Starting phenix.real_space_refine on Fri Jul 3 16:14:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fwu_29519/07_2026/8fwu_29519.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwu_29519/07_2026/8fwu_29519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fwu_29519/07_2026/8fwu_29519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwu_29519/07_2026/8fwu_29519.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fwu_29519/07_2026/8fwu_29519.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fwu_29519/07_2026/8fwu_29519.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fwu_29519/07_2026/8fwu_29519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwu_29519/07_2026/8fwu_29519.map" } resolution = 3.18 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= 0.028 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 8 4.78 5 C 9464 2.51 5 N 2206 2.21 5 O 2716 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 26 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: 14496 Number of models: 1 Model: "" Number of chains: 17 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: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 349 Unusual residues: {' CL': 1, ' NA': 4, 'DNQ': 1, 'NAG': 1, 'POV': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 156 Unusual residues: {' NA': 2, '2J9': 2, 'DNQ': 1, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 398 Unusual residues: {' CL': 1, ' NA': 1, 'DNQ': 1, 'NAG': 1, 'POV': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Unusual residues: {' NA': 1, '2J9': 2, 'DNQ': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.20, per 1000 atoms: 0.22 Number of scatterers: 14496 At special positions: 0 Unit cell: (107.07, 118.69, 136.95, 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 8 11.00 F 4 9.00 O 2716 8.00 N 2206 7.00 C 9464 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=1.99 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=2.06 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 A1006 " - " ASN A 751 " " NAG C1006 " - " ASN C 751 " " NAG E 1 " - " ASN A 546 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN B 751 " " NAG H 1 " - " ASN C 546 " " NAG I 1 " - " ASN D 546 " " NAG J 1 " - " ASN D 751 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 604.1 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: 60 helices and 22 sheets defined 49.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.683A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.751A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.681A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.857A 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 562 through 585 removed outlier: 3.530A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 620 Processing helix chain 'A' and resid 630 through 665 removed outlier: 3.776A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 675 removed outlier: 3.516A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.917A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 739 through 746 removed outlier: 3.699A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.706A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 removed outlier: 3.608A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 850 removed outlier: 3.569A pdb=" N VAL A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.565A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.921A pdb=" N ILE B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.509A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.588A pdb=" N PHE B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 661 removed outlier: 3.907A pdb=" N THR B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 677 removed outlier: 3.575A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.677A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.520A pdb=" N TRP B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.503A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 Processing helix chain 'B' and resid 773 through 789 removed outlier: 3.520A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 822 through 850 removed outlier: 3.560A pdb=" N ALA B 828 " --> pdb=" O PHE B 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.684A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.751A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.681A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.857A 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 562 through 585 removed outlier: 3.530A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 620 Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.776A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 removed outlier: 3.515A pdb=" N LEU C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 Processing helix chain 'C' and resid 703 through 712 removed outlier: 3.916A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 746 removed outlier: 3.698A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 749 No H-bonds generated for 'chain 'C' and resid 747 through 749' Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.706A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 3.608A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 800 " --> pdb=" O GLU C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 850 removed outlier: 3.569A pdb=" N VAL C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 850 " --> pdb=" O SER C 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.565A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 507 removed outlier: 3.921A pdb=" N ILE D 506 " --> pdb=" O VAL D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.509A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 580 " --> pdb=" O CYS D 576 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.588A pdb=" N PHE D 614 " --> pdb=" O ASN D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 661 removed outlier: 3.907A pdb=" N THR D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 677 removed outlier: 3.575A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.677A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.520A pdb=" N TRP D 706 " --> pdb=" O TYR D 702 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 730 removed outlier: 3.504A pdb=" N GLY D 724 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 773 through 789 removed outlier: 3.520A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 Processing helix chain 'D' and resid 822 through 850 removed outlier: 3.561A pdb=" N ALA D 828 " --> pdb=" O PHE D 824 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 435 removed outlier: 6.415A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 446 removed outlier: 3.536A pdb=" N GLU A 460 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.575A pdb=" N ALA A 490 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 499 " --> pdb=" O ALA A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.927A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 683 removed outlier: 6.417A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'B' and resid 534 through 536 removed outlier: 3.736A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.037A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 684 through 685 removed outlier: 6.067A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 433 through 435 removed outlier: 6.416A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 445 through 446 removed outlier: 3.537A pdb=" N GLU C 460 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 489 through 490 removed outlier: 3.575A pdb=" N ALA C 490 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 499 " --> pdb=" O ALA C 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AB7, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.926A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 681 through 683 removed outlier: 6.417A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AC1, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AC2, first strand: chain 'D' and resid 534 through 536 removed outlier: 3.736A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 735 through 738 removed outlier: 4.037A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 684 through 685 removed outlier: 6.067A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 566 hydrogen bonds defined for protein. 1656 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: 2.22 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2224 1.31 - 1.43: 3964 1.43 - 1.56: 8402 1.56 - 1.68: 62 1.68 - 1.81: 132 Bond restraints: 14784 Sorted by residual: bond pdb=" N3 DNQ B1002 " pdb=" O5 DNQ B1002 " ideal model delta sigma weight residual 1.205 1.446 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" N3 DNQ C1001 " pdb=" O5 DNQ C1001 " ideal model delta sigma weight residual 1.205 1.446 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" N3 DNQ A1001 " pdb=" O5 DNQ A1001 " ideal model delta sigma weight residual 1.205 1.446 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" N3 DNQ D1003 " pdb=" O5 DNQ D1003 " ideal model delta sigma weight residual 1.205 1.446 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C1 DNQ A1001 " pdb=" O1 DNQ A1001 " ideal model delta sigma weight residual 1.197 1.417 -0.220 2.00e-02 2.50e+03 1.21e+02 ... (remaining 14779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.47: 19680 6.47 - 12.94: 201 12.94 - 19.40: 5 19.40 - 25.87: 0 25.87 - 32.34: 8 Bond angle restraints: 19894 Sorted by residual: angle pdb=" CAG 2J9 B1001 " pdb=" CAN 2J9 B1001 " pdb=" NAO 2J9 B1001 " ideal model delta sigma weight residual 118.82 151.16 -32.34 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CAG 2J9 D1001 " pdb=" CAN 2J9 D1001 " pdb=" NAO 2J9 D1001 " ideal model delta sigma weight residual 118.82 151.07 -32.25 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CAG 2J9 B1005 " pdb=" CAN 2J9 B1005 " pdb=" NAO 2J9 B1005 " ideal model delta sigma weight residual 118.82 150.74 -31.92 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CAG 2J9 D1002 " pdb=" CAN 2J9 D1002 " pdb=" NAO 2J9 D1002 " ideal model delta sigma weight residual 118.82 150.65 -31.83 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CAH 2J9 D1002 " pdb=" CAN 2J9 D1002 " pdb=" NAO 2J9 D1002 " ideal model delta sigma weight residual 117.67 149.38 -31.71 3.00e+00 1.11e-01 1.12e+02 ... (remaining 19889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8366 35.43 - 70.86: 269 70.86 - 106.30: 34 106.30 - 141.73: 9 141.73 - 177.16: 4 Dihedral angle restraints: 8682 sinusoidal: 3842 harmonic: 4840 Sorted by residual: dihedral pdb=" CA ASP D 732 " pdb=" C ASP D 732 " pdb=" N TYR D 733 " pdb=" CA TYR D 733 " ideal model delta harmonic sigma weight residual 180.00 110.45 69.55 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA ASP B 732 " pdb=" C ASP B 732 " pdb=" N TYR B 733 " pdb=" CA TYR B 733 " ideal model delta harmonic sigma weight residual 180.00 110.53 69.47 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA GLU D 811 " pdb=" C GLU D 811 " pdb=" N ALA D 812 " pdb=" CA ALA D 812 " ideal model delta harmonic sigma weight residual -180.00 -135.50 -44.50 0 5.00e+00 4.00e-02 7.92e+01 ... (remaining 8679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.460: 2152 0.460 - 0.919: 2 0.919 - 1.379: 0 1.379 - 1.838: 0 1.838 - 2.298: 4 Chirality restraints: 2158 Sorted by residual: chirality pdb=" CAN 2J9 D1001 " pdb=" CAG 2J9 D1001 " pdb=" CAH 2J9 D1001 " pdb=" NAO 2J9 D1001 " both_signs ideal model delta sigma weight residual True 2.32 -0.02 2.30 2.00e-01 2.50e+01 1.32e+02 chirality pdb=" CAN 2J9 D1002 " pdb=" CAG 2J9 D1002 " pdb=" CAH 2J9 D1002 " pdb=" NAO 2J9 D1002 " both_signs ideal model delta sigma weight residual True 2.32 -0.02 2.30 2.00e-01 2.50e+01 1.32e+02 chirality pdb=" CAN 2J9 B1005 " pdb=" CAG 2J9 B1005 " pdb=" CAH 2J9 B1005 " pdb=" NAO 2J9 B1005 " both_signs ideal model delta sigma weight residual True 2.32 -0.02 2.29 2.00e-01 2.50e+01 1.32e+02 ... (remaining 2155 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 478 " 0.031 2.00e-02 2.50e+03 1.77e-02 6.23e+00 pdb=" CG TYR D 478 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR D 478 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR D 478 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 478 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 478 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 478 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 478 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 478 " -0.031 2.00e-02 2.50e+03 1.76e-02 6.22e+00 pdb=" CG TYR B 478 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 478 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 478 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 478 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 478 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 478 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 478 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 481 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ARG B 481 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG B 481 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 482 " 0.014 2.00e-02 2.50e+03 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3406 2.78 - 3.31: 12328 3.31 - 3.84: 23024 3.84 - 4.37: 28960 4.37 - 4.90: 48950 Nonbonded interactions: 116668 Sorted by model distance: nonbonded pdb=" OE2 GLU B 787 " pdb=" OG1 THR C 520 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 554 " pdb=" O ASN A 819 " model vdw 2.294 3.040 nonbonded pdb=" OG SER C 554 " pdb=" O ASN C 819 " model vdw 2.294 3.040 nonbonded pdb=" O3 DNQ A1001 " pdb=" O4 DNQ A1001 " model vdw 2.308 3.040 ... (remaining 116663 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 1004)) selection = (chain 'B' and (resid 431 through 850 or resid 1004)) selection = (chain 'C' and (resid 431 through 850 or resid 1004)) selection = (chain 'D' and (resid 431 through 850 or resid 1004)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.620 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.015 0.241 14808 Z= 0.759 Angle : 1.703 32.340 19960 Z= 0.791 Chirality : 0.119 2.298 2158 Planarity : 0.007 0.056 2402 Dihedral : 17.397 177.161 5568 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.21 % Favored : 90.55 % Rotamer: Outliers : 0.97 % Allowed : 4.14 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -6.02 (0.14), residues: 1672 helix: -4.25 (0.09), residues: 842 sheet: -3.17 (0.38), residues: 166 loop : -3.63 (0.18), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 663 TYR 0.037 0.003 TYR D 478 PHE 0.028 0.003 PHE B 658 TRP 0.019 0.003 TRP C 706 HIS 0.008 0.002 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.01547 / 0.76 (14784) covalent geometry : angle 1.66985 / 0.78 (19894) SS BOND : bond 0.01921 / 0.99 ( 6) SS BOND : angle 1.60190 / 1.13 ( 12) hydrogen bonds : bond 0.30601 / 19.71 ( 566) hydrogen bonds : angle 10.86562 / 7.46 ( 1656) link_BETA1-3 : bond 0.00019 / 0.01 ( 2) link_BETA1-3 : angle 3.40132 / 1.69 ( 6) link_BETA1-4 : bond 0.01380 / 0.81 ( 8) link_BETA1-4 : angle 3.70886 / 2.27 ( 24) link_NAG-ASN : bond 0.02138 / 1.25 ( 8) link_NAG-ASN : angle 9.11817 / 6.18 ( 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 334 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 320 time to evaluate : 0.493 Fit side-chains REVERT: C 780 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7355 (mp) REVERT: D 587 TYR cc_start: 0.8216 (m-80) cc_final: 0.7939 (m-80) REVERT: D 719 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7384 (mmtm) outliers start: 14 outliers final: 2 residues processed: 333 average time/residue: 0.1264 time to fit residues: 61.2291 Evaluate side-chains 179 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 791 LEU 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: 0.9980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 GLN B 591 ASN ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN B 621 GLN B 721 ASN C 604 ASN C 621 GLN D 591 ASN D 593 HIS D 610 ASN D 721 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.178435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136494 restraints weight = 15836.190| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.21 r_work: 0.3339 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 14808 Z= 0.158 Angle : 0.790 13.430 19960 Z= 0.384 Chirality : 0.047 0.370 2158 Planarity : 0.005 0.047 2402 Dihedral : 20.329 151.300 2434 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.07 % Favored : 91.69 % Rotamer: Outliers : 2.00 % Allowed : 9.88 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.17), residues: 1672 helix: -2.12 (0.15), residues: 838 sheet: -2.31 (0.45), residues: 122 loop : -3.09 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 712 TYR 0.027 0.002 TYR D 478 PHE 0.026 0.002 PHE D 842 TRP 0.016 0.001 TRP B 798 HIS 0.007 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (14784) covalent geometry : angle 0.75409 / 0.38 (19894) SS BOND : bond 0.00198 / 0.10 ( 6) SS BOND : angle 0.38877 / 0.25 ( 12) hydrogen bonds : bond 0.04865 / 3.18 ( 566) hydrogen bonds : angle 4.72711 / 3.23 ( 1656) link_BETA1-3 : bond 0.00223 / 0.11 ( 2) link_BETA1-3 : angle 2.44310 / 1.31 ( 6) link_BETA1-4 : bond 0.00824 / 0.41 ( 8) link_BETA1-4 : angle 1.84157 / 1.12 ( 24) link_NAG-ASN : bond 0.01141 / 0.68 ( 8) link_NAG-ASN : angle 6.52826 / 4.33 ( 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 245 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.595 Fit side-chains REVERT: A 677 GLN cc_start: 0.5886 (mp10) cc_final: 0.5622 (mt0) REVERT: A 799 TRP cc_start: 0.8677 (m-90) cc_final: 0.8416 (m-90) REVERT: B 672 ASP cc_start: 0.7988 (p0) cc_final: 0.7604 (t0) REVERT: C 670 SER cc_start: 0.8410 (t) cc_final: 0.8088 (m) REVERT: C 703 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: C 780 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7153 (mp) REVERT: D 587 TYR cc_start: 0.8168 (m-80) cc_final: 0.7813 (m-80) REVERT: D 691 MET cc_start: 0.8440 (ttp) cc_final: 0.8228 (tmm) REVERT: D 719 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7524 (mmtm) REVERT: D 733 TYR cc_start: 0.5994 (t80) cc_final: 0.5553 (t80) outliers start: 29 outliers final: 15 residues processed: 239 average time/residue: 0.1214 time to fit residues: 43.1561 Evaluate side-chains 189 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 791 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 130 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 GLN ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 GLN C 792 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.175755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133125 restraints weight = 15876.915| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.21 r_work: 0.3308 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14808 Z= 0.143 Angle : 0.703 12.200 19960 Z= 0.342 Chirality : 0.046 0.335 2158 Planarity : 0.004 0.044 2402 Dihedral : 18.901 140.685 2434 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.06 % Favored : 92.82 % Rotamer: Outliers : 2.42 % Allowed : 11.53 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.19), residues: 1672 helix: -0.56 (0.17), residues: 840 sheet: -2.12 (0.47), residues: 120 loop : -2.79 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 712 TYR 0.020 0.002 TYR D 478 PHE 0.016 0.001 PHE D 842 TRP 0.015 0.001 TRP B 798 HIS 0.003 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (14784) covalent geometry : angle 0.66956 / 0.33 (19894) SS BOND : bond 0.00173 / 0.09 ( 6) SS BOND : angle 0.25956 / 0.17 ( 12) hydrogen bonds : bond 0.03900 / 2.54 ( 566) hydrogen bonds : angle 4.16445 / 2.83 ( 1656) link_BETA1-3 : bond 0.00327 / 0.17 ( 2) link_BETA1-3 : angle 2.14077 / 1.14 ( 6) link_BETA1-4 : bond 0.00677 / 0.37 ( 8) link_BETA1-4 : angle 1.73607 / 1.05 ( 24) link_NAG-ASN : bond 0.01111 / 0.67 ( 8) link_NAG-ASN : angle 5.95592 / 3.90 ( 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 204 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.508 Fit side-chains REVERT: B 499 ASN cc_start: 0.7956 (m110) cc_final: 0.7581 (m-40) REVERT: B 672 ASP cc_start: 0.8073 (p0) cc_final: 0.7566 (t0) REVERT: B 747 GLN cc_start: 0.7624 (mt0) cc_final: 0.7366 (mm-40) REVERT: B 836 PHE cc_start: 0.7825 (m-10) cc_final: 0.7620 (m-10) REVERT: C 670 SER cc_start: 0.8227 (t) cc_final: 0.7927 (m) REVERT: C 780 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7142 (mp) REVERT: D 565 MET cc_start: 0.7600 (tmm) cc_final: 0.7000 (mtt) REVERT: D 587 TYR cc_start: 0.8143 (m-80) cc_final: 0.7808 (m-80) REVERT: D 674 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8725 (tp) REVERT: D 719 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7534 (mmtm) REVERT: D 733 TYR cc_start: 0.5860 (t80) cc_final: 0.4922 (t80) outliers start: 35 outliers final: 16 residues processed: 197 average time/residue: 0.1192 time to fit residues: 35.5309 Evaluate side-chains 177 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 133 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.174689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130892 restraints weight = 15815.714| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.29 r_work: 0.3266 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14808 Z= 0.145 Angle : 0.685 11.826 19960 Z= 0.329 Chirality : 0.045 0.330 2158 Planarity : 0.004 0.042 2402 Dihedral : 17.790 140.860 2432 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.12 % Favored : 92.76 % Rotamer: Outliers : 3.25 % Allowed : 12.29 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.20), residues: 1672 helix: 0.21 (0.18), residues: 840 sheet: -2.24 (0.45), residues: 126 loop : -2.57 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.024 0.002 TYR B 478 PHE 0.016 0.001 PHE A 735 TRP 0.014 0.001 TRP D 798 HIS 0.004 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.14 (14784) covalent geometry : angle 0.65534 / 0.32 (19894) SS BOND : bond 0.00146 / 0.08 ( 6) SS BOND : angle 0.28752 / 0.21 ( 12) hydrogen bonds : bond 0.03571 / 2.31 ( 566) hydrogen bonds : angle 3.96068 / 2.68 ( 1656) link_BETA1-3 : bond 0.00329 / 0.16 ( 2) link_BETA1-3 : angle 2.02179 / 1.10 ( 6) link_BETA1-4 : bond 0.00674 / 0.35 ( 8) link_BETA1-4 : angle 1.64020 / 1.00 ( 24) link_NAG-ASN : bond 0.01078 / 0.65 ( 8) link_NAG-ASN : angle 5.52889 / 3.61 ( 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 217 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.445 Fit side-chains REVERT: B 499 ASN cc_start: 0.8061 (m110) cc_final: 0.7651 (m110) REVERT: B 672 ASP cc_start: 0.8116 (p0) cc_final: 0.7551 (t0) REVERT: B 810 LYS cc_start: 0.5947 (ttpt) cc_final: 0.5678 (pttm) REVERT: C 603 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 670 SER cc_start: 0.8158 (t) cc_final: 0.7878 (m) REVERT: C 780 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7136 (mp) REVERT: D 565 MET cc_start: 0.7653 (tmm) cc_final: 0.7125 (mtt) REVERT: D 587 TYR cc_start: 0.8189 (m-80) cc_final: 0.7955 (m-80) REVERT: D 719 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7580 (mmtm) REVERT: D 733 TYR cc_start: 0.5917 (t80) cc_final: 0.5154 (t80) outliers start: 47 outliers final: 26 residues processed: 202 average time/residue: 0.1227 time to fit residues: 37.1811 Evaluate side-chains 184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 118 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129663 restraints weight = 15804.986| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.30 r_work: 0.3251 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14808 Z= 0.145 Angle : 0.662 11.238 19960 Z= 0.320 Chirality : 0.045 0.333 2158 Planarity : 0.004 0.040 2402 Dihedral : 17.132 140.841 2430 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.64 % Favored : 93.24 % Rotamer: Outliers : 3.04 % Allowed : 13.12 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1672 helix: 0.63 (0.19), residues: 840 sheet: -2.21 (0.46), residues: 126 loop : -2.40 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 468 TYR 0.021 0.002 TYR B 478 PHE 0.029 0.001 PHE D 842 TRP 0.013 0.001 TRP D 798 HIS 0.005 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.14 (14784) covalent geometry : angle 0.63502 / 0.31 (19894) SS BOND : bond 0.00253 / 0.10 ( 6) SS BOND : angle 0.35297 / 0.25 ( 12) hydrogen bonds : bond 0.03430 / 2.22 ( 566) hydrogen bonds : angle 3.83221 / 2.59 ( 1656) link_BETA1-3 : bond 0.00284 / 0.14 ( 2) link_BETA1-3 : angle 1.88106 / 1.03 ( 6) link_BETA1-4 : bond 0.00678 / 0.36 ( 8) link_BETA1-4 : angle 1.56305 / 0.96 ( 24) link_NAG-ASN : bond 0.01008 / 0.60 ( 8) link_NAG-ASN : angle 5.16024 / 3.35 ( 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 213 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.474 Fit side-chains REVERT: B 672 ASP cc_start: 0.8125 (p0) cc_final: 0.7635 (t0) REVERT: B 810 LYS cc_start: 0.6149 (ttpt) cc_final: 0.5880 (pttm) REVERT: C 603 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7523 (mt-10) REVERT: C 670 SER cc_start: 0.8198 (t) cc_final: 0.7914 (m) REVERT: D 565 MET cc_start: 0.7657 (tmm) cc_final: 0.7080 (mtt) REVERT: D 587 TYR cc_start: 0.8306 (m-80) cc_final: 0.8081 (m-80) REVERT: D 719 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7561 (mmtm) REVERT: D 733 TYR cc_start: 0.5940 (t80) cc_final: 0.4865 (t80) outliers start: 44 outliers final: 31 residues processed: 200 average time/residue: 0.1292 time to fit residues: 38.0597 Evaluate side-chains 187 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.168933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124940 restraints weight = 15891.665| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.25 r_work: 0.3195 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 14808 Z= 0.229 Angle : 0.732 11.648 19960 Z= 0.354 Chirality : 0.048 0.356 2158 Planarity : 0.005 0.042 2402 Dihedral : 17.372 140.842 2428 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.19 % Favored : 91.69 % Rotamer: Outliers : 3.31 % Allowed : 13.81 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.21), residues: 1672 helix: 0.43 (0.18), residues: 848 sheet: -2.31 (0.45), residues: 130 loop : -2.44 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 468 TYR 0.025 0.002 TYR D 478 PHE 0.027 0.002 PHE D 842 TRP 0.015 0.002 TRP D 798 HIS 0.005 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.23 (14784) covalent geometry : angle 0.70615 / 0.35 (19894) SS BOND : bond 0.00120 / 0.06 ( 6) SS BOND : angle 0.49084 / 0.35 ( 12) hydrogen bonds : bond 0.03914 / 2.54 ( 566) hydrogen bonds : angle 4.00401 / 2.70 ( 1656) link_BETA1-3 : bond 0.00188 / 0.09 ( 2) link_BETA1-3 : angle 1.89478 / 1.04 ( 6) link_BETA1-4 : bond 0.00477 / 0.25 ( 8) link_BETA1-4 : angle 1.58631 / 0.96 ( 24) link_NAG-ASN : bond 0.00964 / 0.60 ( 8) link_NAG-ASN : angle 5.34679 / 3.56 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.561 Fit side-chains REVERT: A 674 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7104 (mp) REVERT: B 672 ASP cc_start: 0.8169 (p0) cc_final: 0.7611 (t0) REVERT: B 810 LYS cc_start: 0.6415 (ttpt) cc_final: 0.6130 (pttm) REVERT: C 568 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7781 (tt) REVERT: C 603 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7500 (mt-10) REVERT: C 670 SER cc_start: 0.8328 (t) cc_final: 0.7995 (m) REVERT: C 698 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7634 (mmtp) REVERT: D 479 GLU cc_start: 0.5286 (tp30) cc_final: 0.4431 (mp0) REVERT: D 587 TYR cc_start: 0.8554 (m-80) cc_final: 0.8293 (m-80) REVERT: D 719 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7636 (mptt) REVERT: D 810 LYS cc_start: 0.6433 (ttpt) cc_final: 0.6121 (pttm) outliers start: 48 outliers final: 36 residues processed: 204 average time/residue: 0.1265 time to fit residues: 38.3652 Evaluate side-chains 200 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 88 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.172207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128282 restraints weight = 15712.440| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.30 r_work: 0.3227 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14808 Z= 0.140 Angle : 0.657 10.902 19960 Z= 0.317 Chirality : 0.045 0.336 2158 Planarity : 0.004 0.044 2402 Dihedral : 16.943 140.756 2428 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.88 % Favored : 93.00 % Rotamer: Outliers : 3.11 % Allowed : 14.78 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.21), residues: 1672 helix: 0.81 (0.19), residues: 848 sheet: -2.27 (0.45), residues: 130 loop : -2.36 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 468 TYR 0.016 0.001 TYR D 733 PHE 0.023 0.001 PHE D 842 TRP 0.014 0.001 TRP D 798 HIS 0.004 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (14784) covalent geometry : angle 0.63010 / 0.31 (19894) SS BOND : bond 0.00119 / 0.06 ( 6) SS BOND : angle 0.49216 / 0.32 ( 12) hydrogen bonds : bond 0.03415 / 2.21 ( 566) hydrogen bonds : angle 3.84353 / 2.59 ( 1656) link_BETA1-3 : bond 0.00241 / 0.12 ( 2) link_BETA1-3 : angle 1.87169 / 1.02 ( 6) link_BETA1-4 : bond 0.00691 / 0.36 ( 8) link_BETA1-4 : angle 1.60064 / 1.01 ( 24) link_NAG-ASN : bond 0.01050 / 0.64 ( 8) link_NAG-ASN : angle 5.12320 / 3.38 ( 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 207 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.556 Fit side-chains REVERT: A 780 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7116 (mp) REVERT: B 479 GLU cc_start: 0.5356 (tp30) cc_final: 0.4654 (mp0) REVERT: B 531 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7635 (mttp) REVERT: B 565 MET cc_start: 0.7846 (ttp) cc_final: 0.7215 (mtt) REVERT: B 672 ASP cc_start: 0.8162 (p0) cc_final: 0.7603 (t0) REVERT: B 810 LYS cc_start: 0.6150 (ttpt) cc_final: 0.5891 (pttm) REVERT: C 568 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7770 (tt) REVERT: C 603 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 670 SER cc_start: 0.8251 (t) cc_final: 0.7934 (m) REVERT: C 698 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7625 (mmtp) REVERT: C 780 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7066 (mp) REVERT: D 531 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7627 (mttp) REVERT: D 565 MET cc_start: 0.7918 (ttp) cc_final: 0.7218 (mtt) REVERT: D 719 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7615 (mptt) outliers start: 45 outliers final: 33 residues processed: 194 average time/residue: 0.1253 time to fit residues: 36.1671 Evaluate side-chains 192 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.172256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128926 restraints weight = 15663.211| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.24 r_work: 0.3246 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14808 Z= 0.139 Angle : 0.649 10.410 19960 Z= 0.314 Chirality : 0.045 0.338 2158 Planarity : 0.004 0.042 2402 Dihedral : 16.595 140.842 2428 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.42 % Favored : 92.46 % Rotamer: Outliers : 3.25 % Allowed : 14.43 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1672 helix: 1.02 (0.19), residues: 850 sheet: -2.25 (0.45), residues: 130 loop : -2.29 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 468 TYR 0.023 0.002 TYR B 478 PHE 0.030 0.001 PHE D 842 TRP 0.015 0.001 TRP D 798 HIS 0.003 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (14784) covalent geometry : angle 0.62406 / 0.31 (19894) SS BOND : bond 0.00114 / 0.06 ( 6) SS BOND : angle 0.43921 / 0.30 ( 12) hydrogen bonds : bond 0.03345 / 2.17 ( 566) hydrogen bonds : angle 3.79458 / 2.55 ( 1656) link_BETA1-3 : bond 0.00284 / 0.14 ( 2) link_BETA1-3 : angle 1.80676 / 0.99 ( 6) link_BETA1-4 : bond 0.00647 / 0.33 ( 8) link_BETA1-4 : angle 1.51000 / 0.94 ( 24) link_NAG-ASN : bond 0.01051 / 0.63 ( 8) link_NAG-ASN : angle 4.95297 / 3.26 ( 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 210 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.600 Fit side-chains REVERT: A 780 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7084 (mp) REVERT: B 479 GLU cc_start: 0.5337 (tp30) cc_final: 0.4874 (mp0) REVERT: B 531 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7537 (mttm) REVERT: B 644 THR cc_start: 0.8802 (m) cc_final: 0.8401 (p) REVERT: B 672 ASP cc_start: 0.8151 (p0) cc_final: 0.7634 (t0) REVERT: B 810 LYS cc_start: 0.5980 (ttpt) cc_final: 0.5770 (pttm) REVERT: C 568 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7708 (tt) REVERT: C 603 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 670 SER cc_start: 0.8251 (t) cc_final: 0.7928 (m) REVERT: C 698 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7586 (mmtp) REVERT: C 780 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.6998 (mp) REVERT: C 817 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8492 (t) REVERT: D 479 GLU cc_start: 0.5564 (tp30) cc_final: 0.4697 (mp0) REVERT: D 531 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7499 (mttp) REVERT: D 719 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7570 (mptt) outliers start: 47 outliers final: 34 residues processed: 198 average time/residue: 0.1236 time to fit residues: 36.8120 Evaluate side-chains 195 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 755 ILE 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 150 optimal weight: 0.0170 chunk 91 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 491 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129847 restraints weight = 15755.061| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.28 r_work: 0.3245 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14808 Z= 0.129 Angle : 0.645 11.742 19960 Z= 0.309 Chirality : 0.044 0.336 2158 Planarity : 0.004 0.043 2402 Dihedral : 16.108 140.851 2428 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.18 % Favored : 92.70 % Rotamer: Outliers : 3.18 % Allowed : 14.57 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1672 helix: 1.20 (0.19), residues: 850 sheet: -2.25 (0.45), residues: 130 loop : -2.20 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 468 TYR 0.019 0.002 TYR D 478 PHE 0.026 0.001 PHE D 842 TRP 0.015 0.001 TRP D 798 HIS 0.003 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (14784) covalent geometry : angle 0.61932 / 0.30 (19894) SS BOND : bond 0.00121 / 0.06 ( 6) SS BOND : angle 0.42447 / 0.28 ( 12) hydrogen bonds : bond 0.03247 / 2.10 ( 566) hydrogen bonds : angle 3.74238 / 2.51 ( 1656) link_BETA1-3 : bond 0.00374 / 0.19 ( 2) link_BETA1-3 : angle 1.73266 / 0.95 ( 6) link_BETA1-4 : bond 0.00659 / 0.35 ( 8) link_BETA1-4 : angle 1.51358 / 0.96 ( 24) link_NAG-ASN : bond 0.01132 / 0.67 ( 8) link_NAG-ASN : angle 5.02033 / 3.41 ( 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 206 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.572 Fit side-chains REVERT: A 568 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7722 (tt) REVERT: A 780 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7130 (mp) REVERT: B 531 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7552 (mttm) REVERT: B 565 MET cc_start: 0.7847 (ttp) cc_final: 0.7216 (mtt) REVERT: B 644 THR cc_start: 0.8809 (m) cc_final: 0.8279 (p) REVERT: B 672 ASP cc_start: 0.8142 (p0) cc_final: 0.7653 (t0) REVERT: C 568 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7733 (tt) REVERT: C 603 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7456 (mt-10) REVERT: C 670 SER cc_start: 0.8198 (t) cc_final: 0.7905 (m) REVERT: C 698 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7547 (mmtp) REVERT: C 712 ARG cc_start: 0.6719 (mtt90) cc_final: 0.6421 (mtt90) REVERT: C 780 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.6992 (mp) REVERT: C 817 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8488 (t) REVERT: D 479 GLU cc_start: 0.5401 (tp30) cc_final: 0.4801 (mp0) REVERT: D 531 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7452 (mttp) REVERT: D 719 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7676 (mptt) REVERT: D 749 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.7213 (t0) REVERT: D 810 LYS cc_start: 0.5978 (ttpt) cc_final: 0.5756 (pttm) outliers start: 46 outliers final: 34 residues processed: 194 average time/residue: 0.1305 time to fit residues: 37.4804 Evaluate side-chains 196 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 749 ASN Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 0.0170 chunk 158 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.172746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128521 restraints weight = 15521.965| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.29 r_work: 0.3236 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14808 Z= 0.131 Angle : 0.647 11.721 19960 Z= 0.309 Chirality : 0.045 0.338 2158 Planarity : 0.004 0.044 2402 Dihedral : 15.815 140.857 2428 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Rotamer: Outliers : 2.83 % Allowed : 14.85 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1672 helix: 1.27 (0.19), residues: 850 sheet: -2.28 (0.45), residues: 130 loop : -2.20 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 468 TYR 0.017 0.002 TYR D 478 PHE 0.026 0.001 PHE D 842 TRP 0.015 0.001 TRP D 798 HIS 0.004 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (14784) covalent geometry : angle 0.61922 / 0.30 (19894) SS BOND : bond 0.00110 / 0.06 ( 6) SS BOND : angle 0.46398 / 0.32 ( 12) hydrogen bonds : bond 0.03241 / 2.10 ( 566) hydrogen bonds : angle 3.72977 / 2.50 ( 1656) link_BETA1-3 : bond 0.00348 / 0.17 ( 2) link_BETA1-3 : angle 1.68320 / 0.92 ( 6) link_BETA1-4 : bond 0.00675 / 0.35 ( 8) link_BETA1-4 : angle 1.50498 / 0.94 ( 24) link_NAG-ASN : bond 0.01131 / 0.65 ( 8) link_NAG-ASN : angle 5.26731 / 3.54 ( 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 197 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.510 Fit side-chains REVERT: A 568 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7602 (tt) REVERT: A 780 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7106 (mp) REVERT: B 511 ASP cc_start: 0.8010 (m-30) cc_final: 0.7757 (m-30) REVERT: B 531 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7545 (mttp) REVERT: B 565 MET cc_start: 0.7845 (ttp) cc_final: 0.7255 (mtt) REVERT: B 672 ASP cc_start: 0.8128 (p0) cc_final: 0.7633 (t0) REVERT: C 568 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7682 (tt) REVERT: C 603 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7446 (mt-10) REVERT: C 670 SER cc_start: 0.8231 (t) cc_final: 0.7942 (m) REVERT: C 698 LYS cc_start: 0.7776 (mtmm) cc_final: 0.7568 (mmtp) REVERT: C 712 ARG cc_start: 0.6769 (mtt90) cc_final: 0.6491 (mtt90) REVERT: C 780 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7030 (mp) REVERT: C 817 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8490 (t) REVERT: D 479 GLU cc_start: 0.5377 (tp30) cc_final: 0.4752 (mp0) REVERT: D 531 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7592 (mttp) REVERT: D 719 LYS cc_start: 0.7851 (mtmm) cc_final: 0.7645 (mptt) REVERT: D 749 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.7195 (t0) outliers start: 41 outliers final: 30 residues processed: 185 average time/residue: 0.1236 time to fit residues: 34.2411 Evaluate side-chains 192 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 749 ASN Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 118 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 104 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 HIS ** 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 = 0.3975 r_free = 0.3975 target = 0.173362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129366 restraints weight = 15547.821| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.30 r_work: 0.3242 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14808 Z= 0.124 Angle : 0.634 11.691 19960 Z= 0.303 Chirality : 0.044 0.333 2158 Planarity : 0.004 0.045 2402 Dihedral : 15.436 140.805 2428 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.76 % Favored : 93.12 % Rotamer: Outliers : 2.62 % Allowed : 15.33 % Favored : 82.04 % 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: -0.49 (0.22), residues: 1672 helix: 1.36 (0.19), residues: 850 sheet: -2.30 (0.44), residues: 130 loop : -2.16 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 468 TYR 0.016 0.001 TYR D 478 PHE 0.025 0.001 PHE D 842 TRP 0.014 0.001 TRP D 798 HIS 0.003 0.001 HIS D 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (14784) covalent geometry : angle 0.60585 / 0.30 (19894) SS BOND : bond 0.00124 / 0.06 ( 6) SS BOND : angle 0.59729 / 0.42 ( 12) hydrogen bonds : bond 0.03193 / 2.07 ( 566) hydrogen bonds : angle 3.69884 / 2.48 ( 1656) link_BETA1-3 : bond 0.00391 / 0.20 ( 2) link_BETA1-3 : angle 1.63402 / 0.90 ( 6) link_BETA1-4 : bond 0.00714 / 0.37 ( 8) link_BETA1-4 : angle 1.47899 / 0.93 ( 24) link_NAG-ASN : bond 0.01111 / 0.64 ( 8) link_NAG-ASN : angle 5.17596 / 3.45 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.12 seconds wall clock time: 63 minutes 22.10 seconds (3802.10 seconds total)