Starting phenix.real_space_refine on Fri Jul 3 16:51:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fww_29521/07_2026/8fww_29521.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fww_29521/07_2026/8fww_29521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fww_29521/07_2026/8fww_29521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fww_29521/07_2026/8fww_29521.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fww_29521/07_2026/8fww_29521.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fww_29521/07_2026/8fww_29521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fww_29521/07_2026/8fww_29521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fww_29521/07_2026/8fww_29521.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 16 5.49 5 S 80 5.16 5 Cl 2 4.86 5 Na 7 4.78 5 C 9478 2.51 5 N 2196 2.21 5 O 2688 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14471 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 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 chiralities: 1 Chain: "D" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {' NA': 1, 'POV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.36, per 1000 atoms: 0.23 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: 1.09 Conformation dependent library (CDL) restraints added in 610.0 milliseconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 20 sheets defined 50.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.787A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.538A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.615A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.585A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 557 " --> pdb=" O SER A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 557' Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.685A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.575A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 665 removed outlier: 3.850A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.605A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.592A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.510A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.700A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 788 Processing helix chain 'A' and resid 789 through 799 removed outlier: 3.758A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 850 removed outlier: 3.676A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.623A pdb=" N LEU B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.547A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.656A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 630 through 659 removed outlier: 3.886A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 677 removed outlier: 3.705A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.704A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.603A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.547A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 Processing helix chain 'B' and resid 774 through 789 removed outlier: 3.545A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 822 through 850 removed outlier: 3.556A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 473 removed outlier: 3.787A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.539A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.615A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.585A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN C 557 " --> pdb=" O SER C 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 557' Processing helix chain 'C' and resid 560 through 585 removed outlier: 3.686A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 583 " --> pdb=" O PHE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.575A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.849A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.604A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.592A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.511A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.700A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 788 Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.758A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 850 removed outlier: 3.676A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.622A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.547A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 removed outlier: 3.656A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 630 through 659 removed outlier: 3.887A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 677 removed outlier: 3.705A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.704A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.602A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 730 removed outlier: 3.546A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 774 through 789 removed outlier: 3.545A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 Processing helix chain 'D' and resid 822 through 850 removed outlier: 3.554A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 437 removed outlier: 6.641A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA3, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.967A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 736 through 738 removed outlier: 4.060A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 432 through 435 removed outlier: 6.435A pdb=" N LEU B 433 " --> pdb=" O GLU B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA7, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AA8, first strand: chain 'B' and resid 534 through 536 removed outlier: 3.969A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 735 through 738 Processing sheet with id=AB1, first strand: chain 'B' and resid 684 through 685 removed outlier: 5.593A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 433 through 437 removed outlier: 6.641A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AB4, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.967A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 736 through 738 removed outlier: 4.060A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 432 through 435 removed outlier: 6.434A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AB9, first strand: chain 'D' and resid 534 through 536 removed outlier: 3.969A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 735 through 738 Processing sheet with id=AC2, first strand: chain 'D' and resid 684 through 685 removed outlier: 5.594A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 572 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.31 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: 8274 30.70 - 61.40: 354 61.40 - 92.09: 47 92.09 - 122.79: 7 122.79 - 153.49: 6 Dihedral angle restraints: 8688 sinusoidal: 3848 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 8685 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: 4.980 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.100 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 16.816 153.489 5574 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 1.17 % Allowed : 3.66 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.95 (0.13), residues: 1672 helix: -4.16 (0.09), residues: 842 sheet: -3.04 (0.36), residues: 150 loop : -3.68 (0.17), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG D 543 TYR 0.024 0.003 TYR C 733 PHE 0.037 0.003 PHE D 584 TRP 0.020 0.003 TRP D 799 HIS 0.003 0.001 HIS A 508 Details of bonding type rmsd/Z covalent geometry : bond 0.01328 / 0.62 (14768) covalent geometry : angle 1.64469 / 0.76 (19864) SS BOND : bond 0.06387 / 3.28 ( 6) SS BOND : angle 4.40994 / 3.90 ( 12) hydrogen bonds : bond 0.30798 / 20.00 ( 572) hydrogen bonds : angle 10.43992 / 7.19 ( 1686) link_BETA1-3 : bond 0.00115 / 0.06 ( 2) link_BETA1-3 : angle 2.36031 / 1.29 ( 6) link_BETA1-4 : bond 0.01829 / 1.06 ( 8) link_BETA1-4 : angle 3.97780 / 2.81 ( 24) link_NAG-ASN : bond 0.01279 / 0.75 ( 8) link_NAG-ASN : angle 7.46923 / 5.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 281 time to evaluate : 0.504 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: 0.8209 (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: 0.1274 time to fit residues: 53.9182 Evaluate side-chains 201 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 791 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0060 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 ASN A 557 ASN A 605 ASN A 849 ASN B 456 ASN B 621 GLN ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN C 557 ASN C 621 GLN C 792 HIS C 849 ASN D 456 ASN D 604 ASN D 621 GLN D 849 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.186951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145363 restraints weight = 14529.066| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.09 r_work: 0.3374 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14792 Z= 0.153 Angle : 0.742 11.554 19930 Z= 0.352 Chirality : 0.045 0.246 2158 Planarity : 0.005 0.049 2398 Dihedral : 18.671 149.077 2455 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.00 % Allowed : 7.94 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.17), residues: 1672 helix: -1.86 (0.14), residues: 848 sheet: -2.82 (0.36), residues: 164 loop : -3.34 (0.19), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 663 TYR 0.023 0.002 TYR D 590 PHE 0.021 0.002 PHE C 579 TRP 0.016 0.001 TRP C 706 HIS 0.001 0.000 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14768) covalent geometry : angle 0.71509 / 0.35 (19864) SS BOND : bond 0.00349 / 0.13 ( 6) SS BOND : angle 1.14807 / 0.74 ( 12) hydrogen bonds : bond 0.04921 / 3.12 ( 572) hydrogen bonds : angle 4.56597 / 3.13 ( 1686) link_BETA1-3 : bond 0.00843 / 0.42 ( 2) link_BETA1-3 : angle 1.91529 / 1.04 ( 6) link_BETA1-4 : bond 0.00992 / 0.53 ( 8) link_BETA1-4 : angle 2.69998 / 1.82 ( 24) link_NAG-ASN : bond 0.00575 / 0.32 ( 8) link_NAG-ASN : angle 4.95075 / 3.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.5122 (mp0) cc_final: 0.4882 (mp0) REVERT: A 487 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8247 (mttt) REVERT: A 531 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8185 (mttp) REVERT: A 629 LYS cc_start: 0.8294 (ttmp) cc_final: 0.7232 (tptp) REVERT: A 691 MET cc_start: 0.7336 (ptm) cc_final: 0.6817 (ptt) REVERT: A 695 LYS cc_start: 0.6532 (mttt) cc_final: 0.6326 (mtpp) REVERT: B 499 ASN cc_start: 0.7528 (m-40) cc_final: 0.7249 (m-40) REVERT: B 509 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7583 (mttt) REVERT: B 669 ASP cc_start: 0.8086 (t0) cc_final: 0.7563 (t0) REVERT: B 719 LYS cc_start: 0.8516 (pttp) cc_final: 0.8024 (mttp) REVERT: B 722 GLU cc_start: 0.7477 (tp30) cc_final: 0.6809 (mt-10) REVERT: B 762 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7847 (mttt) REVERT: B 793 MET cc_start: 0.7623 (mtm) cc_final: 0.6891 (mmm) REVERT: B 796 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7620 (mm-30) REVERT: B 798 TRP cc_start: 0.7864 (m100) cc_final: 0.7468 (m100) REVERT: C 485 ASP cc_start: 0.7959 (t0) cc_final: 0.7736 (t0) REVERT: C 487 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8155 (mttt) REVERT: C 531 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7769 (mmtp) REVERT: C 665 GLU cc_start: 0.6473 (pt0) cc_final: 0.6046 (mt-10) REVERT: C 677 GLN cc_start: 0.6133 (mm-40) cc_final: 0.5924 (mp10) REVERT: C 712 ARG cc_start: 0.6624 (ttp-110) cc_final: 0.6208 (ttm170) REVERT: D 509 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7853 (mttt) REVERT: D 669 ASP cc_start: 0.8043 (t0) cc_final: 0.7711 (t0) REVERT: D 719 LYS cc_start: 0.8407 (pttp) cc_final: 0.7854 (mttp) REVERT: D 722 GLU cc_start: 0.7739 (tp30) cc_final: 0.7412 (tp30) REVERT: D 796 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7581 (mm-30) REVERT: D 797 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7994 (ttpt) REVERT: D 798 TRP cc_start: 0.7967 (m100) cc_final: 0.6850 (m100) outliers start: 29 outliers final: 13 residues processed: 229 average time/residue: 0.1048 time to fit residues: 35.6104 Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 107 optimal weight: 0.0070 chunk 29 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.181485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140935 restraints weight = 14646.509| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.06 r_work: 0.3194 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- 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: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2431 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= 0.163 Angle : 0.678 10.936 19930 Z= 0.322 Chirality : 0.044 0.238 2158 Planarity : 0.005 0.045 2398 Dihedral : 17.449 144.629 2446 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.04 % Allowed : 9.46 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.19), residues: 1672 helix: -0.39 (0.17), residues: 870 sheet: -2.39 (0.41), residues: 140 loop : -3.15 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 481 TYR 0.021 0.002 TYR B 844 PHE 0.022 0.002 PHE C 584 TRP 0.013 0.001 TRP C 706 HIS 0.002 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (14768) covalent geometry : angle 0.65230 / 0.32 (19864) SS BOND : bond 0.00313 / 0.16 ( 6) SS BOND : angle 1.60970 / 0.98 ( 12) hydrogen bonds : bond 0.04180 / 2.65 ( 572) hydrogen bonds : angle 4.01991 / 2.74 ( 1686) link_BETA1-3 : bond 0.00691 / 0.35 ( 2) link_BETA1-3 : angle 1.87100 / 1.05 ( 6) link_BETA1-4 : bond 0.00942 / 0.53 ( 8) link_BETA1-4 : angle 2.45520 / 1.60 ( 24) link_NAG-ASN : bond 0.00668 / 0.39 ( 8) link_NAG-ASN : angle 4.66241 / 3.58 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 484 GLU cc_start: 0.5484 (mp0) cc_final: 0.5263 (mp0) REVERT: A 487 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8241 (mttt) REVERT: A 629 LYS cc_start: 0.8323 (ttmp) cc_final: 0.7170 (tptp) REVERT: A 691 MET cc_start: 0.7380 (ptm) cc_final: 0.6808 (ptt) REVERT: A 695 LYS cc_start: 0.6672 (mttt) cc_final: 0.6441 (mtpp) REVERT: A 780 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7151 (mp) REVERT: B 499 ASN cc_start: 0.7469 (m-40) cc_final: 0.7251 (m-40) REVERT: B 509 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7596 (mttt) REVERT: B 669 ASP cc_start: 0.8138 (t0) cc_final: 0.7724 (t0) REVERT: B 719 LYS cc_start: 0.8457 (pttp) cc_final: 0.8017 (mttp) REVERT: B 722 GLU cc_start: 0.7511 (tp30) cc_final: 0.6808 (mt-10) REVERT: B 796 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 798 TRP cc_start: 0.7948 (m100) cc_final: 0.7102 (m100) REVERT: C 487 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8094 (mttt) REVERT: C 665 GLU cc_start: 0.6572 (pt0) cc_final: 0.6199 (mt-10) REVERT: C 780 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7119 (mp) REVERT: D 509 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7804 (mtmt) REVERT: D 669 ASP cc_start: 0.8151 (t0) cc_final: 0.7737 (t0) REVERT: D 682 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: D 719 LYS cc_start: 0.8444 (pttp) cc_final: 0.7968 (mttp) REVERT: D 722 GLU cc_start: 0.7746 (tp30) cc_final: 0.7357 (tp30) REVERT: D 796 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7616 (mm-30) REVERT: D 797 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7910 (ttpt) REVERT: D 798 TRP cc_start: 0.7923 (m100) cc_final: 0.6912 (m100) outliers start: 44 outliers final: 26 residues processed: 225 average time/residue: 0.1045 time to fit residues: 35.3416 Evaluate side-chains 200 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 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 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 142 optimal weight: 0.0070 chunk 97 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 792 HIS ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN C 621 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.182044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141452 restraints weight = 14558.380| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.05 r_work: 0.3368 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14792 Z= 0.123 Angle : 0.620 10.307 19930 Z= 0.292 Chirality : 0.042 0.230 2158 Planarity : 0.004 0.043 2398 Dihedral : 16.534 142.455 2436 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.62 % Allowed : 11.19 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.20), residues: 1672 helix: 0.40 (0.18), residues: 870 sheet: -2.33 (0.41), residues: 140 loop : -3.00 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 712 TYR 0.020 0.001 TYR B 844 PHE 0.015 0.001 PHE D 584 TRP 0.009 0.001 TRP C 706 HIS 0.002 0.000 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (14768) covalent geometry : angle 0.59717 / 0.29 (19864) SS BOND : bond 0.00192 / 0.09 ( 6) SS BOND : angle 1.12763 / 0.73 ( 12) hydrogen bonds : bond 0.03486 / 2.21 ( 572) hydrogen bonds : angle 3.78010 / 2.59 ( 1686) link_BETA1-3 : bond 0.00579 / 0.29 ( 2) link_BETA1-3 : angle 1.96051 / 1.10 ( 6) link_BETA1-4 : bond 0.00985 / 0.55 ( 8) link_BETA1-4 : angle 2.37073 / 1.56 ( 24) link_NAG-ASN : bond 0.00570 / 0.32 ( 8) link_NAG-ASN : angle 4.15908 / 3.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 484 GLU cc_start: 0.5565 (mp0) cc_final: 0.5274 (mp0) REVERT: A 487 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8228 (mttt) REVERT: A 629 LYS cc_start: 0.8402 (ttmp) cc_final: 0.7270 (tptp) REVERT: A 691 MET cc_start: 0.7340 (ptm) cc_final: 0.6777 (ptt) REVERT: A 780 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7119 (mp) REVERT: B 499 ASN cc_start: 0.7459 (m-40) cc_final: 0.7255 (m-40) REVERT: B 509 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7692 (mtmt) REVERT: B 565 MET cc_start: 0.8305 (ttm) cc_final: 0.8079 (ttm) REVERT: B 669 ASP cc_start: 0.8086 (t0) cc_final: 0.7625 (t0) REVERT: B 719 LYS cc_start: 0.8444 (pttp) cc_final: 0.8031 (mttp) REVERT: B 722 GLU cc_start: 0.7586 (tp30) cc_final: 0.6857 (mt-10) REVERT: B 796 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 798 TRP cc_start: 0.7936 (m100) cc_final: 0.7134 (m100) REVERT: C 487 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8105 (mttt) REVERT: C 665 GLU cc_start: 0.6423 (pt0) cc_final: 0.6103 (mt-10) REVERT: C 780 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7126 (mp) REVERT: D 509 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7786 (mtmt) REVERT: D 669 ASP cc_start: 0.8047 (t0) cc_final: 0.7596 (t0) REVERT: D 682 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7244 (m-10) REVERT: D 719 LYS cc_start: 0.8477 (pttp) cc_final: 0.7978 (mttp) REVERT: D 722 GLU cc_start: 0.7662 (tp30) cc_final: 0.7283 (tp30) REVERT: D 796 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7633 (mm-30) REVERT: D 797 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7816 (ttpt) REVERT: D 798 TRP cc_start: 0.7938 (m100) cc_final: 0.6884 (m100) outliers start: 38 outliers final: 25 residues processed: 215 average time/residue: 0.1041 time to fit residues: 33.2536 Evaluate side-chains 202 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 438 ILE 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 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 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 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 772 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 29 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 160 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.182140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146834 restraints weight = 14603.511| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.81 r_work: 0.3374 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14792 Z= 0.125 Angle : 0.600 9.556 19930 Z= 0.283 Chirality : 0.042 0.232 2158 Planarity : 0.004 0.042 2398 Dihedral : 15.839 142.700 2436 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.18 % Allowed : 11.33 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1672 helix: 0.82 (0.18), residues: 870 sheet: -2.24 (0.41), residues: 140 loop : -2.86 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 712 TYR 0.020 0.001 TYR B 844 PHE 0.014 0.001 PHE D 584 TRP 0.009 0.001 TRP C 706 HIS 0.001 0.000 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (14768) covalent geometry : angle 0.57909 / 0.28 (19864) SS BOND : bond 0.00200 / 0.09 ( 6) SS BOND : angle 0.94032 / 0.58 ( 12) hydrogen bonds : bond 0.03358 / 2.13 ( 572) hydrogen bonds : angle 3.64830 / 2.50 ( 1686) link_BETA1-3 : bond 0.00588 / 0.30 ( 2) link_BETA1-3 : angle 1.97528 / 1.11 ( 6) link_BETA1-4 : bond 0.00911 / 0.50 ( 8) link_BETA1-4 : angle 2.28486 / 1.51 ( 24) link_NAG-ASN : bond 0.00551 / 0.32 ( 8) link_NAG-ASN : angle 3.82280 / 2.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 484 GLU cc_start: 0.5699 (mp0) cc_final: 0.5482 (mp0) REVERT: A 487 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8409 (mttt) REVERT: A 691 MET cc_start: 0.7514 (ptm) cc_final: 0.7043 (ptt) REVERT: A 695 LYS cc_start: 0.6929 (mttt) cc_final: 0.6699 (mtpp) REVERT: A 780 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7218 (mp) REVERT: A 836 PHE cc_start: 0.7366 (m-10) cc_final: 0.7136 (m-10) REVERT: B 509 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7805 (mttt) REVERT: B 565 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8393 (ttm) REVERT: B 620 MET cc_start: 0.8758 (mmt) cc_final: 0.7955 (mmt) REVERT: B 625 GLU cc_start: 0.7438 (pm20) cc_final: 0.6807 (pm20) REVERT: B 669 ASP cc_start: 0.7877 (t0) cc_final: 0.7439 (t0) REVERT: B 722 GLU cc_start: 0.7531 (tp30) cc_final: 0.7052 (mt-10) REVERT: B 796 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 797 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7941 (ttpp) REVERT: B 798 TRP cc_start: 0.7838 (m100) cc_final: 0.7185 (m100) REVERT: C 487 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8363 (mttt) REVERT: C 665 GLU cc_start: 0.6520 (pt0) cc_final: 0.6298 (mt-10) REVERT: C 780 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7235 (mp) REVERT: D 509 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7924 (mtmt) REVERT: D 669 ASP cc_start: 0.7957 (t0) cc_final: 0.7507 (t0) REVERT: D 682 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.7321 (m-10) REVERT: D 719 LYS cc_start: 0.8317 (pttp) cc_final: 0.8071 (mttp) REVERT: D 722 GLU cc_start: 0.7618 (tp30) cc_final: 0.7305 (tp30) REVERT: D 796 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7711 (mm-30) outliers start: 46 outliers final: 31 residues processed: 220 average time/residue: 0.0984 time to fit residues: 32.6924 Evaluate side-chains 209 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 565 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR 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 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 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 682 TYR Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 5 optimal weight: 0.0050 chunk 41 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.0370 chunk 140 optimal weight: 1.9990 overall best weight: 0.7674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.182558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142521 restraints weight = 14459.245| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.07 r_work: 0.3262 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3134 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= 0.155 Angle : 0.617 9.734 19930 Z= 0.293 Chirality : 0.043 0.233 2158 Planarity : 0.004 0.042 2398 Dihedral : 15.544 142.948 2436 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.18 % Allowed : 11.95 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.21), residues: 1672 helix: 0.92 (0.18), residues: 870 sheet: -2.21 (0.42), residues: 140 loop : -2.75 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 712 TYR 0.021 0.001 TYR B 844 PHE 0.015 0.002 PHE D 584 TRP 0.013 0.001 TRP D 798 HIS 0.001 0.000 HIS C 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.15 (14768) covalent geometry : angle 0.59809 / 0.29 (19864) SS BOND : bond 0.00194 / 0.09 ( 6) SS BOND : angle 0.88926 / 0.54 ( 12) hydrogen bonds : bond 0.03468 / 2.20 ( 572) hydrogen bonds : angle 3.66909 / 2.52 ( 1686) link_BETA1-3 : bond 0.00586 / 0.29 ( 2) link_BETA1-3 : angle 1.96029 / 1.11 ( 6) link_BETA1-4 : bond 0.00883 / 0.49 ( 8) link_BETA1-4 : angle 2.26520 / 1.50 ( 24) link_NAG-ASN : bond 0.00489 / 0.29 ( 8) link_NAG-ASN : angle 3.73327 / 2.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8269 (mttt) REVERT: A 691 MET cc_start: 0.7406 (ptm) cc_final: 0.6804 (ptt) REVERT: A 695 LYS cc_start: 0.6630 (mttt) cc_final: 0.6402 (mtpp) REVERT: A 780 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7137 (mp) REVERT: A 836 PHE cc_start: 0.7068 (m-10) cc_final: 0.6850 (m-10) REVERT: B 509 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7689 (mtmt) REVERT: B 565 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8174 (ttm) REVERT: B 620 MET cc_start: 0.8881 (mmt) cc_final: 0.8132 (mmt) REVERT: B 625 GLU cc_start: 0.7341 (pm20) cc_final: 0.6687 (pm20) REVERT: B 722 GLU cc_start: 0.7641 (tp30) cc_final: 0.6911 (mt-10) REVERT: B 796 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 798 TRP cc_start: 0.7907 (m100) cc_final: 0.7110 (m100) REVERT: C 487 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8173 (mttt) REVERT: C 665 GLU cc_start: 0.6225 (pt0) cc_final: 0.5926 (mt-10) REVERT: C 780 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7159 (mp) REVERT: D 509 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7824 (mtmt) REVERT: D 620 MET cc_start: 0.8921 (mmt) cc_final: 0.8256 (mmt) REVERT: D 669 ASP cc_start: 0.8105 (t0) cc_final: 0.7682 (t0) REVERT: D 682 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: D 719 LYS cc_start: 0.8445 (pttp) cc_final: 0.8025 (mttp) REVERT: D 722 GLU cc_start: 0.7724 (tp30) cc_final: 0.7314 (tp30) REVERT: D 796 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7619 (mm-30) REVERT: D 798 TRP cc_start: 0.7821 (m100) cc_final: 0.6964 (m100) outliers start: 46 outliers final: 38 residues processed: 210 average time/residue: 0.0932 time to fit residues: 29.8921 Evaluate side-chains 212 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 626 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 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 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 682 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 137 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.177580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137045 restraints weight = 14553.810| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.04 r_work: 0.3236 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14792 Z= 0.163 Angle : 0.618 10.199 19930 Z= 0.294 Chirality : 0.043 0.233 2158 Planarity : 0.004 0.041 2398 Dihedral : 15.371 142.821 2436 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.31 % Allowed : 12.02 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.21), residues: 1672 helix: 0.98 (0.18), residues: 870 sheet: -2.19 (0.43), residues: 140 loop : -2.69 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 712 TYR 0.021 0.001 TYR B 844 PHE 0.015 0.002 PHE D 584 TRP 0.009 0.001 TRP D 798 HIS 0.001 0.000 HIS C 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 (14768) covalent geometry : angle 0.59968 / 0.29 (19864) SS BOND : bond 0.00190 / 0.09 ( 6) SS BOND : angle 0.86425 / 0.52 ( 12) hydrogen bonds : bond 0.03467 / 2.20 ( 572) hydrogen bonds : angle 3.67151 / 2.52 ( 1686) link_BETA1-3 : bond 0.00544 / 0.27 ( 2) link_BETA1-3 : angle 1.94822 / 1.11 ( 6) link_BETA1-4 : bond 0.00862 / 0.48 ( 8) link_BETA1-4 : angle 2.28104 / 1.52 ( 24) link_NAG-ASN : bond 0.00470 / 0.28 ( 8) link_NAG-ASN : angle 3.65487 / 2.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8220 (mttt) REVERT: A 691 MET cc_start: 0.7396 (ptm) cc_final: 0.6769 (ptt) REVERT: A 695 LYS cc_start: 0.6619 (mttt) cc_final: 0.6394 (mtpp) REVERT: A 780 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7078 (mp) REVERT: A 836 PHE cc_start: 0.7031 (m-10) cc_final: 0.6808 (m-10) REVERT: B 509 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7681 (mtmt) REVERT: B 565 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8091 (ttm) REVERT: B 620 MET cc_start: 0.8824 (mmt) cc_final: 0.8092 (mmt) REVERT: B 625 GLU cc_start: 0.7337 (pm20) cc_final: 0.6661 (pm20) REVERT: B 722 GLU cc_start: 0.7687 (tp30) cc_final: 0.7229 (tp30) REVERT: B 796 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7697 (mm-30) REVERT: B 798 TRP cc_start: 0.7902 (m100) cc_final: 0.7066 (m100) REVERT: C 487 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8145 (mttt) REVERT: C 665 GLU cc_start: 0.6109 (pt0) cc_final: 0.5807 (mt-10) REVERT: C 780 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7105 (mp) REVERT: D 509 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7811 (mtmt) REVERT: D 620 MET cc_start: 0.8896 (mmt) cc_final: 0.8233 (mmt) REVERT: D 669 ASP cc_start: 0.8093 (t0) cc_final: 0.7671 (t0) REVERT: D 719 LYS cc_start: 0.8433 (pttp) cc_final: 0.8010 (mttp) REVERT: D 722 GLU cc_start: 0.7717 (tp30) cc_final: 0.6939 (mm-30) REVERT: D 796 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 798 TRP cc_start: 0.7854 (m100) cc_final: 0.6954 (m100) outliers start: 48 outliers final: 39 residues processed: 209 average time/residue: 0.0952 time to fit residues: 30.6110 Evaluate side-chains 208 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 626 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 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 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 87 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 68 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.180645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140411 restraints weight = 14431.183| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.04 r_work: 0.3196 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14792 Z= 0.129 Angle : 0.592 9.709 19930 Z= 0.280 Chirality : 0.042 0.227 2158 Planarity : 0.004 0.042 2398 Dihedral : 15.018 142.429 2436 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.31 % Allowed : 12.36 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1672 helix: 1.14 (0.18), residues: 870 sheet: -2.12 (0.43), residues: 140 loop : -2.62 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 712 TYR 0.021 0.001 TYR B 844 PHE 0.014 0.001 PHE D 584 TRP 0.009 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (14768) covalent geometry : angle 0.57424 / 0.28 (19864) SS BOND : bond 0.00185 / 0.09 ( 6) SS BOND : angle 0.84699 / 0.50 ( 12) hydrogen bonds : bond 0.03220 / 2.04 ( 572) hydrogen bonds : angle 3.58415 / 2.46 ( 1686) link_BETA1-3 : bond 0.00558 / 0.28 ( 2) link_BETA1-3 : angle 2.02683 / 1.15 ( 6) link_BETA1-4 : bond 0.00893 / 0.50 ( 8) link_BETA1-4 : angle 2.27859 / 1.53 ( 24) link_NAG-ASN : bond 0.00497 / 0.30 ( 8) link_NAG-ASN : angle 3.39626 / 2.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8212 (mttt) REVERT: A 780 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7108 (mp) REVERT: A 836 PHE cc_start: 0.7060 (m-10) cc_final: 0.6834 (m-10) REVERT: B 509 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7685 (mttt) REVERT: B 565 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8117 (ttm) REVERT: B 620 MET cc_start: 0.8834 (mmt) cc_final: 0.8135 (mmt) REVERT: B 625 GLU cc_start: 0.7354 (pm20) cc_final: 0.6544 (pm20) REVERT: B 722 GLU cc_start: 0.7697 (tp30) cc_final: 0.7247 (tp30) REVERT: B 796 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 798 TRP cc_start: 0.7889 (m100) cc_final: 0.7059 (m100) REVERT: B 800 ARG cc_start: 0.7571 (tpt-90) cc_final: 0.7080 (ttp-170) REVERT: C 487 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8064 (mttt) REVERT: C 488 TYR cc_start: 0.7738 (m-80) cc_final: 0.7439 (m-80) REVERT: C 665 GLU cc_start: 0.6134 (pt0) cc_final: 0.5855 (mt-10) REVERT: C 780 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7140 (mp) REVERT: D 509 LYS cc_start: 0.8369 (mtpp) cc_final: 0.7830 (mtmt) REVERT: D 620 MET cc_start: 0.8854 (mmt) cc_final: 0.8200 (mmt) REVERT: D 669 ASP cc_start: 0.8008 (t0) cc_final: 0.7540 (t0) REVERT: D 719 LYS cc_start: 0.8407 (pttp) cc_final: 0.7993 (mttp) REVERT: D 722 GLU cc_start: 0.7682 (tp30) cc_final: 0.6928 (mm-30) REVERT: D 796 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7528 (mm-30) REVERT: D 800 ARG cc_start: 0.7570 (tpt-90) cc_final: 0.7225 (ttp-170) outliers start: 48 outliers final: 37 residues processed: 217 average time/residue: 0.1046 time to fit residues: 34.0847 Evaluate side-chains 207 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 626 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.184910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144782 restraints weight = 14664.084| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.03 r_work: 0.3344 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14792 Z= 0.142 Angle : 0.603 10.259 19930 Z= 0.287 Chirality : 0.042 0.228 2158 Planarity : 0.004 0.041 2398 Dihedral : 14.891 142.701 2436 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.83 % Allowed : 12.78 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1672 helix: 1.20 (0.18), residues: 870 sheet: -2.09 (0.43), residues: 140 loop : -2.59 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 481 TYR 0.021 0.001 TYR B 844 PHE 0.014 0.001 PHE D 584 TRP 0.028 0.001 TRP D 798 HIS 0.001 0.000 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (14768) covalent geometry : angle 0.58554 / 0.28 (19864) SS BOND : bond 0.00199 / 0.09 ( 6) SS BOND : angle 1.47702 / 0.75 ( 12) hydrogen bonds : bond 0.03275 / 2.07 ( 572) hydrogen bonds : angle 3.59411 / 2.47 ( 1686) link_BETA1-3 : bond 0.00553 / 0.28 ( 2) link_BETA1-3 : angle 1.99459 / 1.13 ( 6) link_BETA1-4 : bond 0.00866 / 0.49 ( 8) link_BETA1-4 : angle 2.25058 / 1.51 ( 24) link_NAG-ASN : bond 0.00474 / 0.29 ( 8) link_NAG-ASN : angle 3.39172 / 2.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8289 (mttt) REVERT: A 780 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7135 (mp) REVERT: A 836 PHE cc_start: 0.7104 (m-10) cc_final: 0.6875 (m-10) REVERT: B 468 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.6168 (ttp-110) REVERT: B 509 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7718 (mtmt) REVERT: B 565 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8174 (ttm) REVERT: B 620 MET cc_start: 0.8882 (mmt) cc_final: 0.8221 (mmt) REVERT: B 625 GLU cc_start: 0.7423 (pm20) cc_final: 0.6612 (pm20) REVERT: B 679 LYS cc_start: 0.6171 (ttpt) cc_final: 0.5835 (tptt) REVERT: B 722 GLU cc_start: 0.7735 (tp30) cc_final: 0.7280 (tp30) REVERT: B 796 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 798 TRP cc_start: 0.7902 (m100) cc_final: 0.7108 (m100) REVERT: B 800 ARG cc_start: 0.7636 (tpt-90) cc_final: 0.7167 (ttp-170) REVERT: C 487 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8166 (mttt) REVERT: C 488 TYR cc_start: 0.7685 (m-80) cc_final: 0.7412 (m-80) REVERT: C 665 GLU cc_start: 0.6131 (pt0) cc_final: 0.5842 (mt-10) REVERT: C 780 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7158 (mp) REVERT: D 468 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.6117 (ttp-110) REVERT: D 509 LYS cc_start: 0.8388 (mtpp) cc_final: 0.7853 (mtmt) REVERT: D 620 MET cc_start: 0.8900 (mmt) cc_final: 0.8268 (mmt) REVERT: D 669 ASP cc_start: 0.7958 (t0) cc_final: 0.7468 (t0) REVERT: D 719 LYS cc_start: 0.8442 (pttp) cc_final: 0.8037 (mttp) REVERT: D 722 GLU cc_start: 0.7767 (tp30) cc_final: 0.6994 (mm-30) REVERT: D 796 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7553 (mm-30) REVERT: D 797 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8199 (ttpp) REVERT: D 800 ARG cc_start: 0.7609 (tpt-90) cc_final: 0.7263 (ttp-170) outliers start: 41 outliers final: 35 residues processed: 206 average time/residue: 0.1042 time to fit residues: 31.8011 Evaluate side-chains 209 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 626 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain 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 565 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 468 ARG Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 111 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.178759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139486 restraints weight = 14556.402| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.00 r_work: 0.3186 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14792 Z= 0.178 Angle : 0.637 10.822 19930 Z= 0.304 Chirality : 0.044 0.230 2158 Planarity : 0.004 0.041 2398 Dihedral : 14.997 142.934 2436 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.97 % Allowed : 12.85 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1672 helix: 1.09 (0.18), residues: 870 sheet: -2.07 (0.43), residues: 140 loop : -2.57 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 481 TYR 0.023 0.002 TYR B 590 PHE 0.015 0.002 PHE D 584 TRP 0.020 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (14768) covalent geometry : angle 0.61918 / 0.30 (19864) SS BOND : bond 0.00212 / 0.10 ( 6) SS BOND : angle 1.46924 / 0.77 ( 12) hydrogen bonds : bond 0.03537 / 2.24 ( 572) hydrogen bonds : angle 3.68384 / 2.52 ( 1686) link_BETA1-3 : bond 0.00550 / 0.28 ( 2) link_BETA1-3 : angle 1.95328 / 1.11 ( 6) link_BETA1-4 : bond 0.00851 / 0.48 ( 8) link_BETA1-4 : angle 2.28110 / 1.52 ( 24) link_NAG-ASN : bond 0.00454 / 0.28 ( 8) link_NAG-ASN : angle 3.49985 / 2.73 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8279 (mttt) REVERT: A 780 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7148 (mp) REVERT: A 836 PHE cc_start: 0.7089 (m-10) cc_final: 0.6863 (m-10) REVERT: B 468 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.6082 (ttp-110) REVERT: B 509 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7756 (mtmt) REVERT: B 565 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8153 (ttm) REVERT: B 620 MET cc_start: 0.8872 (mmt) cc_final: 0.8208 (mmt) REVERT: B 679 LYS cc_start: 0.6165 (ttpt) cc_final: 0.5826 (tptt) REVERT: B 722 GLU cc_start: 0.7748 (tp30) cc_final: 0.6933 (mm-30) REVERT: B 796 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 800 ARG cc_start: 0.7686 (tpt-90) cc_final: 0.7208 (ttp-170) REVERT: C 487 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8128 (mttt) REVERT: C 665 GLU cc_start: 0.6270 (pt0) cc_final: 0.5917 (mt-10) REVERT: C 780 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7160 (mp) REVERT: D 468 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6067 (ttp-110) REVERT: D 509 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7850 (mtmt) REVERT: D 620 MET cc_start: 0.8896 (mmt) cc_final: 0.8264 (mmt) REVERT: D 669 ASP cc_start: 0.8009 (t0) cc_final: 0.7492 (t0) REVERT: D 719 LYS cc_start: 0.8447 (pttp) cc_final: 0.8041 (mttp) REVERT: D 722 GLU cc_start: 0.7773 (tp30) cc_final: 0.6999 (mm-30) REVERT: D 796 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7484 (mm-30) REVERT: D 800 ARG cc_start: 0.7578 (tpt-90) cc_final: 0.7223 (ttp-170) outliers start: 43 outliers final: 34 residues processed: 210 average time/residue: 0.1088 time to fit residues: 34.1171 Evaluate side-chains 208 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 626 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain 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 565 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 468 ARG Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 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 148 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 107 optimal weight: 0.0000 chunk 113 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.181984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143434 restraints weight = 14470.289| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.95 r_work: 0.3337 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3640 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= 0.144 Angle : 0.616 10.086 19930 Z= 0.292 Chirality : 0.043 0.223 2158 Planarity : 0.004 0.041 2398 Dihedral : 14.789 142.511 2436 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.76 % Allowed : 13.26 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1672 helix: 1.20 (0.18), residues: 870 sheet: -2.00 (0.43), residues: 140 loop : -2.53 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 481 TYR 0.022 0.001 TYR B 844 PHE 0.014 0.001 PHE D 584 TRP 0.019 0.001 TRP D 798 HIS 0.001 0.000 HIS C 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 (14768) covalent geometry : angle 0.59826 / 0.29 (19864) SS BOND : bond 0.00238 / 0.12 ( 6) SS BOND : angle 1.74991 / 1.29 ( 12) hydrogen bonds : bond 0.03303 / 2.09 ( 572) hydrogen bonds : angle 3.61793 / 2.48 ( 1686) link_BETA1-3 : bond 0.00540 / 0.27 ( 2) link_BETA1-3 : angle 2.00980 / 1.14 ( 6) link_BETA1-4 : bond 0.00884 / 0.50 ( 8) link_BETA1-4 : angle 2.28973 / 1.54 ( 24) link_NAG-ASN : bond 0.00476 / 0.28 ( 8) link_NAG-ASN : angle 3.34143 / 2.59 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3738.70 seconds wall clock time: 64 minutes 38.82 seconds (3878.82 seconds total)