Starting phenix.real_space_refine on Sat Aug 23 22:36:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fww_29521/08_2025/8fww_29521.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fww_29521/08_2025/8fww_29521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fww_29521/08_2025/8fww_29521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fww_29521/08_2025/8fww_29521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fww_29521/08_2025/8fww_29521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fww_29521/08_2025/8fww_29521.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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 7 4.78 5 C 9478 2.51 5 N 2196 2.21 5 O 2688 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14471 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 338 Unusual residues: {' CL': 1, ' NA': 4, '2J9': 2, '6ZP': 1, 'NAG': 1, 'POV': 5} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 189 Unusual residues: {' NA': 1, '2J9': 2, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 251 Unusual residues: {' CL': 1, ' NA': 1, '6ZP': 1, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {' NA': 1, 'POV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.81, per 1000 atoms: 0.26 Number of scatterers: 14471 At special positions: 0 Unit cell: (87.36, 131.456, 138.944, 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 7 11.00 F 4 9.00 O 2688 8.00 N 2196 7.00 C 9478 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=2.14 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS D 595 " distance=1.92 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 A1005 " - " ASN A 751 " " NAG C1004 " - " 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: 0.97 Conformation dependent library (CDL) restraints added in 512.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 58 helices and 20 sheets defined 50.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.787A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.538A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.615A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.585A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 557 " --> pdb=" O SER A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 557' Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.685A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.575A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 665 removed outlier: 3.850A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.605A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.592A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.510A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.700A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 788 Processing helix chain 'A' and resid 789 through 799 removed outlier: 3.758A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 850 removed outlier: 3.676A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.623A pdb=" N LEU B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.547A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.656A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 630 through 659 removed outlier: 3.886A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 677 removed outlier: 3.705A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.704A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.603A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.547A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 Processing helix chain 'B' and resid 774 through 789 removed outlier: 3.545A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 822 through 850 removed outlier: 3.556A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 473 removed outlier: 3.787A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.539A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.615A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.585A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN C 557 " --> pdb=" O SER C 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 557' Processing helix chain 'C' and resid 560 through 585 removed outlier: 3.686A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 583 " --> pdb=" O PHE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.575A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.849A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.604A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.592A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.511A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.700A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 788 Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.758A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 850 removed outlier: 3.676A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.622A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.547A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 removed outlier: 3.656A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 630 through 659 removed outlier: 3.887A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 677 removed outlier: 3.705A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.704A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.602A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 730 removed outlier: 3.546A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 774 through 789 removed outlier: 3.545A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 Processing helix chain 'D' and resid 822 through 850 removed outlier: 3.554A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 437 removed outlier: 6.641A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.467A 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 527 through 529 Processing sheet with id=AA3, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.967A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 736 through 738 removed outlier: 4.060A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 432 through 435 removed outlier: 6.435A pdb=" N LEU B 433 " --> pdb=" O GLU B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 445 through 446 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: 3.969A 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 Processing sheet with id=AB1, first strand: chain 'B' and resid 684 through 685 removed outlier: 5.593A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 433 through 437 removed outlier: 6.641A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AB4, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.967A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 736 through 738 removed outlier: 4.060A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 432 through 435 removed outlier: 6.434A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AB9, first strand: chain 'D' and resid 534 through 536 removed outlier: 3.969A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 735 through 738 Processing sheet with id=AC2, first strand: chain 'D' and resid 684 through 685 removed outlier: 5.594A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 572 hydrogen bonds defined for protein. 1686 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: 2.10 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2226 1.28 - 1.41: 3591 1.41 - 1.55: 8495 1.55 - 1.68: 324 1.68 - 1.82: 132 Bond restraints: 14768 Sorted by residual: bond pdb=" OAA 2J9 A1001 " pdb=" SAP 2J9 A1001 " 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 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" OAA 2J9 B1004 " pdb=" SAP 2J9 B1004 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" OAA 2J9 B1001 " pdb=" SAP 2J9 B1001 " ideal model delta sigma weight residual 1.452 1.651 -0.199 2.00e-02 2.50e+03 9.95e+01 bond pdb=" OAB 2J9 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.647 -0.195 2.00e-02 2.50e+03 9.55e+01 ... (remaining 14763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.56: 19676 6.56 - 13.12: 177 13.12 - 19.68: 3 19.68 - 26.24: 0 26.24 - 32.80: 8 Bond angle restraints: 19864 Sorted by residual: angle pdb=" CAH 2J9 B1001 " pdb=" CAN 2J9 B1001 " pdb=" NAO 2J9 B1001 " ideal model delta sigma weight residual 117.67 150.47 -32.80 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CAH 2J9 A1009 " pdb=" CAN 2J9 A1009 " pdb=" NAO 2J9 A1009 " ideal model delta sigma weight residual 117.67 150.29 -32.62 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAG 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 118.82 150.78 -31.96 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CAG 2J9 B1004 " pdb=" CAN 2J9 B1004 " pdb=" NAO 2J9 B1004 " ideal model delta sigma weight residual 118.82 150.59 -31.77 3.00e+00 1.11e-01 1.12e+02 angle pdb=" CAH 2J9 B1004 " pdb=" CAN 2J9 B1004 " pdb=" NAO 2J9 B1004 " ideal model delta sigma weight residual 117.67 149.36 -31.69 3.00e+00 1.11e-01 1.12e+02 ... (remaining 19859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 8569 30.70 - 61.40: 467 61.40 - 92.09: 97 92.09 - 122.79: 39 122.79 - 153.49: 6 Dihedral angle restraints: 9178 sinusoidal: 4338 harmonic: 4840 Sorted by residual: dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual 93.00 176.48 -83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual 93.00 176.43 -83.43 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS C 750 " pdb=" SG CYS C 750 " pdb=" SG CYS C 804 " pdb=" CB CYS C 804 " ideal model delta sinusoidal sigma weight residual 93.00 157.23 -64.23 1 1.00e+01 1.00e-02 5.43e+01 ... (remaining 9175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.463: 2154 0.463 - 0.926: 0 0.926 - 1.390: 0 1.390 - 1.853: 0 1.853 - 2.316: 4 Chirality restraints: 2158 Sorted by residual: chirality pdb=" CAN 2J9 B1001 " pdb=" CAG 2J9 B1001 " pdb=" CAH 2J9 B1001 " pdb=" NAO 2J9 B1001 " 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 A1009 " pdb=" CAG 2J9 A1009 " pdb=" CAH 2J9 A1009 " pdb=" NAO 2J9 A1009 " both_signs ideal model delta sigma weight residual True 2.32 -0.01 2.31 2.00e-01 2.50e+01 1.33e+02 chirality pdb=" CAN 2J9 B1004 " pdb=" CAG 2J9 B1004 " pdb=" CAH 2J9 B1004 " pdb=" NAO 2J9 B1004 " both_signs ideal model delta sigma weight residual True 2.32 -0.03 2.29 2.00e-01 2.50e+01 1.31e+02 ... (remaining 2155 not shown) Planarity restraints: 2406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 553 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C PHE B 553 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE B 553 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 554 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 553 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C PHE D 553 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE D 553 " 0.018 2.00e-02 2.50e+03 pdb=" N SER D 554 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 716 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C VAL C 716 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL C 716 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU C 717 " -0.014 2.00e-02 2.50e+03 ... (remaining 2403 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1802 2.74 - 3.28: 12806 3.28 - 3.82: 22623 3.82 - 4.36: 28730 4.36 - 4.90: 48980 Nonbonded interactions: 114941 Sorted by model distance: nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.206 3.040 nonbonded pdb=" NH2 ARG D 543 " pdb=" O LEU D 729 " model vdw 2.249 3.120 nonbonded pdb=" NH2 ARG B 543 " pdb=" O LEU B 729 " model vdw 2.250 3.120 nonbonded pdb=" OG SER A 585 " pdb=" OE1 GLU B 841 " model vdw 2.263 3.040 nonbonded pdb=" NH2 ARG B 634 " pdb=" OE2 GLU C 625 " model vdw 2.278 3.120 ... (remaining 114936 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 1002 through 1003)) selection = (chain 'B' and (resid 431 through 850 or resid 1002 through 1003)) selection = (chain 'C' and (resid 431 through 850 or resid 1002 through 1003)) selection = (chain 'D' and (resid 431 through 850 or resid 1002 through 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: 5.690 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.440 Find NCS groups from input model: 0.300 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.013 0.202 14792 Z= 0.625 Angle : 1.672 32.801 19930 Z= 0.766 Chirality : 0.118 2.316 2158 Planarity : 0.007 0.054 2398 Dihedral : 20.284 153.489 6064 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 1.17 % Allowed : 3.66 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: -5.95 (0.13), residues: 1672 helix: -4.16 (0.09), residues: 842 sheet: -3.04 (0.36), residues: 150 loop : -3.68 (0.17), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG D 543 TYR 0.024 0.003 TYR C 733 PHE 0.037 0.003 PHE D 584 TRP 0.020 0.003 TRP D 799 HIS 0.003 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.01328 (14768) covalent geometry : angle 1.64469 (19864) SS BOND : bond 0.06387 ( 6) SS BOND : angle 4.40994 ( 12) hydrogen bonds : bond 0.30798 ( 572) hydrogen bonds : angle 10.43992 ( 1686) link_BETA1-3 : bond 0.00115 ( 2) link_BETA1-3 : angle 2.36031 ( 6) link_BETA1-4 : bond 0.01829 ( 8) link_BETA1-4 : angle 3.97780 ( 24) link_NAG-ASN : bond 0.01279 ( 8) link_NAG-ASN : angle 7.46923 ( 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 298 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 281 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7012 (tt0) cc_final: 0.6686 (tt0) REVERT: A 487 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8032 (mttt) REVERT: A 531 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7381 (ttmm) REVERT: A 629 LYS cc_start: 0.7826 (ttmp) cc_final: 0.6784 (tptp) REVERT: A 691 MET cc_start: 0.7048 (ptm) cc_final: 0.6318 (ptt) REVERT: A 695 LYS cc_start: 0.6854 (mttt) cc_final: 0.6486 (mtpt) REVERT: A 780 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7152 (mt) REVERT: B 499 ASN cc_start: 0.6914 (m-40) cc_final: 0.6566 (m-40) REVERT: B 509 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7523 (mtmt) REVERT: B 719 LYS cc_start: 0.8335 (pttp) cc_final: 0.7878 (mttp) REVERT: B 722 GLU cc_start: 0.7173 (tp30) cc_final: 0.6890 (tp30) REVERT: B 762 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7979 (mttt) REVERT: B 793 MET cc_start: 0.7149 (mtm) cc_final: 0.6707 (mmm) REVERT: B 797 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7680 (ttpp) REVERT: C 479 GLU cc_start: 0.7987 (tt0) cc_final: 0.7648 (tp30) REVERT: C 487 LYS cc_start: 0.8474 (mtpp) cc_final: 0.7856 (mttt) REVERT: C 531 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7331 (ttmm) REVERT: C 780 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.7020 (mt) REVERT: D 509 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7767 (mttt) REVERT: D 566 TYR cc_start: 0.7796 (m-10) cc_final: 0.7563 (m-80) REVERT: D 662 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7154 (mp0) REVERT: D 719 LYS cc_start: 0.8204 (pttp) cc_final: 0.7763 (mttp) REVERT: D 720 SER cc_start: 0.8186 (t) cc_final: 0.7589 (p) REVERT: D 722 GLU cc_start: 0.7486 (tp30) cc_final: 0.7285 (tp30) REVERT: D 762 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8057 (mttt) REVERT: D 784 GLN cc_start: 0.7586 (tt0) cc_final: 0.7171 (tm-30) REVERT: D 793 MET cc_start: 0.7129 (mtm) cc_final: 0.6572 (mmm) REVERT: D 797 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7932 (ttpt) outliers start: 17 outliers final: 5 residues processed: 295 average time/residue: 0.1327 time to fit residues: 55.9979 Evaluate side-chains 201 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 791 LEU 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: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0060 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN A 557 ASN A 605 ASN A 849 ASN B 456 ASN B 621 GLN ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN C 557 ASN C 621 GLN C 792 HIS C 849 ASN D 456 ASN D 604 ASN D 621 GLN D 849 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.185727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143186 restraints weight = 14542.853| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.28 r_work: 0.3381 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 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 = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14792 Z= 0.154 Angle : 0.774 11.595 19930 Z= 0.359 Chirality : 0.045 0.227 2158 Planarity : 0.005 0.049 2398 Dihedral : 22.449 148.496 2945 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.07 % Allowed : 8.08 % Favored : 89.85 % 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 aren not related in a simple way. whole: -3.90 (0.17), residues: 1672 helix: -1.91 (0.14), residues: 852 sheet: -2.82 (0.36), residues: 164 loop : -3.34 (0.19), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 663 TYR 0.024 0.002 TYR D 590 PHE 0.021 0.002 PHE C 579 TRP 0.017 0.001 TRP C 706 HIS 0.001 0.000 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00352 (14768) covalent geometry : angle 0.73889 (19864) SS BOND : bond 0.00602 ( 6) SS BOND : angle 1.12553 ( 12) hydrogen bonds : bond 0.04908 ( 572) hydrogen bonds : angle 4.56989 ( 1686) link_BETA1-3 : bond 0.00896 ( 2) link_BETA1-3 : angle 3.93773 ( 6) link_BETA1-4 : bond 0.01075 ( 8) link_BETA1-4 : angle 3.35152 ( 24) link_NAG-ASN : bond 0.00647 ( 8) link_NAG-ASN : angle 5.43497 ( 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 239 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8126 (mttt) REVERT: A 531 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7847 (mmtp) REVERT: A 629 LYS cc_start: 0.8025 (ttmp) cc_final: 0.6898 (tptp) REVERT: A 691 MET cc_start: 0.7168 (ptm) cc_final: 0.6631 (ptt) REVERT: B 499 ASN cc_start: 0.7289 (m-40) cc_final: 0.7007 (m-40) REVERT: B 509 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7439 (mttt) REVERT: B 669 ASP cc_start: 0.8006 (t0) cc_final: 0.7501 (t0) REVERT: B 719 LYS cc_start: 0.8361 (pttp) cc_final: 0.7864 (mttp) REVERT: B 722 GLU cc_start: 0.7216 (tp30) cc_final: 0.6546 (mt-10) REVERT: B 762 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7633 (mttt) REVERT: B 793 MET cc_start: 0.7286 (mtm) cc_final: 0.6572 (mmm) REVERT: B 796 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7377 (mm-30) REVERT: B 798 TRP cc_start: 0.7784 (m100) cc_final: 0.7336 (m100) REVERT: C 485 ASP cc_start: 0.7861 (t0) cc_final: 0.7615 (t0) REVERT: C 487 LYS cc_start: 0.8602 (mtpp) cc_final: 0.7983 (mttt) REVERT: C 531 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7626 (mmtp) REVERT: C 661 VAL cc_start: 0.7134 (t) cc_final: 0.6881 (m) REVERT: C 665 GLU cc_start: 0.6233 (pt0) cc_final: 0.5873 (mt-10) REVERT: C 677 GLN cc_start: 0.6004 (mm-40) cc_final: 0.5795 (mp10) REVERT: C 712 ARG cc_start: 0.6459 (ttp-110) cc_final: 0.6095 (ttm170) REVERT: D 509 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7744 (mttt) REVERT: D 669 ASP cc_start: 0.7929 (t0) cc_final: 0.7582 (t0) REVERT: D 719 LYS cc_start: 0.8263 (pttp) cc_final: 0.7686 (mttp) REVERT: D 722 GLU cc_start: 0.7452 (tp30) cc_final: 0.7093 (tp30) REVERT: D 796 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7408 (mm-30) REVERT: D 797 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7814 (ttpt) REVERT: D 798 TRP cc_start: 0.7869 (m100) cc_final: 0.6714 (m100) outliers start: 30 outliers final: 13 residues processed: 234 average time/residue: 0.1162 time to fit residues: 40.0316 Evaluate side-chains 200 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN D 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.177120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136581 restraints weight = 14753.924| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.34 r_work: 0.3255 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14792 Z= 0.206 Angle : 0.759 11.269 19930 Z= 0.354 Chirality : 0.046 0.242 2158 Planarity : 0.005 0.044 2398 Dihedral : 21.178 145.336 2936 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.04 % Allowed : 10.01 % Favored : 86.95 % 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 aren not related in a simple way. whole: -2.65 (0.19), residues: 1672 helix: -0.62 (0.17), residues: 872 sheet: -2.45 (0.41), residues: 140 loop : -3.16 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 481 TYR 0.022 0.002 TYR D 733 PHE 0.023 0.002 PHE A 735 TRP 0.014 0.002 TRP C 706 HIS 0.002 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00509 (14768) covalent geometry : angle 0.72605 (19864) SS BOND : bond 0.00371 ( 6) SS BOND : angle 1.66682 ( 12) hydrogen bonds : bond 0.04592 ( 572) hydrogen bonds : angle 4.12529 ( 1686) link_BETA1-3 : bond 0.00566 ( 2) link_BETA1-3 : angle 3.72204 ( 6) link_BETA1-4 : bond 0.01010 ( 8) link_BETA1-4 : angle 3.14875 ( 24) link_NAG-ASN : bond 0.00740 ( 8) link_NAG-ASN : angle 5.20668 ( 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 222 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.462 Fit side-chains REVERT: A 487 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8233 (mttt) REVERT: A 629 LYS cc_start: 0.8379 (ttmp) cc_final: 0.7234 (tptp) REVERT: A 691 MET cc_start: 0.7354 (ptm) cc_final: 0.6767 (ptt) REVERT: A 780 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7188 (mp) REVERT: A 808 GLU cc_start: 0.5233 (OUTLIER) cc_final: 0.5007 (mp0) REVERT: B 499 ASN cc_start: 0.7560 (m-40) cc_final: 0.7302 (m-40) REVERT: B 509 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7568 (mttt) REVERT: B 620 MET cc_start: 0.8914 (mmt) cc_final: 0.8131 (mmt) REVERT: B 669 ASP cc_start: 0.8207 (t0) cc_final: 0.7792 (t0) REVERT: B 679 LYS cc_start: 0.6084 (ttpt) cc_final: 0.5749 (tptt) REVERT: B 719 LYS cc_start: 0.8512 (pttp) cc_final: 0.8038 (mttp) REVERT: B 722 GLU cc_start: 0.7560 (tp30) cc_final: 0.6885 (mt-10) REVERT: B 796 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7574 (mm-30) REVERT: B 798 TRP cc_start: 0.7953 (m100) cc_final: 0.7110 (m100) REVERT: C 487 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8090 (mttt) REVERT: C 665 GLU cc_start: 0.6561 (pt0) cc_final: 0.6143 (mt-10) REVERT: C 780 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7143 (mp) REVERT: D 509 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7781 (mtmt) REVERT: D 669 ASP cc_start: 0.8288 (t0) cc_final: 0.7869 (t0) REVERT: D 719 LYS cc_start: 0.8489 (pttp) cc_final: 0.8015 (mttp) REVERT: D 722 GLU cc_start: 0.7793 (tp30) cc_final: 0.7390 (tp30) REVERT: D 796 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7594 (mm-30) REVERT: D 797 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7860 (ttpt) REVERT: D 798 TRP cc_start: 0.7968 (m100) cc_final: 0.6951 (m100) outliers start: 44 outliers final: 26 residues processed: 214 average time/residue: 0.1095 time to fit residues: 35.0658 Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 142 optimal weight: 8.9990 chunk 97 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 HIS ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138796 restraints weight = 14590.096| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.33 r_work: 0.3293 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14792 Z= 0.171 Angle : 0.696 9.953 19930 Z= 0.321 Chirality : 0.045 0.255 2158 Planarity : 0.004 0.043 2398 Dihedral : 20.061 143.027 2926 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.59 % Allowed : 11.33 % Favored : 85.08 % 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 aren not related in a simple way. whole: -1.94 (0.20), residues: 1672 helix: 0.13 (0.18), residues: 872 sheet: -2.45 (0.41), residues: 140 loop : -3.02 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 712 TYR 0.021 0.002 TYR B 844 PHE 0.019 0.002 PHE C 584 TRP 0.010 0.001 TRP C 706 HIS 0.002 0.000 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00419 (14768) covalent geometry : angle 0.66418 (19864) SS BOND : bond 0.00182 ( 6) SS BOND : angle 1.23256 ( 12) hydrogen bonds : bond 0.03824 ( 572) hydrogen bonds : angle 3.91814 ( 1686) link_BETA1-3 : bond 0.00279 ( 2) link_BETA1-3 : angle 3.82643 ( 6) link_BETA1-4 : bond 0.01138 ( 8) link_BETA1-4 : angle 3.03682 ( 24) link_NAG-ASN : bond 0.00689 ( 8) link_NAG-ASN : angle 4.89239 ( 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 232 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8155 (mttt) REVERT: A 691 MET cc_start: 0.7260 (ptm) cc_final: 0.6658 (ptt) REVERT: A 780 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.6918 (mp) REVERT: B 509 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7542 (mttt) REVERT: B 565 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7982 (ttm) REVERT: B 669 ASP cc_start: 0.8039 (t0) cc_final: 0.7566 (t0) REVERT: B 719 LYS cc_start: 0.8381 (pttp) cc_final: 0.7992 (mttp) REVERT: B 722 GLU cc_start: 0.7475 (tp30) cc_final: 0.6823 (mt-10) REVERT: B 796 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 798 TRP cc_start: 0.7860 (m100) cc_final: 0.7019 (m100) REVERT: C 487 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8107 (mttt) REVERT: C 665 GLU cc_start: 0.6345 (pt0) cc_final: 0.5999 (mt-10) REVERT: C 780 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.6902 (mp) REVERT: D 509 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7712 (mtmt) REVERT: D 669 ASP cc_start: 0.8090 (t0) cc_final: 0.7648 (t0) REVERT: D 719 LYS cc_start: 0.8492 (pttp) cc_final: 0.8048 (mttp) REVERT: D 722 GLU cc_start: 0.7595 (tp30) cc_final: 0.7171 (tp30) REVERT: D 796 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7487 (mm-30) outliers start: 52 outliers final: 37 residues processed: 224 average time/residue: 0.1035 time to fit residues: 34.5877 Evaluate side-chains 203 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 29 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.180460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138121 restraints weight = 14550.313| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.29 r_work: 0.3135 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14792 Z= 0.157 Angle : 0.673 14.560 19930 Z= 0.309 Chirality : 0.044 0.251 2158 Planarity : 0.004 0.042 2398 Dihedral : 18.627 142.907 2926 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.18 % Allowed : 12.22 % Favored : 84.60 % 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 aren not related in a simple way. whole: -1.39 (0.21), residues: 1672 helix: 0.65 (0.19), residues: 870 sheet: -2.31 (0.42), residues: 140 loop : -2.84 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 712 TYR 0.021 0.002 TYR B 844 PHE 0.015 0.002 PHE D 584 TRP 0.014 0.001 TRP D 798 HIS 0.001 0.000 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00386 (14768) covalent geometry : angle 0.64303 (19864) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.95058 ( 12) hydrogen bonds : bond 0.03582 ( 572) hydrogen bonds : angle 3.75158 ( 1686) link_BETA1-3 : bond 0.00279 ( 2) link_BETA1-3 : angle 3.84508 ( 6) link_BETA1-4 : bond 0.00934 ( 8) link_BETA1-4 : angle 2.88568 ( 24) link_NAG-ASN : bond 0.00681 ( 8) link_NAG-ASN : angle 4.67790 ( 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 216 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.518 Fit side-chains REVERT: A 487 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8079 (mttt) REVERT: A 682 TYR cc_start: 0.7257 (m-10) cc_final: 0.6993 (m-10) REVERT: A 691 MET cc_start: 0.7120 (ptm) cc_final: 0.6503 (ptt) REVERT: A 780 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.6942 (mp) REVERT: A 808 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.4842 (mp0) REVERT: A 836 PHE cc_start: 0.6762 (m-10) cc_final: 0.6543 (m-10) REVERT: B 509 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7543 (mtmt) REVERT: B 565 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7904 (ttm) REVERT: B 620 MET cc_start: 0.8758 (mmt) cc_final: 0.8006 (mmt) REVERT: B 625 GLU cc_start: 0.7207 (pm20) cc_final: 0.6488 (pm20) REVERT: B 669 ASP cc_start: 0.8144 (t0) cc_final: 0.7861 (t0) REVERT: B 719 LYS cc_start: 0.8347 (pttp) cc_final: 0.7851 (mttp) REVERT: B 722 GLU cc_start: 0.7550 (tp30) cc_final: 0.7098 (tp30) REVERT: B 796 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7422 (mm-30) REVERT: B 798 TRP cc_start: 0.7838 (m100) cc_final: 0.6873 (m100) REVERT: C 487 LYS cc_start: 0.8566 (mtpp) cc_final: 0.7941 (mttt) REVERT: C 665 GLU cc_start: 0.6124 (pt0) cc_final: 0.5730 (mt-10) REVERT: C 780 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.6955 (mp) REVERT: D 509 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7637 (mtmt) REVERT: D 620 MET cc_start: 0.8806 (mmt) cc_final: 0.8139 (mmt) REVERT: D 669 ASP cc_start: 0.8192 (t0) cc_final: 0.7757 (t0) REVERT: D 719 LYS cc_start: 0.8444 (pttp) cc_final: 0.7895 (mttp) REVERT: D 722 GLU cc_start: 0.7573 (tp30) cc_final: 0.7152 (tp30) REVERT: D 796 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7438 (mm-30) outliers start: 46 outliers final: 34 residues processed: 207 average time/residue: 0.0976 time to fit residues: 31.4698 Evaluate side-chains 199 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.0020 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.177712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137851 restraints weight = 14593.338| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.10 r_work: 0.3197 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14792 Z= 0.176 Angle : 0.676 11.727 19930 Z= 0.313 Chirality : 0.044 0.228 2158 Planarity : 0.004 0.043 2398 Dihedral : 18.003 143.142 2926 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.73 % Allowed : 12.64 % Favored : 83.63 % 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 aren not related in a simple way. whole: -1.26 (0.21), residues: 1672 helix: 0.75 (0.19), residues: 870 sheet: -2.27 (0.42), residues: 140 loop : -2.76 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 712 TYR 0.021 0.002 TYR B 844 PHE 0.016 0.002 PHE D 584 TRP 0.022 0.001 TRP D 798 HIS 0.001 0.000 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00434 (14768) covalent geometry : angle 0.64555 (19864) SS BOND : bond 0.00192 ( 6) SS BOND : angle 0.86709 ( 12) hydrogen bonds : bond 0.03612 ( 572) hydrogen bonds : angle 3.76339 ( 1686) link_BETA1-3 : bond 0.00129 ( 2) link_BETA1-3 : angle 3.85208 ( 6) link_BETA1-4 : bond 0.00957 ( 8) link_BETA1-4 : angle 2.85915 ( 24) link_NAG-ASN : bond 0.00653 ( 8) link_NAG-ASN : angle 4.68916 ( 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 221 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 0.539 Fit side-chains REVERT: A 487 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8222 (mttt) REVERT: A 682 TYR cc_start: 0.7336 (m-10) cc_final: 0.7072 (m-10) REVERT: A 691 MET cc_start: 0.7284 (ptm) cc_final: 0.6646 (ptt) REVERT: A 780 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7093 (mp) REVERT: A 808 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4964 (mp0) REVERT: A 818 GLN cc_start: 0.7562 (pm20) cc_final: 0.7324 (pm20) REVERT: A 836 PHE cc_start: 0.7019 (m-10) cc_final: 0.6809 (m-10) REVERT: B 509 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7716 (mtmt) REVERT: B 565 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8096 (ttm) REVERT: B 620 MET cc_start: 0.8820 (mmt) cc_final: 0.8109 (mmt) REVERT: B 625 GLU cc_start: 0.7365 (pm20) cc_final: 0.6642 (pm20) REVERT: B 719 LYS cc_start: 0.8472 (pttp) cc_final: 0.8040 (mttp) REVERT: B 722 GLU cc_start: 0.7699 (tp30) cc_final: 0.7277 (tp30) REVERT: B 796 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7567 (mm-30) REVERT: B 798 TRP cc_start: 0.7905 (m100) cc_final: 0.6994 (m100) REVERT: C 487 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8085 (mttt) REVERT: C 664 MET cc_start: 0.8202 (mtp) cc_final: 0.7964 (mtp) REVERT: C 665 GLU cc_start: 0.6380 (pt0) cc_final: 0.5962 (mt-10) REVERT: C 780 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7100 (mp) REVERT: D 509 LYS cc_start: 0.8331 (mtpp) cc_final: 0.7798 (mtmt) REVERT: D 620 MET cc_start: 0.8884 (mmt) cc_final: 0.8259 (mmt) REVERT: D 669 ASP cc_start: 0.8160 (t0) cc_final: 0.7642 (t0) REVERT: D 719 LYS cc_start: 0.8487 (pttp) cc_final: 0.8018 (mttp) REVERT: D 722 GLU cc_start: 0.7715 (tp30) cc_final: 0.7304 (tp30) REVERT: D 796 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7571 (mm-30) outliers start: 54 outliers final: 39 residues processed: 211 average time/residue: 0.0999 time to fit residues: 33.1353 Evaluate side-chains 202 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 137 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.176884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137248 restraints weight = 14567.456| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.10 r_work: 0.3180 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14792 Z= 0.159 Angle : 0.652 11.308 19930 Z= 0.302 Chirality : 0.043 0.243 2158 Planarity : 0.004 0.042 2398 Dihedral : 17.312 142.744 2926 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.73 % Allowed : 13.12 % Favored : 83.15 % 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 aren not related in a simple way. whole: -1.09 (0.21), residues: 1672 helix: 0.91 (0.19), residues: 870 sheet: -2.20 (0.42), residues: 140 loop : -2.69 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 543 TYR 0.020 0.002 TYR B 844 PHE 0.015 0.002 PHE D 584 TRP 0.020 0.001 TRP D 798 HIS 0.001 0.000 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00390 (14768) covalent geometry : angle 0.62225 (19864) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.84747 ( 12) hydrogen bonds : bond 0.03449 ( 572) hydrogen bonds : angle 3.68687 ( 1686) link_BETA1-3 : bond 0.00133 ( 2) link_BETA1-3 : angle 3.58933 ( 6) link_BETA1-4 : bond 0.00989 ( 8) link_BETA1-4 : angle 2.79517 ( 24) link_NAG-ASN : bond 0.00654 ( 8) link_NAG-ASN : angle 4.63203 ( 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 220 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8223 (mttt) REVERT: A 682 TYR cc_start: 0.7361 (m-10) cc_final: 0.7149 (m-10) REVERT: A 691 MET cc_start: 0.7361 (ptm) cc_final: 0.6714 (ptt) REVERT: A 780 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7132 (mp) REVERT: A 808 GLU cc_start: 0.5043 (OUTLIER) cc_final: 0.4831 (mp0) REVERT: A 818 GLN cc_start: 0.7614 (pm20) cc_final: 0.7388 (pm20) REVERT: A 836 PHE cc_start: 0.7058 (m-10) cc_final: 0.6839 (m-10) REVERT: B 509 LYS cc_start: 0.8377 (mtpp) cc_final: 0.7816 (mtmt) REVERT: B 565 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8137 (ttm) REVERT: B 620 MET cc_start: 0.8872 (mmt) cc_final: 0.8195 (mmt) REVERT: B 625 GLU cc_start: 0.7350 (pm20) cc_final: 0.6501 (pm20) REVERT: B 719 LYS cc_start: 0.8464 (pttp) cc_final: 0.8054 (mttp) REVERT: B 722 GLU cc_start: 0.7713 (tp30) cc_final: 0.7291 (tp30) REVERT: B 796 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 798 TRP cc_start: 0.7899 (m100) cc_final: 0.7009 (m100) REVERT: C 487 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8114 (mttt) REVERT: C 488 TYR cc_start: 0.8071 (m-80) cc_final: 0.7746 (m-80) REVERT: C 780 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7135 (mp) REVERT: D 509 LYS cc_start: 0.8381 (mtpp) cc_final: 0.7814 (mtmt) REVERT: D 620 MET cc_start: 0.8887 (mmt) cc_final: 0.8239 (mmt) REVERT: D 669 ASP cc_start: 0.8196 (t0) cc_final: 0.7682 (t0) REVERT: D 670 SER cc_start: 0.8505 (t) cc_final: 0.8092 (p) REVERT: D 719 LYS cc_start: 0.8460 (pttp) cc_final: 0.8018 (mttp) REVERT: D 722 GLU cc_start: 0.7739 (tp30) cc_final: 0.6956 (mm-30) REVERT: D 796 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7560 (mm-30) outliers start: 54 outliers final: 43 residues processed: 208 average time/residue: 0.1016 time to fit residues: 33.4714 Evaluate side-chains 207 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 87 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 135 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.179494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142314 restraints weight = 14489.827| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.05 r_work: 0.3258 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14792 Z= 0.139 Angle : 0.631 10.730 19930 Z= 0.294 Chirality : 0.042 0.202 2158 Planarity : 0.004 0.042 2398 Dihedral : 16.883 142.608 2926 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.59 % Allowed : 13.26 % Favored : 83.15 % 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 aren not related in a simple way. whole: -0.91 (0.21), residues: 1672 helix: 1.07 (0.19), residues: 870 sheet: -2.15 (0.42), residues: 140 loop : -2.62 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 543 TYR 0.019 0.001 TYR B 844 PHE 0.015 0.001 PHE D 584 TRP 0.019 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 Details of bonding type rmsd covalent geometry : bond 0.00338 (14768) covalent geometry : angle 0.60250 (19864) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.78882 ( 12) hydrogen bonds : bond 0.03280 ( 572) hydrogen bonds : angle 3.62350 ( 1686) link_BETA1-3 : bond 0.00108 ( 2) link_BETA1-3 : angle 3.03792 ( 6) link_BETA1-4 : bond 0.00981 ( 8) link_BETA1-4 : angle 2.72254 ( 24) link_NAG-ASN : bond 0.00632 ( 8) link_NAG-ASN : angle 4.50065 ( 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 223 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8305 (mttt) REVERT: A 682 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.7170 (m-10) REVERT: A 691 MET cc_start: 0.7392 (ptm) cc_final: 0.6752 (ptt) REVERT: A 780 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7150 (mp) REVERT: A 808 GLU cc_start: 0.5182 (OUTLIER) cc_final: 0.4907 (mp0) REVERT: A 818 GLN cc_start: 0.7636 (pm20) cc_final: 0.7428 (pm20) REVERT: A 836 PHE cc_start: 0.7063 (m-10) cc_final: 0.6848 (m-10) REVERT: B 509 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7807 (mtmt) REVERT: B 565 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8167 (ttm) REVERT: B 620 MET cc_start: 0.8860 (mmt) cc_final: 0.8219 (mmt) REVERT: B 625 GLU cc_start: 0.7413 (pm20) cc_final: 0.6593 (pm20) REVERT: B 679 LYS cc_start: 0.6072 (ttpt) cc_final: 0.5713 (tptt) REVERT: B 719 LYS cc_start: 0.8475 (pttp) cc_final: 0.8074 (mttp) REVERT: B 722 GLU cc_start: 0.7758 (tp30) cc_final: 0.7339 (tp30) REVERT: B 796 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7634 (mm-30) REVERT: B 798 TRP cc_start: 0.7900 (m100) cc_final: 0.7044 (m100) REVERT: C 487 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8156 (mttt) REVERT: C 488 TYR cc_start: 0.7990 (m-80) cc_final: 0.7707 (m-80) REVERT: C 665 GLU cc_start: 0.6252 (pt0) cc_final: 0.5828 (mt-10) REVERT: C 780 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7125 (mp) REVERT: D 509 LYS cc_start: 0.8407 (mtpp) cc_final: 0.7813 (mtmt) REVERT: D 669 ASP cc_start: 0.7993 (t0) cc_final: 0.7468 (t0) REVERT: D 670 SER cc_start: 0.8441 (t) cc_final: 0.8047 (p) REVERT: D 719 LYS cc_start: 0.8474 (pttp) cc_final: 0.8048 (mttp) REVERT: D 722 GLU cc_start: 0.7762 (tp30) cc_final: 0.6970 (mm-30) REVERT: D 796 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7473 (mm-30) REVERT: D 800 ARG cc_start: 0.7631 (tpt-90) cc_final: 0.7268 (ttp-170) outliers start: 52 outliers final: 37 residues processed: 213 average time/residue: 0.1099 time to fit residues: 36.3406 Evaluate side-chains 207 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.177689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138760 restraints weight = 14730.778| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.07 r_work: 0.3279 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14792 Z= 0.232 Angle : 0.702 12.033 19930 Z= 0.330 Chirality : 0.046 0.265 2158 Planarity : 0.004 0.041 2398 Dihedral : 17.124 143.145 2926 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.52 % Allowed : 13.47 % Favored : 83.01 % 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 aren not related in a simple way. whole: -1.13 (0.21), residues: 1672 helix: 0.82 (0.18), residues: 870 sheet: -2.23 (0.42), residues: 140 loop : -2.63 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 712 TYR 0.020 0.002 TYR B 844 PHE 0.017 0.002 PHE C 533 TRP 0.019 0.002 TRP D 798 HIS 0.001 0.000 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00582 (14768) covalent geometry : angle 0.67347 (19864) SS BOND : bond 0.00171 ( 6) SS BOND : angle 1.30810 ( 12) hydrogen bonds : bond 0.03828 ( 572) hydrogen bonds : angle 3.82655 ( 1686) link_BETA1-3 : bond 0.00121 ( 2) link_BETA1-3 : angle 2.72406 ( 6) link_BETA1-4 : bond 0.00963 ( 8) link_BETA1-4 : angle 2.78432 ( 24) link_NAG-ASN : bond 0.00610 ( 8) link_NAG-ASN : angle 4.86902 ( 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 215 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8322 (mttt) REVERT: A 682 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7301 (m-10) REVERT: A 691 MET cc_start: 0.7497 (ptm) cc_final: 0.6823 (ptt) REVERT: A 780 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7231 (mp) REVERT: A 808 GLU cc_start: 0.5268 (OUTLIER) cc_final: 0.4984 (mp0) REVERT: A 836 PHE cc_start: 0.7175 (m-10) cc_final: 0.6964 (m-10) REVERT: B 509 LYS cc_start: 0.8410 (mtpp) cc_final: 0.7860 (mtmt) REVERT: B 620 MET cc_start: 0.8945 (mmt) cc_final: 0.8304 (mmt) REVERT: B 719 LYS cc_start: 0.8492 (pttp) cc_final: 0.8137 (mttp) REVERT: B 722 GLU cc_start: 0.7832 (tp30) cc_final: 0.7438 (tp30) REVERT: B 796 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7578 (mm-30) REVERT: B 800 ARG cc_start: 0.7818 (tpt-90) cc_final: 0.7337 (ttp-170) REVERT: C 487 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8215 (mttt) REVERT: C 780 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7216 (mp) REVERT: D 454 TYR cc_start: 0.3707 (OUTLIER) cc_final: 0.3145 (m-80) REVERT: D 468 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6091 (ttp-110) REVERT: D 509 LYS cc_start: 0.8387 (mtpp) cc_final: 0.7826 (mtmt) REVERT: D 669 ASP cc_start: 0.8120 (t0) cc_final: 0.7558 (t0) REVERT: D 719 LYS cc_start: 0.8490 (pttp) cc_final: 0.8130 (mttp) REVERT: D 722 GLU cc_start: 0.7824 (tp30) cc_final: 0.7054 (mm-30) REVERT: D 796 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7580 (mm-30) REVERT: D 800 ARG cc_start: 0.7688 (tpt-90) cc_final: 0.7337 (ttp-170) outliers start: 51 outliers final: 38 residues processed: 202 average time/residue: 0.1173 time to fit residues: 36.0030 Evaluate side-chains 205 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 468 ARG Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 96 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.180892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142600 restraints weight = 14468.132| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.98 r_work: 0.3315 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14792 Z= 0.137 Angle : 0.634 10.591 19930 Z= 0.295 Chirality : 0.042 0.173 2158 Planarity : 0.004 0.044 2398 Dihedral : 16.648 142.299 2926 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.97 % Allowed : 14.02 % Favored : 83.01 % 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 aren not related in a simple way. whole: -0.84 (0.21), residues: 1672 helix: 1.09 (0.19), residues: 870 sheet: -2.06 (0.42), residues: 140 loop : -2.55 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 543 TYR 0.019 0.002 TYR B 844 PHE 0.014 0.001 PHE D 584 TRP 0.018 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 Details of bonding type rmsd covalent geometry : bond 0.00333 (14768) covalent geometry : angle 0.60444 (19864) SS BOND : bond 0.00225 ( 6) SS BOND : angle 1.44638 ( 12) hydrogen bonds : bond 0.03293 ( 572) hydrogen bonds : angle 3.64920 ( 1686) link_BETA1-3 : bond 0.00134 ( 2) link_BETA1-3 : angle 2.58353 ( 6) link_BETA1-4 : bond 0.00978 ( 8) link_BETA1-4 : angle 2.74048 ( 24) link_NAG-ASN : bond 0.00618 ( 8) link_NAG-ASN : angle 4.59695 ( 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 212 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.476 Fit side-chains REVERT: A 487 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8324 (mttt) REVERT: A 691 MET cc_start: 0.7424 (ptm) cc_final: 0.6772 (ptt) REVERT: A 780 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7152 (mp) REVERT: A 808 GLU cc_start: 0.5257 (OUTLIER) cc_final: 0.4952 (mp0) REVERT: A 836 PHE cc_start: 0.7096 (m-10) cc_final: 0.6880 (m-10) REVERT: B 468 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.6238 (ttp-110) REVERT: B 509 LYS cc_start: 0.8364 (mtpp) cc_final: 0.7805 (mtmt) REVERT: B 620 MET cc_start: 0.8863 (mmt) cc_final: 0.8200 (mmt) REVERT: B 679 LYS cc_start: 0.6166 (ttpt) cc_final: 0.5797 (tptt) REVERT: B 719 LYS cc_start: 0.8442 (pttp) cc_final: 0.8041 (mttp) REVERT: B 722 GLU cc_start: 0.7754 (tp30) cc_final: 0.6914 (mm-30) REVERT: B 796 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 800 ARG cc_start: 0.7706 (tpt-90) cc_final: 0.7232 (ttp-170) REVERT: C 487 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8176 (mttt) REVERT: C 488 TYR cc_start: 0.7909 (m-80) cc_final: 0.7636 (m-80) REVERT: C 780 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7149 (mp) REVERT: D 468 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.6023 (ttp-110) REVERT: D 509 LYS cc_start: 0.8415 (mtpp) cc_final: 0.7827 (mtmt) REVERT: D 669 ASP cc_start: 0.8086 (t0) cc_final: 0.7718 (t0) REVERT: D 670 SER cc_start: 0.8533 (t) cc_final: 0.8053 (p) REVERT: D 719 LYS cc_start: 0.8468 (pttp) cc_final: 0.8087 (mttp) REVERT: D 722 GLU cc_start: 0.7739 (tp30) cc_final: 0.6985 (mm-30) REVERT: D 796 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7525 (mm-30) REVERT: D 800 ARG cc_start: 0.7601 (tpt-90) cc_final: 0.7242 (ttp-170) outliers start: 43 outliers final: 32 residues processed: 206 average time/residue: 0.1190 time to fit residues: 36.9358 Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 468 ARG Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 148 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 113 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.180006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141260 restraints weight = 14525.812| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.99 r_work: 0.3171 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14792 Z= 0.136 Angle : 0.631 10.633 19930 Z= 0.295 Chirality : 0.043 0.219 2158 Planarity : 0.004 0.042 2398 Dihedral : 16.331 142.643 2924 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.62 % Allowed : 14.30 % Favored : 83.08 % 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 aren not related in a simple way. whole: -0.73 (0.21), residues: 1672 helix: 1.19 (0.19), residues: 870 sheet: -1.98 (0.42), residues: 140 loop : -2.52 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 543 TYR 0.020 0.001 TYR B 844 PHE 0.014 0.001 PHE D 584 TRP 0.028 0.001 TRP B 798 HIS 0.001 0.000 HIS C 792 Details of bonding type rmsd covalent geometry : bond 0.00329 (14768) covalent geometry : angle 0.60203 (19864) SS BOND : bond 0.00237 ( 6) SS BOND : angle 1.81930 ( 12) hydrogen bonds : bond 0.03218 ( 572) hydrogen bonds : angle 3.61371 ( 1686) link_BETA1-3 : bond 0.00170 ( 2) link_BETA1-3 : angle 2.51005 ( 6) link_BETA1-4 : bond 0.01018 ( 8) link_BETA1-4 : angle 2.71066 ( 24) link_NAG-ASN : bond 0.00591 ( 8) link_NAG-ASN : angle 4.49742 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4040.95 seconds wall clock time: 69 minutes 57.41 seconds (4197.41 seconds total)