Starting phenix.real_space_refine on Fri Jul 3 15:54:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fws_29517/07_2026/8fws_29517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fws_29517/07_2026/8fws_29517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8fws_29517/07_2026/8fws_29517.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fws_29517/07_2026/8fws_29517.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fws_29517/07_2026/8fws_29517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fws_29517/07_2026/8fws_29517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fws_29517/07_2026/8fws_29517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fws_29517/07_2026/8fws_29517.map" } resolution = 3.23 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= 0.004 sd= 0.085 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: 8 Type Number sf(0) Gaussians P 16 5.49 5 S 80 5.16 5 Cl 2 4.86 5 Na 6 4.78 5 C 9432 2.51 5 N 2190 2.21 5 O 2686 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14416 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} 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 chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 362 Unusual residues: {' CL': 1, ' NA': 3, '2J9': 2, 'NAG': 1, 'POV': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {' NA': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 256 Unusual residues: {' CL': 1, ' NA': 1, '2J9': 2, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {' NA': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.05, per 1000 atoms: 0.21 Number of scatterers: 14416 At special positions: 0 Unit cell: (115.625, 132.275, 136.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 80 16.00 P 16 15.00 Na 6 11.00 F 4 9.00 O 2686 8.00 N 2190 7.00 C 9432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS B 595 " distance=2.00 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.02 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.02 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS D 595 " distance=2.06 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.02 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " " BMA I 3 " - " BMA I 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1006 " - " ASN A 751 " " NAG C1006 " - " ASN C 751 " " NAG E 1 " - " ASN A 546 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN B 751 " " NAG H 1 " - " ASN C 546 " " NAG I 1 " - " ASN D 546 " " NAG J 1 " - " ASN D 751 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 542.9 milliseconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 18 sheets defined 49.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.946A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 removed outlier: 4.021A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.696A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.516A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 631 through 665 removed outlier: 3.575A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.039A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.688A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 712 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.664A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 removed outlier: 3.710A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.903A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.605A pdb=" N MET A 793 " --> pdb=" O GLY A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 821 through 850 removed outlier: 3.538A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.517A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.680A pdb=" N ASN B 557 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.729A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.618A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 659 removed outlier: 3.570A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.648A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 711 removed outlier: 3.590A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.553A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 removed outlier: 3.704A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 789 removed outlier: 3.856A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 822 through 850 removed outlier: 3.731A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 845 " --> pdb=" O GLU B 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.946A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 removed outlier: 4.022A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.695A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 585 removed outlier: 3.516A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 580 " --> pdb=" O CYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 631 through 665 removed outlier: 3.576A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 removed outlier: 4.040A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.688A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 712 Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.664A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 748 removed outlier: 3.710A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.902A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 removed outlier: 3.604A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 799 Processing helix chain 'C' and resid 821 through 850 removed outlier: 3.538A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.518A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.679A pdb=" N ASN D 557 " --> pdb=" O SER D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.729A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 589 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.618A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 659 removed outlier: 3.569A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.648A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 711 removed outlier: 3.590A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.553A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 removed outlier: 3.703A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 789 removed outlier: 3.857A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 794 through 799 Processing helix chain 'D' and resid 822 through 850 removed outlier: 3.731A pdb=" N VAL D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 845 " --> pdb=" O GLU D 841 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 437 removed outlier: 6.163A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA3, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA4, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.830A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 683 removed outlier: 7.194A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 445 through 446 removed outlier: 3.558A pdb=" N GLU B 460 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AA8, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.058A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.247A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 433 through 437 removed outlier: 6.163A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB3, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AB4, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.830A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 681 through 683 removed outlier: 7.194A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 445 through 446 removed outlier: 3.558A pdb=" N GLU D 460 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AB8, first strand: chain 'D' and resid 534 through 536 removed outlier: 4.058A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 735 through 738 removed outlier: 4.248A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2224 1.31 - 1.44: 3912 1.44 - 1.57: 8392 1.57 - 1.70: 48 1.70 - 1.83: 132 Bond restraints: 14708 Sorted by residual: bond pdb=" OAA 2J9 A1001 " pdb=" SAP 2J9 A1001 " ideal model delta sigma weight residual 1.452 1.655 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAA 2J9 C1002 " pdb=" SAP 2J9 C1002 " ideal model delta sigma weight residual 1.452 1.655 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAA 2J9 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAB 2J9 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAA 2J9 C1001 " pdb=" SAP 2J9 C1001 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 14703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.58: 19590 6.58 - 13.16: 180 13.16 - 19.73: 4 19.73 - 26.31: 0 26.31 - 32.89: 8 Bond angle restraints: 19782 Sorted by residual: angle pdb=" CAH 2J9 A1009 " pdb=" CAN 2J9 A1009 " pdb=" NAO 2J9 A1009 " ideal model delta sigma weight residual 117.67 150.56 -32.89 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CAH 2J9 C1001 " pdb=" CAN 2J9 C1001 " pdb=" NAO 2J9 C1001 " ideal model delta sigma weight residual 117.67 150.26 -32.59 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAH 2J9 C1002 " pdb=" CAN 2J9 C1002 " pdb=" NAO 2J9 C1002 " ideal model delta sigma weight residual 117.67 149.75 -32.08 3.00e+00 1.11e-01 1.14e+02 angle pdb=" CAG 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 118.82 150.74 -31.92 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CAH 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 117.67 149.24 -31.57 3.00e+00 1.11e-01 1.11e+02 ... (remaining 19777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 8216 28.61 - 57.22: 361 57.22 - 85.82: 84 85.82 - 114.43: 9 114.43 - 143.04: 12 Dihedral angle restraints: 8682 sinusoidal: 3842 harmonic: 4840 Sorted by residual: dihedral pdb=" CA TYR D 478 " pdb=" C TYR D 478 " pdb=" N GLU D 479 " pdb=" CA GLU D 479 " ideal model delta harmonic sigma weight residual -180.00 -129.43 -50.57 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA TYR B 478 " pdb=" C TYR B 478 " pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta harmonic sigma weight residual -180.00 -129.48 -50.52 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA VAL B 716 " pdb=" C VAL B 716 " pdb=" N LEU B 717 " pdb=" CA LEU B 717 " ideal model delta harmonic sigma weight residual 180.00 141.31 38.69 0 5.00e+00 4.00e-02 5.99e+01 ... (remaining 8679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.464: 2154 0.464 - 0.927: 0 0.927 - 1.391: 0 1.391 - 1.854: 0 1.854 - 2.318: 4 Chirality restraints: 2158 Sorted by residual: chirality pdb=" CAN 2J9 A1009 " pdb=" CAG 2J9 A1009 " pdb=" CAH 2J9 A1009 " pdb=" NAO 2J9 A1009 " both_signs ideal model delta sigma weight residual True 2.32 -0.00 2.32 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CAN 2J9 C1001 " pdb=" CAG 2J9 C1001 " pdb=" CAH 2J9 C1001 " pdb=" NAO 2J9 C1001 " both_signs ideal model delta sigma weight residual True 2.32 0.02 2.30 2.00e-01 2.50e+01 1.32e+02 chirality pdb=" CAN 2J9 C1002 " pdb=" CAG 2J9 C1002 " pdb=" CAH 2J9 C1002 " pdb=" NAO 2J9 C1002 " both_signs ideal model delta sigma weight residual True 2.32 -0.02 2.30 2.00e-01 2.50e+01 1.32e+02 ... (remaining 2155 not shown) Planarity restraints: 2398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 716 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C VAL D 716 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL D 716 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D 717 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 716 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C VAL B 716 " -0.056 2.00e-02 2.50e+03 pdb=" O VAL B 716 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 717 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 515 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO B 516 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 516 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 516 " -0.033 5.00e-02 4.00e+02 ... (remaining 2395 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3232 2.78 - 3.31: 12234 3.31 - 3.84: 22352 3.84 - 4.37: 27840 4.37 - 4.90: 47421 Nonbonded interactions: 113079 Sorted by model distance: nonbonded pdb=" OG SER C 554 " pdb=" O ASN C 819 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 554 " pdb=" O ASN A 819 " model vdw 2.251 3.040 nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.273 3.040 nonbonded pdb=" O SER C 632 " pdb=" OG SER D 834 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 585 " pdb=" OE2 GLU B 841 " model vdw 2.307 3.040 ... (remaining 113074 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 431 through 850 or resid 1003)) selection = (chain 'B' and (resid 431 through 850 or resid 1003)) selection = (chain 'C' and (resid 431 through 850 or resid 1003)) selection = (chain 'D' and (resid 431 through 850 or resid 1003)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' } 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=0.45 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: 3.810 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.580 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.012 0.203 14732 Z= 0.580 Angle : 1.648 32.889 19848 Z= 0.776 Chirality : 0.116 2.318 2158 Planarity : 0.007 0.058 2390 Dihedral : 17.379 143.040 5568 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.49 % Favored : 91.15 % Rotamer: Outliers : 0.55 % Allowed : 4.28 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.96 (0.13), residues: 1672 helix: -4.37 (0.07), residues: 802 sheet: -3.11 (0.38), residues: 134 loop : -3.49 (0.17), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 713 TYR 0.028 0.003 TYR B 702 PHE 0.029 0.003 PHE D 446 TRP 0.019 0.003 TRP D 706 HIS 0.005 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.01180 / 0.58 (14708) covalent geometry : angle 1.61966 / 0.77 (19782) SS BOND : bond 0.01844 / 0.98 ( 6) SS BOND : angle 1.36329 / 0.93 ( 12) hydrogen bonds : bond 0.30928 / 19.92 ( 558) hydrogen bonds : angle 11.22768 / 7.59 ( 1620) link_BETA1-3 : bond 0.00161 / 0.08 ( 2) link_BETA1-3 : angle 3.28805 / 1.66 ( 6) link_BETA1-4 : bond 0.01669 / 0.99 ( 8) link_BETA1-4 : angle 4.06420 / 2.66 ( 24) link_NAG-ASN : bond 0.01837 / 1.12 ( 8) link_NAG-ASN : angle 7.93277 / 5.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 356 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7629 (t70) cc_final: 0.7262 (t0) REVERT: A 468 ARG cc_start: 0.7093 (ttm110) cc_final: 0.6806 (mtm110) REVERT: A 591 ASN cc_start: 0.8028 (t160) cc_final: 0.7782 (t0) REVERT: A 719 LYS cc_start: 0.7853 (pptt) cc_final: 0.7174 (mtpp) REVERT: A 751 ASN cc_start: 0.6673 (m-40) cc_final: 0.5963 (t0) REVERT: A 776 ASP cc_start: 0.7460 (m-30) cc_final: 0.6979 (m-30) REVERT: A 796 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7208 (mt-10) REVERT: A 845 LYS cc_start: 0.6977 (tptt) cc_final: 0.6703 (tppp) REVERT: B 790 LYS cc_start: 0.7862 (mptp) cc_final: 0.7503 (mmmt) REVERT: B 818 GLN cc_start: 0.8085 (pt0) cc_final: 0.7783 (pm20) REVERT: C 468 ARG cc_start: 0.7114 (ttm110) cc_final: 0.6726 (mtm110) REVERT: C 487 LYS cc_start: 0.7416 (mtpp) cc_final: 0.7138 (mtmt) REVERT: C 584 PHE cc_start: 0.6603 (t80) cc_final: 0.6359 (t80) REVERT: C 591 ASN cc_start: 0.8102 (t160) cc_final: 0.7722 (t0) REVERT: C 677 GLN cc_start: 0.6669 (mp-120) cc_final: 0.6240 (mp10) REVERT: C 696 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7452 (mtmt) REVERT: C 719 LYS cc_start: 0.8313 (pptt) cc_final: 0.7641 (mtpp) REVERT: C 726 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7271 (mm-40) REVERT: C 776 ASP cc_start: 0.7331 (m-30) cc_final: 0.6748 (m-30) REVERT: C 796 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6992 (mt-10) REVERT: C 845 LYS cc_start: 0.6933 (tptt) cc_final: 0.6686 (tppt) REVERT: D 492 ASP cc_start: 0.7492 (t70) cc_final: 0.6809 (m-30) REVERT: D 790 LYS cc_start: 0.7758 (mptp) cc_final: 0.7417 (mmmt) outliers start: 8 outliers final: 0 residues processed: 362 average time/residue: 0.1390 time to fit residues: 70.3402 Evaluate side-chains 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 ASN A 591 ASN A 596 ASN A 604 ASN B 456 ASN B 621 GLN ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN C 591 ASN C 593 HIS C 596 ASN C 604 ASN C 621 GLN D 456 ASN D 604 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.176657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148536 restraints weight = 16070.204| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.81 r_work: 0.3407 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14732 Z= 0.181 Angle : 0.772 9.664 19848 Z= 0.384 Chirality : 0.047 0.216 2158 Planarity : 0.006 0.048 2390 Dihedral : 20.398 139.971 2428 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.01 % Favored : 91.51 % Rotamer: Outliers : 2.28 % Allowed : 10.01 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.16), residues: 1672 helix: -2.25 (0.14), residues: 846 sheet: -3.13 (0.34), residues: 152 loop : -3.12 (0.20), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 712 TYR 0.022 0.002 TYR D 478 PHE 0.017 0.002 PHE B 735 TRP 0.016 0.002 TRP C 706 HIS 0.002 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (14708) covalent geometry : angle 0.74659 / 0.38 (19782) SS BOND : bond 0.00340 / 0.18 ( 6) SS BOND : angle 1.62425 / 1.51 ( 12) hydrogen bonds : bond 0.04948 / 3.17 ( 558) hydrogen bonds : angle 5.13657 / 3.37 ( 1620) link_BETA1-3 : bond 0.00391 / 0.19 ( 2) link_BETA1-3 : angle 2.60210 / 1.42 ( 6) link_BETA1-4 : bond 0.01019 / 0.48 ( 8) link_BETA1-4 : angle 2.01766 / 1.37 ( 24) link_NAG-ASN : bond 0.01081 / 0.69 ( 8) link_NAG-ASN : angle 5.07828 / 3.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 TYR cc_start: 0.8240 (m-10) cc_final: 0.7797 (m-10) REVERT: A 691 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6842 (ttt) REVERT: A 715 SER cc_start: 0.7540 (OUTLIER) cc_final: 0.7174 (p) REVERT: A 719 LYS cc_start: 0.7930 (pptt) cc_final: 0.7682 (mtpp) REVERT: B 691 MET cc_start: 0.7683 (ttp) cc_final: 0.7411 (ttt) REVERT: B 790 LYS cc_start: 0.7822 (mptp) cc_final: 0.7496 (mmmt) REVERT: B 825 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8167 (mt) REVERT: C 584 PHE cc_start: 0.6817 (t80) cc_final: 0.6583 (t80) REVERT: C 696 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7415 (mtmt) REVERT: C 719 LYS cc_start: 0.8233 (pptt) cc_final: 0.8033 (mtpp) REVERT: D 691 MET cc_start: 0.7654 (tmm) cc_final: 0.7434 (ttt) REVERT: D 790 LYS cc_start: 0.7679 (mptp) cc_final: 0.7266 (mmmt) REVERT: D 819 ASN cc_start: 0.8263 (m110) cc_final: 0.7999 (m110) REVERT: D 825 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8196 (mt) outliers start: 33 outliers final: 19 residues processed: 216 average time/residue: 0.1209 time to fit residues: 38.5299 Evaluate side-chains 175 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 0.0030 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 677 GLN A 747 GLN B 456 ASN B 495 ASN D 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.173356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144494 restraints weight = 15988.514| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.71 r_work: 0.3307 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14732 Z= 0.164 Angle : 0.706 10.734 19848 Z= 0.345 Chirality : 0.045 0.205 2158 Planarity : 0.005 0.043 2390 Dihedral : 19.099 140.432 2428 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.66 % Favored : 91.87 % Rotamer: Outliers : 2.76 % Allowed : 11.53 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.19), residues: 1672 helix: -0.79 (0.17), residues: 852 sheet: -2.80 (0.34), residues: 154 loop : -2.92 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 712 TYR 0.022 0.002 TYR A 590 PHE 0.019 0.002 PHE D 579 TRP 0.015 0.001 TRP D 798 HIS 0.003 0.001 HIS B 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (14708) covalent geometry : angle 0.68352 / 0.34 (19782) SS BOND : bond 0.01939 / 0.76 ( 6) SS BOND : angle 1.85662 / 1.60 ( 12) hydrogen bonds : bond 0.03903 / 2.54 ( 558) hydrogen bonds : angle 4.42435 / 2.89 ( 1620) link_BETA1-3 : bond 0.00314 / 0.16 ( 2) link_BETA1-3 : angle 2.28637 / 1.23 ( 6) link_BETA1-4 : bond 0.00698 / 0.36 ( 8) link_BETA1-4 : angle 2.06009 / 1.41 ( 24) link_NAG-ASN : bond 0.00732 / 0.43 ( 8) link_NAG-ASN : angle 4.51685 / 3.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7752 (t70) cc_final: 0.7326 (t0) REVERT: A 566 TYR cc_start: 0.8390 (m-10) cc_final: 0.7846 (m-10) REVERT: A 664 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8193 (mtt) REVERT: A 703 ASP cc_start: 0.7442 (t70) cc_final: 0.6955 (t0) REVERT: A 715 SER cc_start: 0.7444 (OUTLIER) cc_final: 0.6988 (p) REVERT: A 800 ARG cc_start: 0.8161 (tpp-160) cc_final: 0.7689 (tpm170) REVERT: B 677 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.5839 (mp10) REVERT: B 691 MET cc_start: 0.7805 (ttp) cc_final: 0.7471 (ttt) REVERT: B 790 LYS cc_start: 0.7933 (mptp) cc_final: 0.7467 (tptt) REVERT: B 825 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8046 (mt) REVERT: C 584 PHE cc_start: 0.6796 (t80) cc_final: 0.6549 (t80) REVERT: C 661 VAL cc_start: 0.8508 (t) cc_final: 0.8231 (m) REVERT: C 696 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7385 (mtmt) REVERT: C 719 LYS cc_start: 0.8413 (pptt) cc_final: 0.8058 (mtpp) REVERT: C 845 LYS cc_start: 0.7163 (tppt) cc_final: 0.6537 (tppt) REVERT: D 743 GLU cc_start: 0.8348 (mp0) cc_final: 0.7944 (mp0) REVERT: D 790 LYS cc_start: 0.7745 (mptp) cc_final: 0.7252 (tptt) REVERT: D 819 ASN cc_start: 0.8506 (m110) cc_final: 0.8132 (m-40) REVERT: D 825 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8103 (mt) outliers start: 40 outliers final: 23 residues processed: 184 average time/residue: 0.1253 time to fit residues: 33.7304 Evaluate side-chains 171 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.176919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.148014 restraints weight = 16280.918| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.90 r_work: 0.3303 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14732 Z= 0.164 Angle : 0.683 9.663 19848 Z= 0.332 Chirality : 0.045 0.213 2158 Planarity : 0.004 0.050 2390 Dihedral : 18.439 140.526 2428 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.60 % Favored : 92.05 % Rotamer: Outliers : 3.73 % Allowed : 11.74 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.20), residues: 1672 helix: -0.17 (0.18), residues: 864 sheet: -2.65 (0.34), residues: 158 loop : -2.90 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 712 TYR 0.021 0.002 TYR D 844 PHE 0.016 0.002 PHE D 584 TRP 0.011 0.001 TRP A 706 HIS 0.002 0.001 HIS B 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (14708) covalent geometry : angle 0.66183 / 0.33 (19782) SS BOND : bond 0.00308 / 0.18 ( 6) SS BOND : angle 1.28368 / 0.96 ( 12) hydrogen bonds : bond 0.03598 / 2.32 ( 558) hydrogen bonds : angle 4.23183 / 2.77 ( 1620) link_BETA1-3 : bond 0.00426 / 0.21 ( 2) link_BETA1-3 : angle 2.16527 / 1.18 ( 6) link_BETA1-4 : bond 0.00676 / 0.36 ( 8) link_BETA1-4 : angle 1.99392 / 1.37 ( 24) link_NAG-ASN : bond 0.00749 / 0.42 ( 8) link_NAG-ASN : angle 4.27255 / 2.91 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 155 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7683 (t70) cc_final: 0.7337 (t0) REVERT: A 487 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7656 (mtmt) REVERT: A 566 TYR cc_start: 0.8348 (m-10) cc_final: 0.7835 (m-10) REVERT: A 703 ASP cc_start: 0.7368 (t70) cc_final: 0.6986 (t0) REVERT: B 669 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7672 (t70) REVERT: B 691 MET cc_start: 0.7686 (ttp) cc_final: 0.7441 (ttt) REVERT: B 743 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 825 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8129 (mt) REVERT: C 457 ASP cc_start: 0.7587 (t0) cc_final: 0.7236 (t0) REVERT: C 584 PHE cc_start: 0.6877 (t80) cc_final: 0.6592 (t80) REVERT: C 696 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7472 (mtmt) REVERT: C 719 LYS cc_start: 0.8344 (pptt) cc_final: 0.8039 (mtpp) REVERT: C 845 LYS cc_start: 0.7375 (tppt) cc_final: 0.6856 (tppp) REVERT: D 743 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: D 793 MET cc_start: 0.8341 (mmt) cc_final: 0.7541 (mtt) REVERT: D 819 ASN cc_start: 0.8369 (m110) cc_final: 0.8105 (m110) REVERT: D 825 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8125 (mt) outliers start: 54 outliers final: 31 residues processed: 194 average time/residue: 0.1109 time to fit residues: 31.4215 Evaluate side-chains 177 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 754 GLN D 456 ASN D 754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137801 restraints weight = 16418.014| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.52 r_work: 0.3266 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14732 Z= 0.211 Angle : 0.719 9.663 19848 Z= 0.348 Chirality : 0.047 0.200 2158 Planarity : 0.005 0.046 2390 Dihedral : 18.110 140.340 2428 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.07 % Favored : 91.57 % Rotamer: Outliers : 3.87 % Allowed : 12.29 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.20), residues: 1672 helix: -0.07 (0.18), residues: 868 sheet: -2.64 (0.35), residues: 158 loop : -2.83 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 712 TYR 0.022 0.002 TYR D 844 PHE 0.017 0.002 PHE D 584 TRP 0.012 0.002 TRP A 706 HIS 0.003 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.21 (14708) covalent geometry : angle 0.69973 / 0.34 (19782) SS BOND : bond 0.00476 / 0.28 ( 6) SS BOND : angle 0.79085 / 0.61 ( 12) hydrogen bonds : bond 0.03783 / 2.46 ( 558) hydrogen bonds : angle 4.26996 / 2.79 ( 1620) link_BETA1-3 : bond 0.00179 / 0.09 ( 2) link_BETA1-3 : angle 2.00245 / 1.09 ( 6) link_BETA1-4 : bond 0.00641 / 0.34 ( 8) link_BETA1-4 : angle 2.04271 / 1.38 ( 24) link_NAG-ASN : bond 0.00629 / 0.36 ( 8) link_NAG-ASN : angle 4.33615 / 2.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7717 (t70) cc_final: 0.7385 (t0) REVERT: A 566 TYR cc_start: 0.8394 (m-10) cc_final: 0.7889 (m-10) REVERT: A 703 ASP cc_start: 0.7388 (t70) cc_final: 0.7017 (t0) REVERT: A 715 SER cc_start: 0.7454 (OUTLIER) cc_final: 0.7068 (p) REVERT: B 669 ASP cc_start: 0.8327 (t70) cc_final: 0.8022 (t70) REVERT: B 677 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.5672 (mp10) REVERT: B 691 MET cc_start: 0.7745 (ttp) cc_final: 0.7504 (ttt) REVERT: B 796 GLU cc_start: 0.7927 (tt0) cc_final: 0.7725 (tm-30) REVERT: B 825 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8170 (mt) REVERT: C 584 PHE cc_start: 0.7056 (t80) cc_final: 0.6733 (t80) REVERT: C 661 VAL cc_start: 0.8495 (t) cc_final: 0.8227 (m) REVERT: C 696 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7532 (mtmt) REVERT: C 709 MET cc_start: 0.7425 (mtt) cc_final: 0.6739 (mtm) REVERT: C 719 LYS cc_start: 0.8353 (pptt) cc_final: 0.8041 (mtpp) REVERT: C 845 LYS cc_start: 0.7344 (tppt) cc_final: 0.6836 (tppp) REVERT: D 743 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: D 793 MET cc_start: 0.8559 (mmt) cc_final: 0.7753 (mtt) REVERT: D 819 ASN cc_start: 0.8392 (m110) cc_final: 0.8090 (m110) REVERT: D 825 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8169 (mt) outliers start: 56 outliers final: 32 residues processed: 193 average time/residue: 0.1155 time to fit residues: 32.6728 Evaluate side-chains 180 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 129 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 138 optimal weight: 0.0060 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 593 HIS D 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.166848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.138011 restraints weight = 16435.914| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.59 r_work: 0.3348 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14732 Z= 0.124 Angle : 0.637 9.132 19848 Z= 0.310 Chirality : 0.043 0.244 2158 Planarity : 0.004 0.045 2390 Dihedral : 17.429 140.432 2428 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.12 % Favored : 92.64 % Rotamer: Outliers : 2.83 % Allowed : 13.95 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.20), residues: 1672 helix: 0.47 (0.18), residues: 864 sheet: -2.29 (0.37), residues: 130 loop : -2.70 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 712 TYR 0.023 0.001 TYR C 733 PHE 0.012 0.001 PHE A 708 TRP 0.009 0.001 TRP A 706 HIS 0.001 0.001 HIS B 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (14708) covalent geometry : angle 0.61974 / 0.31 (19782) SS BOND : bond 0.00332 / 0.21 ( 6) SS BOND : angle 0.70721 / 0.61 ( 12) hydrogen bonds : bond 0.03166 / 2.05 ( 558) hydrogen bonds : angle 4.02688 / 2.64 ( 1620) link_BETA1-3 : bond 0.00376 / 0.19 ( 2) link_BETA1-3 : angle 1.84957 / 1.01 ( 6) link_BETA1-4 : bond 0.00783 / 0.40 ( 8) link_BETA1-4 : angle 1.93281 / 1.30 ( 24) link_NAG-ASN : bond 0.00966 / 0.53 ( 8) link_NAG-ASN : angle 3.79771 / 2.56 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7673 (t70) cc_final: 0.7327 (t0) REVERT: A 566 TYR cc_start: 0.8529 (m-10) cc_final: 0.8040 (m-10) REVERT: A 703 ASP cc_start: 0.7451 (t70) cc_final: 0.7035 (t0) REVERT: A 715 SER cc_start: 0.7402 (OUTLIER) cc_final: 0.7060 (p) REVERT: B 677 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.5718 (mp10) REVERT: B 691 MET cc_start: 0.7788 (ttp) cc_final: 0.7510 (ttt) REVERT: B 793 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.7967 (mtt) REVERT: C 584 PHE cc_start: 0.7078 (t80) cc_final: 0.6769 (t80) REVERT: C 661 VAL cc_start: 0.8484 (t) cc_final: 0.8121 (m) REVERT: C 696 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7533 (mtmt) REVERT: C 719 LYS cc_start: 0.8439 (pptt) cc_final: 0.8065 (mtpp) REVERT: D 677 GLN cc_start: 0.6869 (mp10) cc_final: 0.6515 (mm-40) REVERT: D 743 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: D 793 MET cc_start: 0.8570 (mmt) cc_final: 0.7673 (mtt) REVERT: D 819 ASN cc_start: 0.8465 (m110) cc_final: 0.8125 (m110) REVERT: D 825 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8111 (mt) outliers start: 41 outliers final: 26 residues processed: 176 average time/residue: 0.0979 time to fit residues: 25.6477 Evaluate side-chains 167 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.165769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142079 restraints weight = 16281.351| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.14 r_work: 0.3381 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14732 Z= 0.139 Angle : 0.648 8.738 19848 Z= 0.314 Chirality : 0.043 0.275 2158 Planarity : 0.004 0.045 2390 Dihedral : 17.100 140.530 2428 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.48 % Favored : 92.17 % Rotamer: Outliers : 3.25 % Allowed : 14.02 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.21), residues: 1672 helix: 0.70 (0.18), residues: 864 sheet: -2.31 (0.38), residues: 132 loop : -2.59 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.022 0.001 TYR D 844 PHE 0.012 0.001 PHE D 584 TRP 0.010 0.001 TRP A 706 HIS 0.003 0.001 HIS B 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (14708) covalent geometry : angle 0.63217 / 0.31 (19782) SS BOND : bond 0.00301 / 0.18 ( 6) SS BOND : angle 0.65102 / 0.55 ( 12) hydrogen bonds : bond 0.03214 / 2.08 ( 558) hydrogen bonds : angle 3.96614 / 2.60 ( 1620) link_BETA1-3 : bond 0.00445 / 0.22 ( 2) link_BETA1-3 : angle 1.77010 / 0.97 ( 6) link_BETA1-4 : bond 0.00741 / 0.39 ( 8) link_BETA1-4 : angle 1.89646 / 1.27 ( 24) link_NAG-ASN : bond 0.00933 / 0.50 ( 8) link_NAG-ASN : angle 3.67432 / 2.49 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7661 (t70) cc_final: 0.7346 (t0) REVERT: A 566 TYR cc_start: 0.8457 (m-10) cc_final: 0.7973 (m-10) REVERT: A 715 SER cc_start: 0.7358 (OUTLIER) cc_final: 0.7045 (p) REVERT: B 677 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.5817 (mp10) REVERT: B 682 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.7016 (m-10) REVERT: B 691 MET cc_start: 0.7733 (ttp) cc_final: 0.7470 (ttt) REVERT: B 793 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7670 (mtt) REVERT: C 584 PHE cc_start: 0.7063 (t80) cc_final: 0.6764 (t80) REVERT: C 661 VAL cc_start: 0.8513 (t) cc_final: 0.8124 (m) REVERT: C 696 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7537 (mtmt) REVERT: C 719 LYS cc_start: 0.8369 (pptt) cc_final: 0.8045 (mtpp) REVERT: D 677 GLN cc_start: 0.6866 (mp10) cc_final: 0.6522 (mm-40) REVERT: D 743 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: D 793 MET cc_start: 0.8504 (mmt) cc_final: 0.7675 (mtt) REVERT: D 819 ASN cc_start: 0.8455 (m110) cc_final: 0.8137 (m110) REVERT: D 825 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8132 (mt) outliers start: 47 outliers final: 32 residues processed: 171 average time/residue: 0.1133 time to fit residues: 28.7137 Evaluate side-chains 174 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 154 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.165263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138681 restraints weight = 16326.830| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.36 r_work: 0.3378 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14732 Z= 0.152 Angle : 0.651 8.606 19848 Z= 0.316 Chirality : 0.044 0.245 2158 Planarity : 0.004 0.045 2390 Dihedral : 16.895 140.496 2428 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.66 % Favored : 91.99 % Rotamer: Outliers : 3.25 % Allowed : 14.50 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.21), residues: 1672 helix: 0.75 (0.18), residues: 864 sheet: -2.30 (0.38), residues: 132 loop : -2.58 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.025 0.002 TYR A 542 PHE 0.013 0.001 PHE D 584 TRP 0.023 0.001 TRP D 798 HIS 0.001 0.001 HIS B 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (14708) covalent geometry : angle 0.63521 / 0.31 (19782) SS BOND : bond 0.00282 / 0.15 ( 6) SS BOND : angle 0.62315 / 0.51 ( 12) hydrogen bonds : bond 0.03280 / 2.12 ( 558) hydrogen bonds : angle 3.95460 / 2.59 ( 1620) link_BETA1-3 : bond 0.00401 / 0.20 ( 2) link_BETA1-3 : angle 1.67448 / 0.91 ( 6) link_BETA1-4 : bond 0.00702 / 0.36 ( 8) link_BETA1-4 : angle 1.88776 / 1.26 ( 24) link_NAG-ASN : bond 0.00742 / 0.42 ( 8) link_NAG-ASN : angle 3.61385 / 2.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7645 (t70) cc_final: 0.7311 (t0) REVERT: A 715 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.7045 (p) REVERT: B 677 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.5708 (mp10) REVERT: B 682 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.7072 (m-10) REVERT: B 691 MET cc_start: 0.7769 (ttp) cc_final: 0.7507 (ttt) REVERT: B 743 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: B 793 MET cc_start: 0.8586 (tpt) cc_final: 0.7759 (mtt) REVERT: C 584 PHE cc_start: 0.7023 (t80) cc_final: 0.6732 (t80) REVERT: C 661 VAL cc_start: 0.8501 (t) cc_final: 0.8088 (m) REVERT: C 696 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7503 (mtmt) REVERT: C 709 MET cc_start: 0.7336 (mtm) cc_final: 0.6807 (mtm) REVERT: C 719 LYS cc_start: 0.8377 (pptt) cc_final: 0.8037 (mtpp) REVERT: D 677 GLN cc_start: 0.6826 (mp10) cc_final: 0.6508 (mm-40) REVERT: D 743 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: D 793 MET cc_start: 0.8571 (mmt) cc_final: 0.7727 (mtt) REVERT: D 825 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8128 (mt) outliers start: 47 outliers final: 33 residues processed: 172 average time/residue: 0.1143 time to fit residues: 29.1149 Evaluate side-chains 174 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 147 optimal weight: 0.4980 chunk 136 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.164155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133751 restraints weight = 16501.447| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.51 r_work: 0.3267 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14732 Z= 0.141 Angle : 0.641 8.820 19848 Z= 0.313 Chirality : 0.043 0.281 2158 Planarity : 0.004 0.045 2390 Dihedral : 16.661 140.540 2428 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.36 % Favored : 92.34 % Rotamer: Outliers : 3.11 % Allowed : 14.30 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.21), residues: 1672 helix: 0.93 (0.19), residues: 850 sheet: -2.27 (0.39), residues: 130 loop : -2.59 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.022 0.002 TYR B 844 PHE 0.013 0.001 PHE D 584 TRP 0.017 0.001 TRP D 798 HIS 0.001 0.000 HIS B 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (14708) covalent geometry : angle 0.62637 / 0.31 (19782) SS BOND : bond 0.00315 / 0.20 ( 6) SS BOND : angle 0.62709 / 0.50 ( 12) hydrogen bonds : bond 0.03196 / 2.08 ( 558) hydrogen bonds : angle 3.91030 / 2.56 ( 1620) link_BETA1-3 : bond 0.00374 / 0.19 ( 2) link_BETA1-3 : angle 1.54817 / 0.85 ( 6) link_BETA1-4 : bond 0.00722 / 0.38 ( 8) link_BETA1-4 : angle 1.85848 / 1.23 ( 24) link_NAG-ASN : bond 0.00894 / 0.48 ( 8) link_NAG-ASN : angle 3.54392 / 2.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7552 (t70) cc_final: 0.7256 (t0) REVERT: A 715 SER cc_start: 0.7397 (OUTLIER) cc_final: 0.7073 (p) REVERT: A 760 ASP cc_start: 0.8050 (t0) cc_final: 0.7846 (t70) REVERT: A 800 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.7262 (ptp-110) REVERT: A 818 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: B 677 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.5702 (mp10) REVERT: B 682 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: B 691 MET cc_start: 0.7678 (ttp) cc_final: 0.7436 (ttt) REVERT: B 743 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: B 793 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7774 (mtt) REVERT: C 584 PHE cc_start: 0.6984 (t80) cc_final: 0.6701 (t80) REVERT: C 661 VAL cc_start: 0.8529 (t) cc_final: 0.8119 (m) REVERT: C 696 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7515 (mtmt) REVERT: C 709 MET cc_start: 0.7330 (mtm) cc_final: 0.6877 (mtm) REVERT: C 719 LYS cc_start: 0.8357 (pptt) cc_final: 0.8023 (mtpp) REVERT: D 677 GLN cc_start: 0.6866 (mp10) cc_final: 0.6500 (mm-40) REVERT: D 743 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: D 825 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8119 (mt) outliers start: 45 outliers final: 33 residues processed: 170 average time/residue: 0.1194 time to fit residues: 30.0130 Evaluate side-chains 178 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.170112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141741 restraints weight = 16166.021| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.45 r_work: 0.3371 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14732 Z= 0.130 Angle : 0.625 9.169 19848 Z= 0.304 Chirality : 0.043 0.263 2158 Planarity : 0.004 0.046 2390 Dihedral : 16.355 140.523 2428 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.12 % Favored : 92.64 % Rotamer: Outliers : 2.97 % Allowed : 14.64 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1672 helix: 1.09 (0.19), residues: 852 sheet: -2.18 (0.39), residues: 130 loop : -2.54 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.022 0.001 TYR D 844 PHE 0.011 0.001 PHE B 584 TRP 0.017 0.001 TRP D 798 HIS 0.001 0.000 HIS D 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (14708) covalent geometry : angle 0.60873 / 0.30 (19782) SS BOND : bond 0.00269 / 0.15 ( 6) SS BOND : angle 0.59425 / 0.53 ( 12) hydrogen bonds : bond 0.03096 / 2.02 ( 558) hydrogen bonds : angle 3.84053 / 2.52 ( 1620) link_BETA1-3 : bond 0.00484 / 0.24 ( 2) link_BETA1-3 : angle 1.45126 / 0.80 ( 6) link_BETA1-4 : bond 0.00723 / 0.38 ( 8) link_BETA1-4 : angle 1.80309 / 1.19 ( 24) link_NAG-ASN : bond 0.01084 / 0.50 ( 8) link_NAG-ASN : angle 3.64351 / 2.37 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7514 (t70) cc_final: 0.7216 (t0) REVERT: A 715 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.7113 (p) REVERT: A 800 ARG cc_start: 0.7910 (tpp-160) cc_final: 0.7084 (ptp-110) REVERT: A 818 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: B 677 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.5699 (mp10) REVERT: B 682 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6942 (m-10) REVERT: B 691 MET cc_start: 0.7812 (ttp) cc_final: 0.7554 (ttt) REVERT: B 743 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: B 793 MET cc_start: 0.8543 (tpt) cc_final: 0.7594 (mtt) REVERT: C 584 PHE cc_start: 0.6990 (t80) cc_final: 0.6709 (t80) REVERT: C 661 VAL cc_start: 0.8492 (t) cc_final: 0.8066 (m) REVERT: C 696 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7457 (mtmt) REVERT: C 709 MET cc_start: 0.7258 (mtm) cc_final: 0.6848 (mtm) REVERT: C 719 LYS cc_start: 0.8438 (pptt) cc_final: 0.8039 (mtpp) REVERT: D 677 GLN cc_start: 0.6893 (mp10) cc_final: 0.6541 (mm-40) REVERT: D 743 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: D 796 GLU cc_start: 0.8377 (tt0) cc_final: 0.8157 (tt0) REVERT: D 825 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8099 (mt) outliers start: 43 outliers final: 31 residues processed: 174 average time/residue: 0.1196 time to fit residues: 31.0560 Evaluate side-chains 177 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139465 restraints weight = 16249.116| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.58 r_work: 0.3347 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14732 Z= 0.137 Angle : 0.633 9.664 19848 Z= 0.309 Chirality : 0.043 0.255 2158 Planarity : 0.004 0.046 2390 Dihedral : 16.246 140.524 2428 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.42 % Favored : 92.28 % Rotamer: Outliers : 2.97 % Allowed : 14.85 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.86 (0.21), residues: 1672 helix: 1.11 (0.19), residues: 852 sheet: -2.11 (0.39), residues: 130 loop : -2.52 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 481 TYR 0.022 0.002 TYR B 844 PHE 0.014 0.001 PHE D 584 TRP 0.015 0.001 TRP D 798 HIS 0.001 0.000 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14708) covalent geometry : angle 0.61804 / 0.31 (19782) SS BOND : bond 0.00315 / 0.19 ( 6) SS BOND : angle 0.50626 / 0.40 ( 12) hydrogen bonds : bond 0.03143 / 2.04 ( 558) hydrogen bonds : angle 3.84429 / 2.52 ( 1620) link_BETA1-3 : bond 0.00579 / 0.29 ( 2) link_BETA1-3 : angle 1.48948 / 0.82 ( 6) link_BETA1-4 : bond 0.00712 / 0.38 ( 8) link_BETA1-4 : angle 1.79210 / 1.18 ( 24) link_NAG-ASN : bond 0.00896 / 0.45 ( 8) link_NAG-ASN : angle 3.55137 / 2.34 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3558.51 seconds wall clock time: 61 minutes 41.58 seconds (3701.58 seconds total)