44 ( 1) link_BETA1-4 : bond 0.00422 / 0.21 ( 2) link_BETA1-4 : angle 2.19810 / 1.15 ( 6) link_NAG-ASN : bond 0.00307 / 0.24 ( 7) link_NAG-ASN : angle 1.76382 / 1.22 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 723 ASP cc_start: 0.8469 (m-30) cc_final: 0.8226 (t0) REVERT: B 803 GLU cc_start: 0.8808 (tp30) cc_final: 0.8381 (tt0) REVERT: B 883 LEU cc_start: 0.7700 (pp) cc_final: 0.6550 (tp) REVERT: B 893 GLN cc_start: 0.8350 (tt0) cc_final: 0.7999 (tp40) REVERT: D 834 ASN cc_start: 0.7120 (m-40) cc_final: 0.6772 (m-40) REVERT: D 873 TYR cc_start: 0.9199 (m-10) cc_final: 0.8953 (m-80) outliers start: 26 outliers final: 19 residues processed: 196 average time/residue: 0.0835 time to fit residues: 23.0810 Evaluate side-chains 182 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 799 GLU Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 913 CYS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 831 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [64, 87, 103, 34, 11, 23, 77, 3, 19, 39, 63] chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 ASN A 520 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119529 restraints weight = 12500.075| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.45 r_work: 0.3222 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8973 Z= 0.145 Angle : 0.568 7.160 12229 Z= 0.292 Chirality : 0.043 0.193 1407 Planarity : 0.003 0.035 1536 Dihedral : 7.127 85.025 1448 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.91 % Allowed : 14.27 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1110 helix: 1.19 (0.25), residues: 436 sheet: -1.09 (0.43), residues: 161 loop : -0.77 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 671 TYR 0.022 0.002 TYR D 894 PHE 0.016 0.002 PHE A 458 TRP 0.012 0.001 TRP C 498 HIS 0.006 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 8951) covalent geometry : angle 0.56069 / 0.29 (12178) SS BOND : bond 0.00282 / 0.21 ( 12) SS BOND : angle 0.88555 / 0.59 ( 24) hydrogen bonds : bond 0.03033 / 1.94 ( 367) hydrogen bonds : angle 5.53191 / 3.86 ( 1044) Misc. bond : bond 0.00820 / 0.43 ( 1) link_BETA1-4 : bond 0.00339 / 0.17 ( 2) link_BETA1-4 : angle 2.07325 / 1.09 ( 6) link_NAG-ASN : bond 0.00343 / 0.27 ( 7) link_NAG-ASN : angle 1.90745 / 1.33 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 540 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8703 (mm) REVERT: C 672 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7445 (pt) REVERT: B 803 GLU cc_start: 0.8809 (tp30) cc_final: 0.8487 (tt0) REVERT: B 883 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.6206 (tp) REVERT: B 893 GLN cc_start: 0.8366 (tt0) cc_final: 0.7985 (tp40) REVERT: D 834 ASN cc_start: 0.7081 (m-40) cc_final: 0.6700 (m-40) REVERT: D 844 MET cc_start: 0.9101 (tpt) cc_final: 0.8868 (tpt) outliers start: 34 outliers final: 21 residues processed: 190 average time/residue: 0.0860 time to fit residues: 22.7301 Evaluate side-chains 182 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 799 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 831 TYR Chi-restraints excluded: chain D residue 883 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [28, 34, 50, 81, 88, 14, 104, 89, 72, 46, 67] chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 520 ASN B 821 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121485 restraints weight = 12358.749| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.38 r_work: 0.3302 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8973 Z= 0.131 Angle : 0.592 15.644 12229 Z= 0.292 Chirality : 0.043 0.228 1407 Planarity : 0.003 0.035 1536 Dihedral : 7.310 86.086 1448 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.68 % Allowed : 14.50 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.26), residues: 1110 helix: 1.18 (0.24), residues: 436 sheet: -1.13 (0.42), residues: 165 loop : -0.81 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 671 TYR 0.018 0.002 TYR D 894 PHE 0.014 0.001 PHE A 458 TRP 0.020 0.001 TRP C 498 HIS 0.006 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8951) covalent geometry : angle 0.55971 / 0.29 (12178) SS BOND : bond 0.00249 / 0.18 ( 12) SS BOND : angle 0.79343 / 0.51 ( 24) hydrogen bonds : bond 0.02929 / 1.89 ( 367) hydrogen bonds : angle 5.37881 / 3.76 ( 1044) Misc. bond : bond 0.00807 / 0.42 ( 1) link_BETA1-4 : bond 0.00227 / 0.12 ( 2) link_BETA1-4 : angle 2.01298 / 1.06 ( 6) link_NAG-ASN : bond 0.00381 / 0.30 ( 7) link_NAG-ASN : angle 4.51961 / 3.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 540 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8710 (mm) REVERT: C 672 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7558 (pt) REVERT: B 803 GLU cc_start: 0.8776 (tp30) cc_final: 0.8466 (tt0) REVERT: B 883 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.6494 (tp) REVERT: B 893 GLN cc_start: 0.8361 (tt0) cc_final: 0.8018 (tp40) REVERT: D 834 ASN cc_start: 0.7102 (m-40) cc_final: 0.6691 (m-40) REVERT: D 844 MET cc_start: 0.9088 (tpt) cc_final: 0.8877 (tpt) REVERT: D 873 TYR cc_start: 0.9187 (m-10) cc_final: 0.8934 (m-80) outliers start: 32 outliers final: 20 residues processed: 198 average time/residue: 0.0867 time to fit residues: 24.0782 Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 799 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 831 TYR Chi-restraints excluded: chain D residue 859 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [85, 39, 89, 83, 38, 54, 44, 49, 104, 50, 103] chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 705 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120452 restraints weight = 12188.521| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.34 r_work: 0.3279 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8973 Z= 0.150 Angle : 0.588 12.503 12229 Z= 0.295 Chirality : 0.043 0.324 1407 Planarity : 0.003 0.037 1536 Dihedral : 6.968 87.095 1448 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.60 % Allowed : 14.50 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.26), residues: 1110 helix: 1.14 (0.25), residues: 437 sheet: -1.16 (0.42), residues: 165 loop : -0.78 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 671 TYR 0.016 0.002 TYR D 894 PHE 0.016 0.002 PHE A 458 TRP 0.019 0.001 TRP C 498 HIS 0.007 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 8951) covalent geometry : angle 0.56637 / 0.29 (12178) SS BOND : bond 0.00258 / 0.19 ( 12) SS BOND : angle 0.81886 / 0.54 ( 24) hydrogen bonds : bond 0.02970 / 1.90 ( 367) hydrogen bonds : angle 5.33178 / 3.75 ( 1044) Misc. bond : bond 0.00820 / 0.43 ( 1) link_BETA1-4 : bond 0.00360 / 0.18 ( 2) link_BETA1-4 : angle 1.97798 / 1.06 ( 6) link_NAG-ASN : bond 0.00528 / 0.41 ( 7) link_NAG-ASN : angle 3.67463 / 2.49 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ASP cc_start: 0.9011 (t0) cc_final: 0.8776 (t70) REVERT: A 680 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7478 (tt) REVERT: C 422 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8350 (pm20) REVERT: C 540 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8754 (mm) REVERT: C 672 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7557 (pt) REVERT: C 689 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7918 (t) REVERT: B 803 GLU cc_start: 0.8765 (tp30) cc_final: 0.8482 (tt0) REVERT: B 813 MET cc_start: 0.8688 (tpp) cc_final: 0.8418 (ttp) REVERT: B 866 LYS cc_start: 0.9029 (tttt) cc_final: 0.8794 (tttm) REVERT: B 883 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.6527 (tt) REVERT: D 834 ASN cc_start: 0.7093 (m-40) cc_final: 0.6656 (m-40) outliers start: 40 outliers final: 26 residues processed: 194 average time/residue: 0.0907 time to fit residues: 24.4051 Evaluate side-chains 189 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 799 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 831 TYR Chi-restraints excluded: chain D residue 859 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 913 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [33, 9, 110, 26, 28, 30, 35, 92, 44, 36, 106] chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.0010 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 44 optimal weight: 0.0040 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 0.0030 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123206 restraints weight = 12300.186| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.36 r_work: 0.3348 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8973 Z= 0.111 Angle : 0.564 11.907 12229 Z= 0.284 Chirality : 0.042 0.224 1407 Planarity : 0.003 0.038 1536 Dihedral : 6.884 88.629 1448 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.68 % Allowed : 15.65 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1110 helix: 1.29 (0.25), residues: 429 sheet: -1.22 (0.41), residues: 172 loop : -0.78 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 798 TYR 0.015 0.001 TYR D 894 PHE 0.030 0.001 PHE D 593 TRP 0.017 0.001 TRP C 498 HIS 0.006 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8951) covalent geometry : angle 0.54421 / 0.28 (12178) SS BOND : bond 0.00199 / 0.15 ( 12) SS BOND : angle 0.68953 / 0.44 ( 24) hydrogen bonds : bond 0.02744 / 1.75 ( 367) hydrogen bonds : angle 5.23618 / 3.66 ( 1044) Misc. bond : bond 0.00779 / 0.41 ( 1) link_BETA1-4 : bond 0.00287 / 0.15 ( 2) link_BETA1-4 : angle 1.97973 / 1.05 ( 6) link_NAG-ASN : bond 0.00648 / 0.51 ( 7) link_NAG-ASN : angle 3.40838 / 2.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ASP cc_start: 0.8937 (t0) cc_final: 0.8667 (t70) REVERT: C 422 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: C 453 GLN cc_start: 0.8703 (mp10) cc_final: 0.8137 (mp10) REVERT: C 672 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7534 (pt) REVERT: C 755 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8380 (tpp80) REVERT: C 789 ASP cc_start: 0.8455 (t70) cc_final: 0.8157 (t0) REVERT: B 803 GLU cc_start: 0.8751 (tp30) cc_final: 0.8481 (tt0) REVERT: B 866 LYS cc_start: 0.9080 (tttt) cc_final: 0.8844 (tttm) REVERT: B 883 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.6453 (tt) REVERT: B 889 GLU cc_start: 0.8111 (mp0) cc_final: 0.7729 (mp0) REVERT: D 834 ASN cc_start: 0.7074 (m-40) cc_final: 0.6666 (m-40) REVERT: D 873 TYR cc_start: 0.9136 (m-10) cc_final: 0.8910 (m-80) outliers start: 32 outliers final: 20 residues processed: 196 average time/residue: 0.0858 time to fit residues: 23.6273 Evaluate side-chains 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 831 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [40, 32, 51, 105, 70, 62, 9, 38, 66, 53, 109] chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 70 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123058 restraints weight = 12146.662| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.33 r_work: 0.3363 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8973 Z= 0.124 Angle : 0.576 11.610 12229 Z= 0.288 Chirality : 0.042 0.217 1407 Planarity : 0.004 0.039 1536 Dihedral : 6.847 87.957 1448 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.34 % Allowed : 16.00 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1110 helix: 1.31 (0.25), residues: 430 sheet: -1.25 (0.41), residues: 172 loop : -0.75 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 793 TYR 0.014 0.002 TYR D 894 PHE 0.025 0.001 PHE D 593 TRP 0.024 0.001 TRP C 498 HIS 0.005 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8951) covalent geometry : angle 0.55822 / 0.28 (12178) SS BOND : bond 0.00213 / 0.16 ( 12) SS BOND : angle 0.70774 / 0.45 ( 24) hydrogen bonds : bond 0.02742 / 1.75 ( 367) hydrogen bonds : angle 5.19080 / 3.63 ( 1044) Misc. bond : bond 0.00751 / 0.40 ( 1) link_BETA1-4 : bond 0.00283 / 0.14 ( 2) link_BETA1-4 : angle 1.96961 / 1.05 ( 6) link_NAG-ASN : bond 0.00674 / 0.53 ( 7) link_NAG-ASN : angle 3.32387 / 2.21 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ASP cc_start: 0.8893 (t0) cc_final: 0.8628 (t70) REVERT: A 680 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7451 (tt) REVERT: A 760 ILE cc_start: 0.9163 (mm) cc_final: 0.8922 (mm) REVERT: C 422 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: C 453 GLN cc_start: 0.8731 (mp10) cc_final: 0.8159 (mp10) REVERT: C 789 ASP cc_start: 0.8451 (t70) cc_final: 0.8179 (t0) REVERT: B 803 GLU cc_start: 0.8726 (tp30) cc_final: 0.8468 (tt0) REVERT: B 866 LYS cc_start: 0.9122 (tttt) cc_final: 0.8919 (tttm) REVERT: B 883 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6439 (tt) REVERT: B 889 GLU cc_start: 0.8132 (mp0) cc_final: 0.7511 (mp0) REVERT: D 834 ASN cc_start: 0.7072 (m-40) cc_final: 0.6674 (m-40) outliers start: 29 outliers final: 21 residues processed: 185 average time/residue: 0.0929 time to fit residues: 23.9796 Evaluate side-chains 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 831 TYR Chi-restraints excluded: chain D residue 913 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [105, 13, 7, 75, 95, 80, 83, 74, 76, 42, 18] chunk 105 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122225 restraints weight = 12124.110| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.36 r_work: 0.3347 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8973 Z= 0.141 Angle : 0.587 11.325 12229 Z= 0.296 Chirality : 0.043 0.217 1407 Planarity : 0.004 0.042 1536 Dihedral : 6.877 88.402 1448 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.22 % Allowed : 16.23 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1110 helix: 1.30 (0.25), residues: 430 sheet: -1.27 (0.40), residues: 172 loop : -0.79 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 793 TYR 0.015 0.002 TYR D 894 PHE 0.024 0.002 PHE D 593 TRP 0.022 0.001 TRP C 498 HIS 0.005 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8951) covalent geometry : angle 0.56867 / 0.29 (12178) SS BOND : bond 0.00222 / 0.16 ( 12) SS BOND : angle 1.20823 / 0.91 ( 24) hydrogen bonds : bond 0.02794 / 1.78 ( 367) hydrogen bonds : angle 5.21384 / 3.66 ( 1044) Misc. bond : bond 0.00771 / 0.41 ( 1) link_BETA1-4 : bond 0.00267 / 0.14 ( 2) link_BETA1-4 : angle 1.98191 / 1.06 ( 6) link_NAG-ASN : bond 0.00684 / 0.54 ( 7) link_NAG-ASN : angle 3.26284 / 2.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ASP cc_start: 0.8890 (t0) cc_final: 0.8623 (t70) REVERT: A 680 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7459 (tt) REVERT: A 760 ILE cc_start: 0.9171 (mm) cc_final: 0.8923 (mm) REVERT: C 422 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: C 453 GLN cc_start: 0.8738 (mp10) cc_final: 0.8151 (mp10) REVERT: C 789 ASP cc_start: 0.8460 (t70) cc_final: 0.8191 (t0) REVERT: B 803 GLU cc_start: 0.8767 (tp30) cc_final: 0.8501 (tt0) REVERT: B 866 LYS cc_start: 0.9144 (tttt) cc_final: 0.8932 (tttm) REVERT: B 883 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.6430 (tt) REVERT: B 889 GLU cc_start: 0.8133 (mp0) cc_final: 0.7514 (mp0) REVERT: D 545 ASP cc_start: 0.8449 (m-30) cc_final: 0.8034 (m-30) REVERT: D 834 ASN cc_start: 0.7052 (m-40) cc_final: 0.6640 (m-40) outliers start: 28 outliers final: 21 residues processed: 186 average time/residue: 0.0990 time to fit residues: 25.4268 Evaluate side-chains 187 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 831 TYR Chi-restraints excluded: chain D residue 913 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [16, 58, 95, 91, 12, 96, 43, 54, 52, 77, 36] chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 95 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123003 restraints weight = 12149.356| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.36 r_work: 0.3357 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8973 Z= 0.127 Angle : 0.584 11.156 12229 Z= 0.294 Chirality : 0.043 0.252 1407 Planarity : 0.004 0.041 1536 Dihedral : 6.827 89.068 1448 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.99 % Allowed : 16.34 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 1110 helix: 1.34 (0.25), residues: 430 sheet: -1.26 (0.41), residues: 172 loop : -0.75 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 671 TYR 0.015 0.001 TYR D 894 PHE 0.017 0.001 PHE D 593 TRP 0.020 0.001 TRP C 498 HIS 0.004 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8951) covalent geometry : angle 0.56602 / 0.29 (12178) SS BOND : bond 0.00266 / 0.21 ( 12) SS BOND : angle 1.02884 / 0.77 ( 24) hydrogen bonds : bond 0.02699 / 1.72 ( 367) hydrogen bonds : angle 5.19437 / 3.65 ( 1044) Misc. bond : bond 0.00765 / 0.40 ( 1) link_BETA1-4 : bond 0.00299 / 0.15 ( 2) link_BETA1-4 : angle 1.97805 / 1.06 ( 6) link_NAG-ASN : bond 0.00672 / 0.53 ( 7) link_NAG-ASN : angle 3.19119 / 2.11 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ASP cc_start: 0.8857 (t0) cc_final: 0.8620 (t70) REVERT: A 680 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7470 (tt) REVERT: A 760 ILE cc_start: 0.9174 (mm) cc_final: 0.8930 (mm) REVERT: C 422 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8337 (pm20) REVERT: C 453 GLN cc_start: 0.8738 (mp10) cc_final: 0.8151 (mp10) REVERT: C 754 PHE cc_start: 0.8634 (t80) cc_final: 0.8272 (t80) REVERT: C 789 ASP cc_start: 0.8454 (t70) cc_final: 0.8180 (t0) REVERT: B 803 GLU cc_start: 0.8742 (tp30) cc_final: 0.8477 (tt0) REVERT: B 866 LYS cc_start: 0.9155 (tttt) cc_final: 0.8940 (tttm) REVERT: B 883 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6339 (tt) REVERT: B 889 GLU cc_start: 0.8154 (mp0) cc_final: 0.7539 (mp0) REVERT: D 545 ASP cc_start: 0.8433 (m-30) cc_final: 0.8033 (m-30) REVERT: D 834 ASN cc_start: 0.7020 (m-40) cc_final: 0.6612 (m-40) outliers start: 26 outliers final: 20 residues processed: 189 average time/residue: 0.0887 time to fit residues: 23.3987 Evaluate side-chains 186 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 831 TYR Chi-restraints excluded: chain D residue 913 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [55, 0, 22, 62, 95, 102, 36, 78, 109, 35, 28] chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 ASN B 626 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122392 restraints weight = 12186.824| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.37 r_work: 0.3338 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8973 Z= 0.137 Angle : 0.591 10.960 12229 Z= 0.299 Chirality : 0.043 0.212 1407 Planarity : 0.004 0.041 1536 Dihedral : 6.822 88.721 1448 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.99 % Allowed : 16.92 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1110 helix: 1.32 (0.25), residues: 430 sheet: -1.26 (0.39), residues: 184 loop : -0.75 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 793 TYR 0.012 0.001 TYR D 894 PHE 0.021 0.001 PHE D 593 TRP 0.020 0.001 TRP C 498 HIS 0.005 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8951) covalent geometry : angle 0.57425 / 0.30 (12178) SS BOND : bond 0.00218 / 0.16 ( 12) SS BOND : angle 0.90020 / 0.67 ( 24) hydrogen bonds : bond 0.02715 / 1.72 ( 367) hydrogen bonds : angle 5.14955 / 3.62 ( 1044) Misc. bond : bond 0.00771 / 0.41 ( 1) link_BETA1-4 : bond 0.00233 / 0.12 ( 2) link_BETA1-4 : angle 1.99299 / 1.06 ( 6) link_NAG-ASN : bond 0.00685 / 0.53 ( 7) link_NAG-ASN : angle 3.15780 / 2.08 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2339.28 seconds wall clock time: 40 minutes 43.64 seconds (2443.64 seconds total)