Starting phenix.real_space_refine on Sat May 17 02:17:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fww_29521/05_2025/8fww_29521.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fww_29521/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fww_29521/05_2025/8fww_29521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fww_29521/05_2025/8fww_29521.map" model { file = "/net/cci-nas-00/data/ceres_data/8fww_29521/05_2025/8fww_29521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fww_29521/05_2025/8fww_29521.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.54, per 1000 atoms: 0.66 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: 4.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.50 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: 3.98 Time building geometry restraints manager: 4.53 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: 7.150 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.960 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.003 TRP D 799 HIS 0.003 0.001 HIS A 508 PHE 0.037 0.003 PHE D 584 TYR 0.024 0.003 TYR C 733 ARG 0.017 0.002 ARG D 543 Details of bonding type rmsd link_NAG-ASN : bond 0.01279 ( 8) link_NAG-ASN : angle 7.46923 ( 24) link_BETA1-4 : bond 0.01829 ( 8) link_BETA1-4 : angle 3.97780 ( 24) hydrogen bonds : bond 0.30798 ( 572) hydrogen bonds : angle 10.43992 ( 1686) SS BOND : bond 0.06387 ( 6) SS BOND : angle 4.40994 ( 12) link_BETA1-3 : bond 0.00115 ( 2) link_BETA1-3 : angle 2.36031 ( 6) covalent geometry : bond 0.01328 (14768) covalent geometry : angle 1.64469 (19864) *********************** 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 : 1.533 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: 0.2845 time to fit residues: 119.1281 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 : 1.501 ------------------------------------------------------------------------------- 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 141 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.184613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142099 restraints weight = 14465.244| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.27 r_work: 0.3308 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1948 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= 0.163 Angle : 0.781 11.596 19930 Z= 0.364 Chirality : 0.046 0.218 2158 Planarity : 0.005 0.049 2398 Dihedral : 22.578 148.741 2945 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.17), residues: 1672 helix: -1.86 (0.14), residues: 852 sheet: -2.70 (0.39), residues: 150 loop : -3.31 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 706 HIS 0.002 0.000 HIS A 792 PHE 0.020 0.002 PHE C 579 TYR 0.024 0.002 TYR D 590 ARG 0.006 0.001 ARG B 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00675 ( 8) link_NAG-ASN : angle 5.49314 ( 24) link_BETA1-4 : bond 0.01046 ( 8) link_BETA1-4 : angle 3.24261 ( 24) hydrogen bonds : bond 0.04817 ( 572) hydrogen bonds : angle 4.53528 ( 1686) SS BOND : bond 0.00200 ( 6) SS BOND : angle 1.10233 ( 12) link_BETA1-3 : bond 0.00597 ( 2) link_BETA1-3 : angle 3.62658 ( 6) covalent geometry : bond 0.00380 (14768) covalent geometry : angle 0.74749 (19864) *********************** 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 234 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8115 (mttt) REVERT: A 531 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7850 (mmtp) REVERT: A 629 LYS cc_start: 0.8033 (ttmp) cc_final: 0.6891 (tptp) REVERT: A 691 MET cc_start: 0.7147 (ptm) cc_final: 0.6596 (ptt) REVERT: B 499 ASN cc_start: 0.7288 (m-40) cc_final: 0.6984 (m-40) REVERT: B 509 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7447 (mttt) REVERT: B 669 ASP cc_start: 0.8025 (t0) cc_final: 0.7502 (t0) REVERT: B 719 LYS cc_start: 0.8372 (pttp) cc_final: 0.7863 (mttp) REVERT: B 722 GLU cc_start: 0.7234 (tp30) cc_final: 0.6551 (mt-10) REVERT: B 762 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7628 (mttt) REVERT: B 793 MET cc_start: 0.7305 (mtm) cc_final: 0.6576 (mmm) REVERT: B 796 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 798 TRP cc_start: 0.7796 (m100) cc_final: 0.7301 (m100) REVERT: C 481 ARG cc_start: 0.7137 (mmt90) cc_final: 0.6880 (mmt90) REVERT: C 487 LYS cc_start: 0.8602 (mtpp) cc_final: 0.7987 (mttt) REVERT: C 531 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7628 (mmtp) REVERT: C 661 VAL cc_start: 0.7163 (t) cc_final: 0.6877 (m) REVERT: C 665 GLU cc_start: 0.6253 (pt0) cc_final: 0.5884 (mt-10) REVERT: C 712 ARG cc_start: 0.6524 (ttp-110) cc_final: 0.6113 (ttm170) REVERT: D 465 ASP cc_start: 0.7305 (m-30) cc_final: 0.7060 (m-30) REVERT: D 509 LYS cc_start: 0.8251 (mtpp) cc_final: 0.7753 (mttt) REVERT: D 669 ASP cc_start: 0.7953 (t0) cc_final: 0.7613 (t0) REVERT: D 719 LYS cc_start: 0.8279 (pttp) cc_final: 0.7696 (mttp) REVERT: D 722 GLU cc_start: 0.7498 (tp30) cc_final: 0.7148 (tp30) REVERT: D 796 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7381 (mm-30) REVERT: D 797 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7820 (ttpt) REVERT: D 798 TRP cc_start: 0.7872 (m100) cc_final: 0.6598 (m100) outliers start: 30 outliers final: 13 residues processed: 230 average time/residue: 0.2571 time to fit residues: 86.3756 Evaluate side-chains 199 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 89 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 0.0010 chunk 52 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.180615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140515 restraints weight = 14616.732| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.12 r_work: 0.3326 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14792 Z= 0.174 Angle : 0.724 10.901 19930 Z= 0.336 Chirality : 0.045 0.233 2158 Planarity : 0.005 0.045 2398 Dihedral : 21.099 143.991 2936 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.90 % Allowed : 9.81 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.19), residues: 1672 helix: -0.45 (0.17), residues: 872 sheet: -2.41 (0.41), residues: 140 loop : -3.15 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 706 HIS 0.002 0.001 HIS A 792 PHE 0.022 0.002 PHE C 584 TYR 0.022 0.002 TYR B 844 ARG 0.005 0.000 ARG A 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 8) link_NAG-ASN : angle 5.12141 ( 24) link_BETA1-4 : bond 0.01017 ( 8) link_BETA1-4 : angle 3.16485 ( 24) hydrogen bonds : bond 0.04264 ( 572) hydrogen bonds : angle 4.04649 ( 1686) SS BOND : bond 0.00514 ( 6) SS BOND : angle 1.61112 ( 12) link_BETA1-3 : bond 0.00462 ( 2) link_BETA1-3 : angle 3.80003 ( 6) covalent geometry : bond 0.00426 (14768) covalent geometry : angle 0.69045 (19864) *********************** 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 225 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8191 (mttt) REVERT: A 629 LYS cc_start: 0.8318 (ttmp) cc_final: 0.7152 (tptp) REVERT: A 691 MET cc_start: 0.7364 (ptm) cc_final: 0.6799 (ptt) REVERT: A 780 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7078 (mp) REVERT: B 499 ASN cc_start: 0.7475 (m-40) cc_final: 0.7264 (m-40) REVERT: B 509 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7598 (mttt) REVERT: B 669 ASP cc_start: 0.8147 (t0) cc_final: 0.7729 (t0) REVERT: B 719 LYS cc_start: 0.8454 (pttp) cc_final: 0.8007 (mttp) REVERT: B 722 GLU cc_start: 0.7504 (tp30) cc_final: 0.6827 (mt-10) REVERT: B 796 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7564 (mm-30) REVERT: B 798 TRP cc_start: 0.7954 (m100) cc_final: 0.7103 (m100) REVERT: C 487 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8077 (mttt) REVERT: C 565 MET cc_start: 0.8192 (mmt) cc_final: 0.7972 (mmt) REVERT: C 665 GLU cc_start: 0.6505 (pt0) cc_final: 0.6102 (mt-10) REVERT: C 780 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7043 (mp) REVERT: D 509 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7788 (mtmt) REVERT: D 669 ASP cc_start: 0.8172 (t0) cc_final: 0.7748 (t0) REVERT: D 682 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7573 (m-10) REVERT: D 719 LYS cc_start: 0.8457 (pttp) cc_final: 0.7930 (mttp) REVERT: D 722 GLU cc_start: 0.7730 (tp30) cc_final: 0.7329 (tp30) REVERT: D 796 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7587 (mm-30) REVERT: D 798 TRP cc_start: 0.7912 (m100) cc_final: 0.7032 (m100) outliers start: 42 outliers final: 25 residues processed: 219 average time/residue: 0.2515 time to fit residues: 81.6900 Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 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 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 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 682 TYR 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 5 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 112 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 121 optimal weight: 0.0970 chunk 166 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.183620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143425 restraints weight = 14408.001| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.04 r_work: 0.3369 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14792 Z= 0.116 Angle : 0.653 9.464 19930 Z= 0.298 Chirality : 0.043 0.253 2158 Planarity : 0.004 0.043 2398 Dihedral : 19.385 142.389 2926 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.76 % Allowed : 11.40 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.20), residues: 1672 helix: 0.48 (0.18), residues: 870 sheet: -2.34 (0.41), residues: 140 loop : -2.98 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 706 HIS 0.002 0.000 HIS A 792 PHE 0.021 0.001 PHE C 584 TYR 0.020 0.001 TYR B 844 ARG 0.007 0.000 ARG C 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 8) link_NAG-ASN : angle 4.57485 ( 24) link_BETA1-4 : bond 0.01017 ( 8) link_BETA1-4 : angle 2.97749 ( 24) hydrogen bonds : bond 0.03359 ( 572) hydrogen bonds : angle 3.72665 ( 1686) SS BOND : bond 0.00222 ( 6) SS BOND : angle 1.24869 ( 12) link_BETA1-3 : bond 0.00318 ( 2) link_BETA1-3 : angle 4.00798 ( 6) covalent geometry : bond 0.00267 (14768) covalent geometry : angle 0.62087 (19864) *********************** 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 228 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8138 (mttt) REVERT: A 629 LYS cc_start: 0.8393 (ttmp) cc_final: 0.7269 (tptp) REVERT: A 691 MET cc_start: 0.7346 (ptm) cc_final: 0.6791 (ptt) REVERT: A 780 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7129 (mp) REVERT: B 509 LYS cc_start: 0.8209 (mtpp) cc_final: 0.7676 (mtmt) REVERT: B 565 MET cc_start: 0.8292 (ttm) cc_final: 0.8078 (ttm) REVERT: B 625 GLU cc_start: 0.7242 (pm20) cc_final: 0.6746 (pm20) REVERT: B 669 ASP cc_start: 0.8025 (t0) cc_final: 0.7569 (t0) REVERT: B 719 LYS cc_start: 0.8426 (pttp) cc_final: 0.8011 (mttp) REVERT: B 722 GLU cc_start: 0.7552 (tp30) cc_final: 0.6826 (mt-10) REVERT: B 796 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 797 LYS cc_start: 0.8368 (ttpt) cc_final: 0.7771 (ttpp) REVERT: B 798 TRP cc_start: 0.7921 (m100) cc_final: 0.7128 (m100) REVERT: C 487 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8084 (mttt) REVERT: C 665 GLU cc_start: 0.6317 (pt0) cc_final: 0.6053 (mt-10) REVERT: C 780 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7093 (mp) REVERT: D 509 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7757 (mtmt) REVERT: D 669 ASP cc_start: 0.8062 (t0) cc_final: 0.7607 (t0) REVERT: D 712 ARG cc_start: 0.6428 (mtp180) cc_final: 0.6097 (mtt90) REVERT: D 719 LYS cc_start: 0.8474 (pttp) cc_final: 0.7957 (mttp) REVERT: D 722 GLU cc_start: 0.7635 (tp30) cc_final: 0.7269 (tp30) REVERT: D 796 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7621 (mm-30) REVERT: D 798 TRP cc_start: 0.7952 (m100) cc_final: 0.7050 (m100) outliers start: 40 outliers final: 24 residues processed: 221 average time/residue: 0.2740 time to fit residues: 88.4713 Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 624 SER Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 536 LEU 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 444 VAL Chi-restraints excluded: chain C residue 536 LEU 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 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 817 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 163 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 D 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.182692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146918 restraints weight = 14678.456| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.82 r_work: 0.3352 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3067 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= 0.155 Angle : 0.675 9.708 19930 Z= 0.309 Chirality : 0.045 0.358 2158 Planarity : 0.004 0.043 2398 Dihedral : 18.454 143.218 2926 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.18 % Allowed : 11.67 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1672 helix: 0.78 (0.18), residues: 870 sheet: -2.25 (0.42), residues: 140 loop : -2.85 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 706 HIS 0.001 0.000 HIS A 508 PHE 0.014 0.002 PHE D 584 TYR 0.021 0.002 TYR B 844 ARG 0.008 0.000 ARG C 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 8) link_NAG-ASN : angle 4.94345 ( 24) link_BETA1-4 : bond 0.00978 ( 8) link_BETA1-4 : angle 2.91039 ( 24) hydrogen bonds : bond 0.03569 ( 572) hydrogen bonds : angle 3.69925 ( 1686) SS BOND : bond 0.00195 ( 6) SS BOND : angle 1.12811 ( 12) link_BETA1-3 : bond 0.00357 ( 2) link_BETA1-3 : angle 3.83767 ( 6) covalent geometry : bond 0.00379 (14768) covalent geometry : angle 0.64154 (19864) *********************** 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 221 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8383 (mttt) REVERT: A 534 MET cc_start: 0.9280 (ttm) cc_final: 0.9045 (ttm) REVERT: A 691 MET cc_start: 0.7535 (ptm) cc_final: 0.7012 (ptt) REVERT: A 780 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7302 (mp) REVERT: A 836 PHE cc_start: 0.7347 (m-10) cc_final: 0.7117 (m-10) REVERT: B 509 LYS cc_start: 0.8333 (mtpp) cc_final: 0.7857 (mtmt) REVERT: B 620 MET cc_start: 0.8927 (mmt) cc_final: 0.8179 (mmt) REVERT: B 625 GLU cc_start: 0.7495 (pm20) cc_final: 0.6873 (pm20) REVERT: B 719 LYS cc_start: 0.8467 (pttp) cc_final: 0.8162 (mttp) REVERT: B 722 GLU cc_start: 0.7713 (tp30) cc_final: 0.7091 (mt-10) REVERT: B 796 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7870 (mm-30) REVERT: B 798 TRP cc_start: 0.7976 (m100) cc_final: 0.7293 (m100) REVERT: B 800 ARG cc_start: 0.7593 (tpt-90) cc_final: 0.7243 (ttp-170) REVERT: C 487 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8370 (mttt) REVERT: C 665 GLU cc_start: 0.6493 (pt0) cc_final: 0.6178 (mt-10) REVERT: C 780 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7296 (mp) REVERT: D 509 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7922 (mtmt) REVERT: D 669 ASP cc_start: 0.8178 (t0) cc_final: 0.7722 (t0) REVERT: D 719 LYS cc_start: 0.8446 (pttp) cc_final: 0.8153 (mttp) REVERT: D 722 GLU cc_start: 0.7862 (tp30) cc_final: 0.7481 (tp30) REVERT: D 796 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7789 (mm-30) REVERT: D 798 TRP cc_start: 0.7986 (m100) cc_final: 0.7221 (m100) outliers start: 46 outliers final: 36 residues processed: 213 average time/residue: 0.2509 time to fit residues: 79.0352 Evaluate side-chains 205 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 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 B residue 438 ILE Chi-restraints excluded: chain B residue 536 LEU 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 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 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 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 674 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 133 optimal weight: 1.9990 chunk 137 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 139 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.178393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137944 restraints weight = 14716.363| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.04 r_work: 0.3315 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3277 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= 0.157 Angle : 0.662 9.890 19930 Z= 0.304 Chirality : 0.044 0.218 2158 Planarity : 0.004 0.041 2398 Dihedral : 17.613 142.743 2926 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.38 % Allowed : 12.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1672 helix: 0.91 (0.18), residues: 870 sheet: -2.16 (0.43), residues: 140 loop : -2.75 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 706 HIS 0.001 0.000 HIS A 508 PHE 0.015 0.002 PHE D 584 TYR 0.021 0.002 TYR B 844 ARG 0.007 0.000 ARG C 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 8) link_NAG-ASN : angle 4.68118 ( 24) link_BETA1-4 : bond 0.01073 ( 8) link_BETA1-4 : angle 2.81473 ( 24) hydrogen bonds : bond 0.03466 ( 572) hydrogen bonds : angle 3.67852 ( 1686) SS BOND : bond 0.00171 ( 6) SS BOND : angle 0.89411 ( 12) link_BETA1-3 : bond 0.00224 ( 2) link_BETA1-3 : angle 3.80571 ( 6) covalent geometry : bond 0.00388 (14768) covalent geometry : angle 0.63191 (19864) *********************** 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 220 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8255 (mttt) REVERT: A 691 MET cc_start: 0.7382 (ptm) cc_final: 0.6811 (ptt) REVERT: A 780 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7150 (mp) REVERT: A 836 PHE cc_start: 0.7104 (m-10) cc_final: 0.6884 (m-10) REVERT: B 468 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.6170 (ttp-110) REVERT: B 509 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7756 (mtmt) REVERT: B 620 MET cc_start: 0.8881 (mmt) cc_final: 0.8141 (mmt) REVERT: B 625 GLU cc_start: 0.7379 (pm20) cc_final: 0.6714 (pm20) REVERT: B 719 LYS cc_start: 0.8475 (pttp) cc_final: 0.8078 (mttp) REVERT: B 722 GLU cc_start: 0.7706 (tp30) cc_final: 0.7267 (tp30) REVERT: B 796 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 798 TRP cc_start: 0.7913 (m100) cc_final: 0.7111 (m100) REVERT: C 487 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8170 (mttt) REVERT: C 665 GLU cc_start: 0.6240 (pt0) cc_final: 0.5892 (mt-10) REVERT: C 780 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7194 (mp) REVERT: D 509 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7781 (mtmt) REVERT: D 620 MET cc_start: 0.8926 (mmt) cc_final: 0.8284 (mmt) REVERT: D 669 ASP cc_start: 0.8110 (t0) cc_final: 0.7664 (t0) REVERT: D 719 LYS cc_start: 0.8458 (pttp) cc_final: 0.8051 (mttp) REVERT: D 722 GLU cc_start: 0.7765 (tp30) cc_final: 0.7345 (tp30) REVERT: D 796 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7647 (mm-30) REVERT: D 798 TRP cc_start: 0.7968 (m100) cc_final: 0.7072 (m100) outliers start: 49 outliers final: 38 residues processed: 212 average time/residue: 0.2445 time to fit residues: 77.2944 Evaluate side-chains 206 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 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 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS 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 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 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 817 VAL Chi-restraints excluded: chain D residue 438 ILE 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 674 LEU 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 92 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** D 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.177109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137849 restraints weight = 14776.666| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.11 r_work: 0.3304 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 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 = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14792 Z= 0.193 Angle : 0.690 11.488 19930 Z= 0.319 Chirality : 0.045 0.263 2158 Planarity : 0.004 0.042 2398 Dihedral : 17.261 143.048 2926 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.38 % Allowed : 12.85 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.21), residues: 1672 helix: 0.87 (0.18), residues: 870 sheet: -2.20 (0.43), residues: 140 loop : -2.70 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 613 HIS 0.001 0.000 HIS A 508 PHE 0.015 0.002 PHE B 584 TYR 0.021 0.002 TYR B 733 ARG 0.006 0.000 ARG A 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 8) link_NAG-ASN : angle 4.75312 ( 24) link_BETA1-4 : bond 0.00968 ( 8) link_BETA1-4 : angle 2.80136 ( 24) hydrogen bonds : bond 0.03712 ( 572) hydrogen bonds : angle 3.75571 ( 1686) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.94973 ( 12) link_BETA1-3 : bond 0.00157 ( 2) link_BETA1-3 : angle 3.53593 ( 6) covalent geometry : bond 0.00481 (14768) covalent geometry : angle 0.66120 (19864) *********************** 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 224 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8233 (mttt) REVERT: A 691 MET cc_start: 0.7339 (ptm) cc_final: 0.6714 (ptt) REVERT: A 780 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7132 (mp) REVERT: A 818 GLN cc_start: 0.7603 (pm20) cc_final: 0.7366 (pm20) REVERT: A 836 PHE cc_start: 0.7081 (m-10) cc_final: 0.6862 (m-10) REVERT: B 468 ARG cc_start: 0.6407 (OUTLIER) cc_final: 0.5828 (ttp-110) REVERT: B 509 LYS cc_start: 0.8328 (mtpp) cc_final: 0.7769 (mtmt) REVERT: B 620 MET cc_start: 0.8915 (mmt) cc_final: 0.8235 (mmt) REVERT: B 719 LYS cc_start: 0.8458 (pttp) cc_final: 0.8041 (mttp) REVERT: B 722 GLU cc_start: 0.7764 (tp30) cc_final: 0.7319 (tp30) REVERT: B 796 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 800 ARG cc_start: 0.7713 (tpt-90) cc_final: 0.7237 (ttp-170) REVERT: C 487 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8185 (mttt) REVERT: C 665 GLU cc_start: 0.6261 (pt0) cc_final: 0.5882 (mt-10) REVERT: C 780 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7154 (mp) REVERT: D 509 LYS cc_start: 0.8329 (mtpp) cc_final: 0.7787 (mtmt) REVERT: D 620 MET cc_start: 0.8931 (mmt) cc_final: 0.8295 (mmt) REVERT: D 669 ASP cc_start: 0.8211 (t0) cc_final: 0.7749 (t0) REVERT: D 719 LYS cc_start: 0.8470 (pttp) cc_final: 0.8067 (mttp) REVERT: D 722 GLU cc_start: 0.7803 (tp30) cc_final: 0.7369 (tp30) REVERT: D 796 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7515 (mm-30) REVERT: D 800 ARG cc_start: 0.7685 (tpt-90) cc_final: 0.7235 (ttp-170) outliers start: 49 outliers final: 38 residues processed: 215 average time/residue: 0.2624 time to fit residues: 83.2439 Evaluate side-chains 206 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 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 717 LEU 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 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 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 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 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 674 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.174724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135041 restraints weight = 14703.957| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.09 r_work: 0.3201 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 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 = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14792 Z= 0.178 Angle : 0.667 10.246 19930 Z= 0.309 Chirality : 0.044 0.183 2158 Planarity : 0.004 0.042 2398 Dihedral : 16.942 142.686 2926 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.45 % Allowed : 13.26 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1672 helix: 0.93 (0.18), residues: 870 sheet: -2.18 (0.43), residues: 140 loop : -2.68 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 798 HIS 0.001 0.000 HIS C 508 PHE 0.015 0.002 PHE D 584 TYR 0.019 0.002 TYR B 844 ARG 0.006 0.000 ARG A 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 8) link_NAG-ASN : angle 4.67342 ( 24) link_BETA1-4 : bond 0.00984 ( 8) link_BETA1-4 : angle 2.77634 ( 24) hydrogen bonds : bond 0.03549 ( 572) hydrogen bonds : angle 3.71200 ( 1686) SS BOND : bond 0.00240 ( 6) SS BOND : angle 1.47145 ( 12) link_BETA1-3 : bond 0.00107 ( 2) link_BETA1-3 : angle 2.99002 ( 6) covalent geometry : bond 0.00444 (14768) covalent geometry : angle 0.63785 (19864) *********************** 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 218 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8215 (mttt) REVERT: A 691 MET cc_start: 0.7312 (ptm) cc_final: 0.6678 (ptt) REVERT: A 780 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7046 (mp) REVERT: A 818 GLN cc_start: 0.7567 (pm20) cc_final: 0.7331 (pm20) REVERT: A 836 PHE cc_start: 0.6983 (m-10) cc_final: 0.6770 (m-10) REVERT: B 468 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5854 (ttp-110) REVERT: B 509 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7723 (mtmt) REVERT: B 620 MET cc_start: 0.8885 (mmt) cc_final: 0.8210 (mmt) REVERT: B 679 LYS cc_start: 0.6102 (ttpt) cc_final: 0.5758 (tptt) REVERT: B 719 LYS cc_start: 0.8422 (pttp) cc_final: 0.7981 (mttp) REVERT: B 722 GLU cc_start: 0.7720 (tp30) cc_final: 0.7274 (tp30) REVERT: B 796 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 798 TRP cc_start: 0.7743 (m100) cc_final: 0.6922 (m100) REVERT: B 800 ARG cc_start: 0.7707 (tpt-90) cc_final: 0.7196 (ttp-170) REVERT: C 487 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8072 (mttt) REVERT: C 665 GLU cc_start: 0.6174 (pt0) cc_final: 0.5794 (mt-10) REVERT: C 780 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7092 (mp) REVERT: D 509 LYS cc_start: 0.8381 (mtpp) cc_final: 0.7795 (mtmt) REVERT: D 620 MET cc_start: 0.8897 (mmt) cc_final: 0.8248 (mmt) REVERT: D 669 ASP cc_start: 0.8086 (t0) cc_final: 0.7584 (t0) REVERT: D 719 LYS cc_start: 0.8435 (pttp) cc_final: 0.7999 (mttp) REVERT: D 722 GLU cc_start: 0.7750 (tp30) cc_final: 0.6958 (mm-30) REVERT: D 796 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7408 (mm-30) REVERT: D 798 TRP cc_start: 0.7880 (m100) cc_final: 0.6983 (m100) REVERT: D 800 ARG cc_start: 0.7610 (tpt-90) cc_final: 0.7207 (ttp-170) outliers start: 50 outliers final: 36 residues processed: 207 average time/residue: 0.2559 time to fit residues: 78.3628 Evaluate side-chains 204 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 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 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 709 MET Chi-restraints excluded: chain C residue 717 LEU 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 817 VAL Chi-restraints excluded: chain D residue 438 ILE 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 674 LEU 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 56 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 132 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 129 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.181918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143433 restraints weight = 14530.910| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.99 r_work: 0.3345 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3647 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 : 0.639 9.747 19930 Z= 0.295 Chirality : 0.042 0.207 2158 Planarity : 0.004 0.042 2398 Dihedral : 16.546 142.337 2926 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.11 % Allowed : 13.60 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1672 helix: 1.12 (0.19), residues: 870 sheet: -2.00 (0.43), residues: 140 loop : -2.60 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 798 HIS 0.001 0.000 HIS C 792 PHE 0.014 0.001 PHE D 584 TYR 0.018 0.001 TYR B 844 ARG 0.008 0.000 ARG A 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 8) link_NAG-ASN : angle 4.49577 ( 24) link_BETA1-4 : bond 0.00971 ( 8) link_BETA1-4 : angle 2.71637 ( 24) hydrogen bonds : bond 0.03266 ( 572) hydrogen bonds : angle 3.60434 ( 1686) SS BOND : bond 0.00352 ( 6) SS BOND : angle 1.83708 ( 12) link_BETA1-3 : bond 0.00141 ( 2) link_BETA1-3 : angle 2.63946 ( 6) covalent geometry : bond 0.00332 (14768) covalent geometry : angle 0.61028 (19864) *********************** 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 213 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8296 (mttt) REVERT: A 488 TYR cc_start: 0.7952 (m-80) cc_final: 0.7669 (m-80) REVERT: A 691 MET cc_start: 0.7392 (ptm) cc_final: 0.6785 (ptt) REVERT: A 780 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7122 (mp) REVERT: A 836 PHE cc_start: 0.7085 (m-10) cc_final: 0.6866 (m-10) REVERT: B 468 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5998 (ttp-110) REVERT: B 509 LYS cc_start: 0.8362 (mtpp) cc_final: 0.7801 (mtmt) REVERT: B 620 MET cc_start: 0.8869 (mmt) cc_final: 0.8199 (mmt) REVERT: B 625 GLU cc_start: 0.7405 (pm20) cc_final: 0.7041 (pm20) REVERT: B 679 LYS cc_start: 0.6167 (ttpt) cc_final: 0.5800 (tptt) REVERT: B 719 LYS cc_start: 0.8450 (pttp) cc_final: 0.8068 (mttp) REVERT: B 722 GLU cc_start: 0.7715 (tp30) cc_final: 0.6887 (mm-30) REVERT: B 796 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 798 TRP cc_start: 0.7784 (m100) cc_final: 0.6995 (m100) REVERT: B 800 ARG cc_start: 0.7734 (tpt-90) cc_final: 0.7256 (ttp-170) REVERT: C 487 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8165 (mttt) REVERT: C 488 TYR cc_start: 0.7908 (m-80) cc_final: 0.7619 (m-80) REVERT: C 665 GLU cc_start: 0.6151 (pt0) cc_final: 0.5770 (mt-10) REVERT: C 780 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7149 (mp) REVERT: D 509 LYS cc_start: 0.8417 (mtpp) cc_final: 0.7841 (mtmt) REVERT: D 620 MET cc_start: 0.8903 (mmt) cc_final: 0.8275 (mmt) REVERT: D 669 ASP cc_start: 0.8056 (t0) cc_final: 0.7545 (t0) REVERT: D 670 SER cc_start: 0.8369 (t) cc_final: 0.7987 (p) REVERT: D 719 LYS cc_start: 0.8450 (pttp) cc_final: 0.8046 (mttp) REVERT: D 722 GLU cc_start: 0.7749 (tp30) cc_final: 0.6998 (mm-30) REVERT: D 796 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7533 (mm-30) REVERT: D 800 ARG cc_start: 0.7645 (tpt-90) cc_final: 0.7247 (ttp-170) outliers start: 45 outliers final: 37 residues processed: 202 average time/residue: 0.2665 time to fit residues: 80.1734 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 : 1.466 ------------------------------------------------------------------------------- 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 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 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 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 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 709 MET Chi-restraints excluded: chain C residue 717 LEU 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 817 VAL Chi-restraints excluded: chain D residue 468 ARG 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 674 LEU 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 62 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 107 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.177869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138630 restraints weight = 14615.263| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.21 r_work: 0.3183 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 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 = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14792 Z= 0.127 Angle : 0.623 9.748 19930 Z= 0.288 Chirality : 0.042 0.246 2158 Planarity : 0.004 0.042 2398 Dihedral : 16.219 142.479 2926 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.62 % Allowed : 13.95 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1672 helix: 1.26 (0.18), residues: 870 sheet: -1.94 (0.43), residues: 140 loop : -2.56 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 PHE 0.014 0.001 PHE D 584 TYR 0.021 0.001 TYR B 590 ARG 0.007 0.000 ARG A 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 8) link_NAG-ASN : angle 4.42055 ( 24) link_BETA1-4 : bond 0.00955 ( 8) link_BETA1-4 : angle 2.67622 ( 24) hydrogen bonds : bond 0.03143 ( 572) hydrogen bonds : angle 3.56241 ( 1686) SS BOND : bond 0.00255 ( 6) SS BOND : angle 1.74497 ( 12) link_BETA1-3 : bond 0.00139 ( 2) link_BETA1-3 : angle 2.47972 ( 6) covalent geometry : bond 0.00307 (14768) covalent geometry : angle 0.59413 (19864) ********************** 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 210 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8228 (mttt) REVERT: A 488 TYR cc_start: 0.7788 (m-80) cc_final: 0.7420 (m-80) REVERT: A 780 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7094 (mp) REVERT: A 836 PHE cc_start: 0.7063 (m-10) cc_final: 0.6844 (m-10) REVERT: B 468 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5970 (ttp-110) REVERT: B 499 ASN cc_start: 0.7485 (m110) cc_final: 0.6967 (p0) REVERT: B 509 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7758 (mtmt) REVERT: B 620 MET cc_start: 0.8804 (mmt) cc_final: 0.8171 (mmt) REVERT: B 625 GLU cc_start: 0.7366 (pm20) cc_final: 0.7015 (pm20) REVERT: B 679 LYS cc_start: 0.6117 (ttpt) cc_final: 0.5753 (tptt) REVERT: B 719 LYS cc_start: 0.8443 (pttp) cc_final: 0.8032 (mttp) REVERT: B 722 GLU cc_start: 0.7700 (tp30) cc_final: 0.6868 (mm-30) REVERT: B 796 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7591 (mm-30) REVERT: B 798 TRP cc_start: 0.7742 (m100) cc_final: 0.6928 (m100) REVERT: B 800 ARG cc_start: 0.7626 (tpt-90) cc_final: 0.7172 (ttp-170) REVERT: C 487 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8078 (mttt) REVERT: C 488 TYR cc_start: 0.7792 (m-80) cc_final: 0.7453 (m-80) REVERT: C 780 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7123 (mp) REVERT: D 509 LYS cc_start: 0.8414 (mtpp) cc_final: 0.7819 (mtmt) REVERT: D 620 MET cc_start: 0.8861 (mmt) cc_final: 0.8171 (mmt) REVERT: D 669 ASP cc_start: 0.7975 (t0) cc_final: 0.7477 (t0) REVERT: D 670 SER cc_start: 0.8157 (t) cc_final: 0.7835 (p) REVERT: D 719 LYS cc_start: 0.8452 (pttp) cc_final: 0.8015 (mttp) REVERT: D 722 GLU cc_start: 0.7745 (tp30) cc_final: 0.6969 (mm-30) REVERT: D 796 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7490 (mm-30) REVERT: D 800 ARG cc_start: 0.7543 (tpt-90) cc_final: 0.7234 (ttp-170) outliers start: 38 outliers final: 31 residues processed: 199 average time/residue: 0.2656 time to fit residues: 77.9939 Evaluate side-chains 199 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 B residue 438 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 536 LEU 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 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 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 755 ILE 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 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 674 LEU 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 161 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 151 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 792 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.182684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144115 restraints weight = 14535.615| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.04 r_work: 0.3327 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14792 Z= 0.138 Angle : 0.634 9.973 19930 Z= 0.294 Chirality : 0.043 0.273 2158 Planarity : 0.004 0.042 2398 Dihedral : 16.060 142.632 2924 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.49 % Allowed : 14.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1672 helix: 1.32 (0.18), residues: 870 sheet: -1.87 (0.43), residues: 140 loop : -2.55 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 PHE 0.014 0.001 PHE D 584 TYR 0.020 0.001 TYR B 844 ARG 0.007 0.000 ARG A 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 8) link_NAG-ASN : angle 4.40954 ( 24) link_BETA1-4 : bond 0.00974 ( 8) link_BETA1-4 : angle 2.67095 ( 24) hydrogen bonds : bond 0.03219 ( 572) hydrogen bonds : angle 3.56200 ( 1686) SS BOND : bond 0.00255 ( 6) SS BOND : angle 1.66368 ( 12) link_BETA1-3 : bond 0.00165 ( 2) link_BETA1-3 : angle 2.45935 ( 6) covalent geometry : bond 0.00338 (14768) covalent geometry : angle 0.60618 (19864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8650.56 seconds wall clock time: 150 minutes 10.19 seconds (9010.19 seconds total)