Starting phenix.real_space_refine on Wed Mar 4 19:25:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ryz_24749/03_2026/7ryz_24749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryz_24749/03_2026/7ryz_24749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ryz_24749/03_2026/7ryz_24749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryz_24749/03_2026/7ryz_24749.map" model { file = "/net/cci-nas-00/data/ceres_data/7ryz_24749/03_2026/7ryz_24749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryz_24749/03_2026/7ryz_24749.cif" } resolution = 4.15 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 10196 2.51 5 N 2556 2.21 5 O 2882 1.98 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15742 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4652 Classifications: {'peptide': 597} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 578} Chain breaks: 3 Chain: "B" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3193 Classifications: {'peptide': 410} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 396} Chain breaks: 1 Chain: "C" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4652 Classifications: {'peptide': 597} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 578} Chain breaks: 3 Chain: "D" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3193 Classifications: {'peptide': 410} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 396} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.25, per 1000 atoms: 0.21 Number of scatterers: 15742 At special positions: 0 Unit cell: (108.73, 126.99, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2882 8.00 N 2556 7.00 C 10196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1099 " - pdb=" SG CYS A1110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1099 " - pdb=" SG CYS C1110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " 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 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 636.3 milliseconds 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 22 sheets defined 56.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.569A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 547 removed outlier: 3.687A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.528A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 627 removed outlier: 3.520A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.531A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.856A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.550A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 770 removed outlier: 3.769A pdb=" N TYR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 792 through 822 removed outlier: 3.544A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1029 Processing helix chain 'A' and resid 1118 through 1148 removed outlier: 3.816A pdb=" N GLY A1123 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL A1124 " --> pdb=" O SER A1120 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1194 removed outlier: 3.858A pdb=" N LEU A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1233 removed outlier: 3.682A pdb=" N MET A1221 " --> pdb=" O PHE A1217 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR A1226 " --> pdb=" O ALA A1222 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A1233 " --> pdb=" O ASN A1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.821A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.608A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.625A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.758A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.680A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 4.353A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.503A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.673A pdb=" N ALA B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.655A pdb=" N ALA B 691 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.876A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 712 " --> pdb=" O MET B 708 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 743 through 756 Processing helix chain 'B' and resid 757 through 770 removed outlier: 3.858A pdb=" N LYS B 765 " --> pdb=" O LYS B 761 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 770 " --> pdb=" O TRP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 792 through 820 removed outlier: 3.914A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.568A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 470 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 547 removed outlier: 3.687A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 545 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.528A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 627 removed outlier: 3.520A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.529A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.857A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.549A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 770 removed outlier: 3.770A pdb=" N TYR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 792 through 822 removed outlier: 3.544A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1029 Processing helix chain 'C' and resid 1118 through 1148 removed outlier: 3.816A pdb=" N GLY C1123 " --> pdb=" O ALA C1119 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL C1124 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C1148 " --> pdb=" O SER C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1194 removed outlier: 3.858A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1233 removed outlier: 3.682A pdb=" N MET C1221 " --> pdb=" O PHE C1217 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR C1226 " --> pdb=" O ALA C1222 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS C1233 " --> pdb=" O ASN C1229 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.821A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.609A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.625A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 519' Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.758A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.678A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 4.353A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.502A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.673A pdb=" N ALA D 677 " --> pdb=" O TYR D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.654A pdb=" N ALA D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.876A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 712 " --> pdb=" O MET D 708 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 743 through 756 Processing helix chain 'D' and resid 757 through 770 removed outlier: 3.858A pdb=" N LYS D 765 " --> pdb=" O LYS D 761 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D 770 " --> pdb=" O TRP D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 Processing helix chain 'D' and resid 792 through 820 removed outlier: 3.914A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.061A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 8.221A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1033 through 1039 Processing sheet with id=AA7, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.580A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 7.008A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 7.008A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 498 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB6, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.059A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 646 through 648 removed outlier: 8.221A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1033 through 1039 Processing sheet with id=AB9, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.580A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 648 removed outlier: 7.007A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 648 removed outlier: 7.007A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU D 498 " --> pdb=" O LYS D 730 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2496 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: 2.60 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4829 1.35 - 1.47: 4215 1.47 - 1.60: 6872 1.60 - 1.72: 4 1.72 - 1.85: 174 Bond restraints: 16094 Sorted by residual: bond pdb=" C05 QUS B1301 " pdb=" O19 QUS B1301 " ideal model delta sigma weight residual 1.203 1.451 -0.248 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C05 QUS D1301 " pdb=" O19 QUS D1301 " ideal model delta sigma weight residual 1.203 1.450 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C05 QUS A1401 " pdb=" O19 QUS A1401 " ideal model delta sigma weight residual 1.203 1.448 -0.245 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C05 QUS C1401 " pdb=" O19 QUS C1401 " ideal model delta sigma weight residual 1.203 1.448 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C04 QUS D1301 " pdb=" O18 QUS D1301 " ideal model delta sigma weight residual 1.212 1.411 -0.199 2.00e-02 2.50e+03 9.93e+01 ... (remaining 16089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 21310 2.74 - 5.47: 366 5.47 - 8.21: 66 8.21 - 10.94: 4 10.94 - 13.68: 8 Bond angle restraints: 21754 Sorted by residual: angle pdb=" CA PRO D 679 " pdb=" C PRO D 679 " pdb=" O PRO D 679 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.24e+00 6.50e-01 2.87e+01 angle pdb=" CA PRO B 679 " pdb=" C PRO B 679 " pdb=" O PRO B 679 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.24e+00 6.50e-01 2.87e+01 angle pdb=" C SER A1153 " pdb=" N SER A1154 " pdb=" CA SER A1154 " ideal model delta sigma weight residual 121.19 129.34 -8.15 1.59e+00 3.96e-01 2.63e+01 angle pdb=" C SER C1153 " pdb=" N SER C1154 " pdb=" CA SER C1154 " ideal model delta sigma weight residual 121.19 129.34 -8.15 1.59e+00 3.96e-01 2.63e+01 angle pdb=" C GLU C1197 " pdb=" N ASP C1198 " pdb=" CA ASP C1198 " ideal model delta sigma weight residual 125.66 134.99 -9.33 1.85e+00 2.92e-01 2.54e+01 ... (remaining 21749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9020 17.95 - 35.90: 363 35.90 - 53.85: 87 53.85 - 71.81: 16 71.81 - 89.76: 12 Dihedral angle restraints: 9498 sinusoidal: 3724 harmonic: 5774 Sorted by residual: dihedral pdb=" CA GLU B 678 " pdb=" C GLU B 678 " pdb=" N PRO B 679 " pdb=" CA PRO B 679 " ideal model delta harmonic sigma weight residual 180.00 130.01 49.99 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA GLU D 678 " pdb=" C GLU D 678 " pdb=" N PRO D 679 " pdb=" CA PRO D 679 " ideal model delta harmonic sigma weight residual 180.00 130.02 49.98 0 5.00e+00 4.00e-02 9.99e+01 dihedral pdb=" CA PRO A1118 " pdb=" C PRO A1118 " pdb=" N ALA A1119 " pdb=" CA ALA A1119 " ideal model delta harmonic sigma weight residual -180.00 -154.15 -25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 9495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1869 0.052 - 0.104: 469 0.104 - 0.156: 84 0.156 - 0.208: 18 0.208 - 0.260: 2 Chirality restraints: 2442 Sorted by residual: chirality pdb=" CG LEU A 498 " pdb=" CB LEU A 498 " pdb=" CD1 LEU A 498 " pdb=" CD2 LEU A 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CG LEU C 498 " pdb=" CB LEU C 498 " pdb=" CD1 LEU C 498 " pdb=" CD2 LEU C 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA CYS D 718 " pdb=" N CYS D 718 " pdb=" C CYS D 718 " pdb=" CB CYS D 718 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2439 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 519 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO A 520 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO C 520 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 493 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO D 494 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 494 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 494 " 0.027 5.00e-02 4.00e+02 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2874 2.76 - 3.30: 14753 3.30 - 3.83: 25858 3.83 - 4.37: 30566 4.37 - 4.90: 51259 Nonbonded interactions: 125310 Sorted by model distance: nonbonded pdb=" OG SER A 729 " pdb=" OG SER D 729 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR C 655 " pdb=" O18 QUS C1401 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR A 655 " pdb=" O18 QUS A1401 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLN A1186 " pdb=" OH TYR B 797 " model vdw 2.286 3.040 nonbonded pdb=" O LEU A 639 " pdb=" OH TYR A 647 " model vdw 2.289 3.040 ... (remaining 125305 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.110 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.008 0.248 16100 Z= 0.373 Angle : 0.980 13.680 21766 Z= 0.544 Chirality : 0.048 0.260 2442 Planarity : 0.006 0.050 2682 Dihedral : 11.657 89.758 5796 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.24 % Allowed : 5.37 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.13), residues: 1990 helix: -3.45 (0.09), residues: 1072 sheet: -1.98 (0.34), residues: 180 loop : -2.24 (0.18), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 599 TYR 0.021 0.002 TYR C1135 PHE 0.021 0.002 PHE D 574 TRP 0.019 0.003 TRP A1032 HIS 0.004 0.002 HIS C1092 Details of bonding type rmsd covalent geometry : bond 0.00759 (16094) covalent geometry : angle 0.97957 (21754) SS BOND : bond 0.00248 ( 6) SS BOND : angle 1.99902 ( 12) hydrogen bonds : bond 0.28459 ( 850) hydrogen bonds : angle 9.38444 ( 2496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 653 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ILE cc_start: 0.8827 (tt) cc_final: 0.8602 (mt) REVERT: A 434 LYS cc_start: 0.8915 (tptt) cc_final: 0.8455 (tmmt) REVERT: A 435 HIS cc_start: 0.7819 (t-90) cc_final: 0.7580 (t-170) REVERT: A 482 THR cc_start: 0.8631 (m) cc_final: 0.8328 (p) REVERT: A 509 LYS cc_start: 0.7353 (pmtt) cc_final: 0.7097 (mmmt) REVERT: A 537 SER cc_start: 0.9256 (p) cc_final: 0.8485 (t) REVERT: A 585 MET cc_start: 0.8202 (mmt) cc_final: 0.7774 (mmt) REVERT: A 611 ILE cc_start: 0.9288 (mm) cc_final: 0.9068 (mm) REVERT: A 626 VAL cc_start: 0.9123 (t) cc_final: 0.8804 (p) REVERT: A 637 GLU cc_start: 0.8190 (tt0) cc_final: 0.7627 (tp30) REVERT: A 642 GLN cc_start: 0.7326 (tt0) cc_final: 0.7011 (pp30) REVERT: A 720 THR cc_start: 0.8012 (p) cc_final: 0.7087 (p) REVERT: A 1015 LEU cc_start: 0.8668 (mt) cc_final: 0.8457 (mt) REVERT: A 1016 ASN cc_start: 0.8337 (m-40) cc_final: 0.7753 (t0) REVERT: A 1022 PHE cc_start: 0.8236 (m-10) cc_final: 0.7150 (m-10) REVERT: A 1131 SER cc_start: 0.9290 (m) cc_final: 0.9084 (p) REVERT: A 1141 VAL cc_start: 0.8890 (t) cc_final: 0.8671 (t) REVERT: A 1175 LEU cc_start: 0.9458 (mt) cc_final: 0.9140 (tp) REVERT: A 1211 CYS cc_start: 0.8755 (m) cc_final: 0.8538 (p) REVERT: A 1219 CYS cc_start: 0.8768 (m) cc_final: 0.8284 (m) REVERT: B 407 MET cc_start: 0.8413 (mtp) cc_final: 0.8051 (mtp) REVERT: B 408 MET cc_start: 0.7184 (mmm) cc_final: 0.6940 (mmm) REVERT: B 445 VAL cc_start: 0.7895 (p) cc_final: 0.7640 (p) REVERT: B 498 LEU cc_start: 0.9019 (pt) cc_final: 0.8759 (pt) REVERT: B 504 ILE cc_start: 0.8946 (pt) cc_final: 0.8639 (pt) REVERT: B 505 LYS cc_start: 0.7832 (tmtm) cc_final: 0.7249 (tptp) REVERT: B 506 LYS cc_start: 0.7906 (ttmp) cc_final: 0.7489 (mtpt) REVERT: B 509 LYS cc_start: 0.7725 (pmtt) cc_final: 0.7176 (tppt) REVERT: B 637 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7856 (tm-30) REVERT: B 670 MET cc_start: 0.8817 (mtp) cc_final: 0.8301 (mtp) REVERT: B 761 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7689 (pttt) REVERT: B 807 MET cc_start: 0.9199 (mmm) cc_final: 0.8656 (mmt) REVERT: C 399 THR cc_start: 0.8006 (t) cc_final: 0.7790 (t) REVERT: C 408 MET cc_start: 0.6750 (tpp) cc_final: 0.6240 (tpt) REVERT: C 434 LYS cc_start: 0.8999 (tptt) cc_final: 0.8478 (pttp) REVERT: C 435 HIS cc_start: 0.7534 (t-90) cc_final: 0.7306 (t-170) REVERT: C 537 SER cc_start: 0.9218 (p) cc_final: 0.8411 (t) REVERT: C 540 LEU cc_start: 0.9181 (tt) cc_final: 0.8968 (mm) REVERT: C 585 MET cc_start: 0.8450 (mmt) cc_final: 0.7883 (mmt) REVERT: C 591 ILE cc_start: 0.8350 (mp) cc_final: 0.7971 (mt) REVERT: C 626 VAL cc_start: 0.9100 (t) cc_final: 0.8775 (p) REVERT: C 637 GLU cc_start: 0.8315 (tt0) cc_final: 0.7419 (mp0) REVERT: C 709 ASN cc_start: 0.8712 (t0) cc_final: 0.8143 (t0) REVERT: C 710 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8538 (mt-10) REVERT: C 714 GLN cc_start: 0.7351 (mt0) cc_final: 0.6352 (tp40) REVERT: C 720 THR cc_start: 0.8071 (p) cc_final: 0.7005 (p) REVERT: C 728 ASP cc_start: 0.7544 (t70) cc_final: 0.6764 (t70) REVERT: C 1016 ASN cc_start: 0.8676 (m-40) cc_final: 0.8330 (t0) REVERT: C 1022 PHE cc_start: 0.8333 (m-10) cc_final: 0.7169 (m-10) REVERT: C 1175 LEU cc_start: 0.9327 (mt) cc_final: 0.9042 (mt) REVERT: C 1219 CYS cc_start: 0.8562 (m) cc_final: 0.7953 (m) REVERT: D 408 MET cc_start: 0.7245 (mmm) cc_final: 0.6941 (mmm) REVERT: D 418 ASN cc_start: 0.6581 (m-40) cc_final: 0.4629 (p0) REVERT: D 497 SER cc_start: 0.8654 (m) cc_final: 0.8317 (t) REVERT: D 504 ILE cc_start: 0.8978 (pt) cc_final: 0.8669 (mt) REVERT: D 506 LYS cc_start: 0.7839 (ttmp) cc_final: 0.7636 (mtpt) REVERT: D 509 LYS cc_start: 0.7906 (pmtt) cc_final: 0.7502 (tppt) REVERT: D 569 ASN cc_start: 0.5653 (m-40) cc_final: 0.5202 (m-40) REVERT: D 590 ASP cc_start: 0.7646 (p0) cc_final: 0.7372 (m-30) REVERT: D 591 ILE cc_start: 0.8505 (pt) cc_final: 0.8278 (pt) REVERT: D 710 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8116 (mt-10) REVERT: D 747 ASN cc_start: 0.8795 (t0) cc_final: 0.8573 (t0) REVERT: D 807 MET cc_start: 0.8962 (mmm) cc_final: 0.8692 (mmt) outliers start: 4 outliers final: 2 residues processed: 655 average time/residue: 0.1216 time to fit residues: 116.5049 Evaluate side-chains 372 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 370 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN A 575 ASN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN B 586 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1186 GLN D 586 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.104402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.082815 restraints weight = 44576.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084053 restraints weight = 27834.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085100 restraints weight = 20808.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085200 restraints weight = 18382.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085303 restraints weight = 17297.657| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16100 Z= 0.132 Angle : 0.589 6.520 21766 Z= 0.315 Chirality : 0.041 0.152 2442 Planarity : 0.005 0.044 2682 Dihedral : 7.138 88.730 2198 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.12 % Allowed : 4.55 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.16), residues: 1990 helix: -0.71 (0.13), residues: 1086 sheet: -1.70 (0.36), residues: 174 loop : -1.75 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1038 TYR 0.021 0.001 TYR A 732 PHE 0.014 0.001 PHE C 574 TRP 0.013 0.001 TRP D 766 HIS 0.005 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00284 (16094) covalent geometry : angle 0.58820 (21754) SS BOND : bond 0.00205 ( 6) SS BOND : angle 1.24796 ( 12) hydrogen bonds : bond 0.04278 ( 850) hydrogen bonds : angle 4.60689 ( 2496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 511 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8838 (tptt) cc_final: 0.8474 (tmmt) REVERT: A 504 ILE cc_start: 0.8774 (tp) cc_final: 0.8420 (tp) REVERT: A 585 MET cc_start: 0.8345 (mmt) cc_final: 0.7697 (mmt) REVERT: A 589 CYS cc_start: 0.7082 (t) cc_final: 0.6665 (t) REVERT: A 591 ILE cc_start: 0.8194 (mp) cc_final: 0.7826 (pt) REVERT: A 619 ASN cc_start: 0.8729 (t0) cc_final: 0.8412 (t0) REVERT: A 637 GLU cc_start: 0.8011 (tt0) cc_final: 0.7664 (tp30) REVERT: A 639 LEU cc_start: 0.8493 (mt) cc_final: 0.8286 (mt) REVERT: A 661 ARG cc_start: 0.8335 (ptm-80) cc_final: 0.8045 (ttp80) REVERT: A 805 LEU cc_start: 0.8979 (mt) cc_final: 0.8431 (tt) REVERT: A 1022 PHE cc_start: 0.8438 (m-10) cc_final: 0.8196 (m-10) REVERT: A 1170 THR cc_start: 0.8578 (p) cc_final: 0.8302 (t) REVERT: A 1175 LEU cc_start: 0.9314 (mt) cc_final: 0.8917 (tp) REVERT: B 407 MET cc_start: 0.8100 (mtp) cc_final: 0.7841 (mtp) REVERT: B 414 MET cc_start: 0.6808 (ttm) cc_final: 0.6606 (ttp) REVERT: B 503 MET cc_start: 0.8890 (tmm) cc_final: 0.8604 (tmm) REVERT: B 542 LEU cc_start: 0.8649 (mt) cc_final: 0.8397 (mp) REVERT: B 633 ILE cc_start: 0.8730 (pt) cc_final: 0.7982 (pt) REVERT: B 637 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7902 (tm-30) REVERT: B 638 ASP cc_start: 0.7241 (m-30) cc_final: 0.6858 (t0) REVERT: B 761 LYS cc_start: 0.8524 (mtpp) cc_final: 0.7687 (mtmm) REVERT: C 434 LYS cc_start: 0.8912 (tptt) cc_final: 0.8581 (tmmt) REVERT: C 504 ILE cc_start: 0.8724 (tp) cc_final: 0.8467 (tp) REVERT: C 585 MET cc_start: 0.8417 (mmt) cc_final: 0.7736 (mmt) REVERT: C 589 CYS cc_start: 0.7576 (t) cc_final: 0.7331 (t) REVERT: C 591 ILE cc_start: 0.8132 (mp) cc_final: 0.7858 (pt) REVERT: C 611 ILE cc_start: 0.9448 (mm) cc_final: 0.9234 (mm) REVERT: C 637 GLU cc_start: 0.8121 (tt0) cc_final: 0.7460 (mp0) REVERT: C 755 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7311 (tm-30) REVERT: C 756 GLN cc_start: 0.8499 (tt0) cc_final: 0.8111 (tt0) REVERT: C 770 LYS cc_start: 0.6361 (mppt) cc_final: 0.5780 (pttt) REVERT: C 808 LEU cc_start: 0.8712 (mt) cc_final: 0.8441 (mm) REVERT: C 815 CYS cc_start: 0.7435 (m) cc_final: 0.7127 (t) REVERT: C 1022 PHE cc_start: 0.8533 (m-10) cc_final: 0.8313 (m-10) REVERT: C 1172 LEU cc_start: 0.9176 (mm) cc_final: 0.8889 (tp) REVERT: C 1211 CYS cc_start: 0.8982 (p) cc_final: 0.8474 (p) REVERT: C 1219 CYS cc_start: 0.8733 (m) cc_final: 0.8267 (m) REVERT: D 408 MET cc_start: 0.7118 (mmm) cc_final: 0.6874 (mmm) REVERT: D 411 ASN cc_start: 0.7412 (t0) cc_final: 0.7145 (t0) REVERT: D 418 ASN cc_start: 0.6565 (m-40) cc_final: 0.5232 (p0) REVERT: D 432 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8553 (tp) REVERT: D 442 LEU cc_start: 0.8026 (mt) cc_final: 0.7682 (mm) REVERT: D 456 ASP cc_start: 0.6981 (m-30) cc_final: 0.6771 (m-30) REVERT: D 479 LEU cc_start: 0.8556 (mt) cc_final: 0.8279 (mp) REVERT: D 503 MET cc_start: 0.8714 (tmm) cc_final: 0.8497 (tmm) REVERT: D 590 ASP cc_start: 0.7683 (p0) cc_final: 0.7354 (m-30) REVERT: D 597 SER cc_start: 0.8803 (p) cc_final: 0.8273 (m) REVERT: D 670 MET cc_start: 0.8423 (mtm) cc_final: 0.7965 (mtp) REVERT: D 815 CYS cc_start: 0.7284 (m) cc_final: 0.7025 (t) outliers start: 2 outliers final: 0 residues processed: 511 average time/residue: 0.1059 time to fit residues: 82.5828 Evaluate side-chains 320 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 71 optimal weight: 0.3980 chunk 96 optimal weight: 0.0770 chunk 182 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN A1016 ASN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.082670 restraints weight = 45418.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084059 restraints weight = 30619.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084674 restraints weight = 22293.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084869 restraints weight = 19089.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084904 restraints weight = 18171.316| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16100 Z= 0.120 Angle : 0.558 6.407 21766 Z= 0.295 Chirality : 0.041 0.149 2442 Planarity : 0.004 0.051 2682 Dihedral : 6.615 87.292 2198 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 1990 helix: 0.61 (0.15), residues: 1080 sheet: -1.22 (0.42), residues: 146 loop : -1.57 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 545 TYR 0.020 0.001 TYR A 732 PHE 0.019 0.001 PHE A1169 TRP 0.013 0.001 TRP C1032 HIS 0.003 0.000 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00258 (16094) covalent geometry : angle 0.55726 (21754) SS BOND : bond 0.00613 ( 6) SS BOND : angle 1.12709 ( 12) hydrogen bonds : bond 0.03751 ( 850) hydrogen bonds : angle 4.29771 ( 2496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8865 (tptt) cc_final: 0.8549 (tmmt) REVERT: A 585 MET cc_start: 0.8492 (mmt) cc_final: 0.7781 (mmt) REVERT: A 589 CYS cc_start: 0.7127 (t) cc_final: 0.6571 (t) REVERT: A 591 ILE cc_start: 0.8073 (mp) cc_final: 0.7775 (pt) REVERT: A 619 ASN cc_start: 0.8818 (t0) cc_final: 0.8383 (t0) REVERT: A 642 GLN cc_start: 0.7939 (pp30) cc_final: 0.7723 (pp30) REVERT: A 661 ARG cc_start: 0.8329 (ptm-80) cc_final: 0.7999 (ttp80) REVERT: A 770 LYS cc_start: 0.6898 (mppt) cc_final: 0.5851 (tptt) REVERT: A 805 LEU cc_start: 0.8977 (mt) cc_final: 0.8413 (tt) REVERT: A 1172 LEU cc_start: 0.9084 (mm) cc_final: 0.8739 (tp) REVERT: A 1175 LEU cc_start: 0.9214 (mt) cc_final: 0.8962 (tp) REVERT: A 1219 CYS cc_start: 0.8671 (m) cc_final: 0.8315 (m) REVERT: B 407 MET cc_start: 0.7965 (mtp) cc_final: 0.7608 (mtp) REVERT: B 503 MET cc_start: 0.8927 (tmm) cc_final: 0.8685 (tmm) REVERT: B 504 ILE cc_start: 0.9262 (pt) cc_final: 0.8919 (pt) REVERT: B 546 PHE cc_start: 0.6300 (m-10) cc_final: 0.5764 (m-80) REVERT: B 637 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7800 (tm-30) REVERT: B 693 VAL cc_start: 0.8645 (t) cc_final: 0.8389 (t) REVERT: B 721 MET cc_start: 0.8787 (ptt) cc_final: 0.8379 (ppp) REVERT: B 761 LYS cc_start: 0.8551 (mtpp) cc_final: 0.7826 (mtmm) REVERT: C 434 LYS cc_start: 0.8928 (tptt) cc_final: 0.8579 (tmmt) REVERT: C 504 ILE cc_start: 0.8773 (tp) cc_final: 0.8569 (tp) REVERT: C 585 MET cc_start: 0.8465 (mmt) cc_final: 0.7634 (mmt) REVERT: C 589 CYS cc_start: 0.7480 (t) cc_final: 0.7231 (t) REVERT: C 591 ILE cc_start: 0.8239 (mp) cc_final: 0.7951 (pt) REVERT: C 637 GLU cc_start: 0.8074 (tt0) cc_final: 0.7383 (mp0) REVERT: C 647 TYR cc_start: 0.5088 (m-80) cc_final: 0.4857 (m-80) REVERT: C 755 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7303 (tm-30) REVERT: C 756 GLN cc_start: 0.8521 (tt0) cc_final: 0.8207 (tt0) REVERT: C 770 LYS cc_start: 0.6454 (mppt) cc_final: 0.5995 (pttt) REVERT: C 815 CYS cc_start: 0.7309 (m) cc_final: 0.7025 (t) REVERT: C 1099 CYS cc_start: 0.5066 (m) cc_final: 0.4588 (m) REVERT: C 1172 LEU cc_start: 0.9137 (mm) cc_final: 0.8853 (tp) REVERT: C 1182 MET cc_start: 0.7769 (mmt) cc_final: 0.7563 (mmt) REVERT: C 1211 CYS cc_start: 0.8792 (p) cc_final: 0.8302 (p) REVERT: C 1219 CYS cc_start: 0.8822 (m) cc_final: 0.8381 (m) REVERT: C 1224 SER cc_start: 0.9063 (t) cc_final: 0.8725 (p) REVERT: D 411 ASN cc_start: 0.7334 (t0) cc_final: 0.7100 (t0) REVERT: D 418 ASN cc_start: 0.6580 (m-40) cc_final: 0.5461 (p0) REVERT: D 432 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8446 (tp) REVERT: D 456 ASP cc_start: 0.6936 (m-30) cc_final: 0.6704 (m-30) REVERT: D 503 MET cc_start: 0.8730 (tmm) cc_final: 0.8386 (tmm) REVERT: D 569 ASN cc_start: 0.5515 (m-40) cc_final: 0.5307 (m110) REVERT: D 590 ASP cc_start: 0.7651 (p0) cc_final: 0.7211 (m-30) REVERT: D 591 ILE cc_start: 0.8439 (pt) cc_final: 0.8212 (pt) REVERT: D 597 SER cc_start: 0.8779 (p) cc_final: 0.8198 (m) REVERT: D 693 VAL cc_start: 0.8788 (t) cc_final: 0.8574 (t) REVERT: D 708 MET cc_start: 0.8418 (mmp) cc_final: 0.8159 (mmp) REVERT: D 721 MET cc_start: 0.8078 (ppp) cc_final: 0.7761 (ppp) REVERT: D 807 MET cc_start: 0.8960 (mmm) cc_final: 0.8319 (mmt) REVERT: D 815 CYS cc_start: 0.7259 (m) cc_final: 0.7018 (t) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.0969 time to fit residues: 69.9620 Evaluate side-chains 318 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN A1186 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1163 ASN C1186 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078510 restraints weight = 45701.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079831 restraints weight = 27611.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080931 restraints weight = 20375.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081048 restraints weight = 18393.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.081259 restraints weight = 17677.709| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16100 Z= 0.203 Angle : 0.628 8.195 21766 Z= 0.334 Chirality : 0.043 0.167 2442 Planarity : 0.004 0.065 2682 Dihedral : 6.345 86.454 2198 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.18), residues: 1990 helix: 0.90 (0.15), residues: 1092 sheet: -1.36 (0.44), residues: 122 loop : -1.52 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 545 TYR 0.023 0.002 TYR A 732 PHE 0.041 0.002 PHE A1022 TRP 0.019 0.002 TRP A1204 HIS 0.006 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00447 (16094) covalent geometry : angle 0.62779 (21754) SS BOND : bond 0.00218 ( 6) SS BOND : angle 0.95061 ( 12) hydrogen bonds : bond 0.03905 ( 850) hydrogen bonds : angle 4.50329 ( 2496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8845 (tptt) cc_final: 0.8519 (tmmt) REVERT: A 585 MET cc_start: 0.8459 (mmt) cc_final: 0.7777 (mmt) REVERT: A 589 CYS cc_start: 0.7402 (t) cc_final: 0.7187 (t) REVERT: A 619 ASN cc_start: 0.8697 (t0) cc_final: 0.8392 (t0) REVERT: A 637 GLU cc_start: 0.8265 (tt0) cc_final: 0.7997 (tp30) REVERT: A 805 LEU cc_start: 0.9085 (mt) cc_final: 0.8499 (tt) REVERT: A 1022 PHE cc_start: 0.8202 (m-80) cc_final: 0.7127 (m-80) REVERT: A 1025 THR cc_start: 0.8949 (p) cc_final: 0.8744 (p) REVERT: A 1143 PHE cc_start: 0.8346 (p90) cc_final: 0.7877 (p90) REVERT: A 1169 PHE cc_start: 0.8061 (m-80) cc_final: 0.7695 (m-80) REVERT: A 1206 TYR cc_start: 0.8541 (m-80) cc_final: 0.8244 (m-80) REVERT: A 1212 LEU cc_start: 0.8573 (tp) cc_final: 0.8344 (tp) REVERT: A 1219 CYS cc_start: 0.8714 (m) cc_final: 0.8248 (m) REVERT: B 407 MET cc_start: 0.7833 (mtp) cc_final: 0.7598 (mtp) REVERT: B 479 LEU cc_start: 0.8644 (tp) cc_final: 0.8296 (mt) REVERT: B 503 MET cc_start: 0.8961 (tmm) cc_final: 0.8582 (tmm) REVERT: B 504 ILE cc_start: 0.9287 (pt) cc_final: 0.8906 (pt) REVERT: B 546 PHE cc_start: 0.6488 (m-10) cc_final: 0.5932 (m-80) REVERT: B 657 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7536 (tp30) REVERT: B 721 MET cc_start: 0.8718 (ptt) cc_final: 0.8187 (ppp) REVERT: B 761 LYS cc_start: 0.8674 (mtpp) cc_final: 0.7904 (mtmm) REVERT: B 764 ASN cc_start: 0.9038 (t0) cc_final: 0.8777 (t0) REVERT: C 434 LYS cc_start: 0.8898 (tptt) cc_final: 0.8600 (tmmt) REVERT: C 585 MET cc_start: 0.8473 (mmt) cc_final: 0.7893 (mmt) REVERT: C 590 ASP cc_start: 0.7767 (p0) cc_final: 0.7487 (p0) REVERT: C 613 ILE cc_start: 0.9347 (mt) cc_final: 0.8915 (mt) REVERT: C 647 TYR cc_start: 0.5545 (m-80) cc_final: 0.5053 (m-80) REVERT: C 734 ILE cc_start: 0.9030 (mt) cc_final: 0.8727 (mt) REVERT: C 755 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7420 (tm-30) REVERT: C 756 GLN cc_start: 0.8650 (tt0) cc_final: 0.8231 (tt0) REVERT: C 770 LYS cc_start: 0.6912 (mptt) cc_final: 0.6129 (pttp) REVERT: C 815 CYS cc_start: 0.7397 (m) cc_final: 0.7054 (t) REVERT: C 1022 PHE cc_start: 0.8232 (m-80) cc_final: 0.7126 (m-80) REVERT: C 1172 LEU cc_start: 0.9274 (mm) cc_final: 0.8951 (mm) REVERT: C 1182 MET cc_start: 0.7957 (mmt) cc_final: 0.7738 (mmt) REVERT: C 1219 CYS cc_start: 0.8811 (m) cc_final: 0.8269 (m) REVERT: D 411 ASN cc_start: 0.7353 (t0) cc_final: 0.7122 (t0) REVERT: D 418 ASN cc_start: 0.6628 (m-40) cc_final: 0.4878 (p0) REVERT: D 432 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8493 (tp) REVERT: D 479 LEU cc_start: 0.8584 (mt) cc_final: 0.8361 (mt) REVERT: D 503 MET cc_start: 0.8716 (tmm) cc_final: 0.8310 (tmm) REVERT: D 569 ASN cc_start: 0.5872 (m-40) cc_final: 0.5654 (m110) REVERT: D 708 MET cc_start: 0.8594 (mmp) cc_final: 0.8192 (mmp) REVERT: D 765 LYS cc_start: 0.8269 (ptmm) cc_final: 0.8027 (ttpp) outliers start: 1 outliers final: 0 residues processed: 405 average time/residue: 0.0929 time to fit residues: 60.0127 Evaluate side-chains 307 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 189 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 117 optimal weight: 0.0370 chunk 86 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 41 optimal weight: 8.9990 chunk 94 optimal weight: 0.0770 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1186 GLN D 619 ASN D 709 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083147 restraints weight = 44485.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084206 restraints weight = 29465.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084526 restraints weight = 20970.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084949 restraints weight = 20873.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085187 restraints weight = 18597.300| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16100 Z= 0.107 Angle : 0.549 6.644 21766 Z= 0.285 Chirality : 0.040 0.152 2442 Planarity : 0.004 0.053 2682 Dihedral : 5.632 88.322 2198 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 1990 helix: 1.33 (0.16), residues: 1088 sheet: -1.09 (0.40), residues: 150 loop : -1.26 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 715 TYR 0.020 0.001 TYR C 424 PHE 0.037 0.001 PHE C1022 TRP 0.013 0.001 TRP A1032 HIS 0.004 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00231 (16094) covalent geometry : angle 0.54871 (21754) SS BOND : bond 0.00522 ( 6) SS BOND : angle 0.83246 ( 12) hydrogen bonds : bond 0.03328 ( 850) hydrogen bonds : angle 4.12601 ( 2496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8811 (tptt) cc_final: 0.8547 (tmmt) REVERT: A 585 MET cc_start: 0.8439 (mmt) cc_final: 0.7635 (mmt) REVERT: A 619 ASN cc_start: 0.8676 (t0) cc_final: 0.8318 (t0) REVERT: A 637 GLU cc_start: 0.8104 (tt0) cc_final: 0.7732 (tp30) REVERT: A 661 ARG cc_start: 0.8369 (ptm-80) cc_final: 0.7961 (tmt170) REVERT: A 805 LEU cc_start: 0.9000 (mt) cc_final: 0.8506 (tt) REVERT: A 1169 PHE cc_start: 0.7969 (m-80) cc_final: 0.7764 (m-80) REVERT: A 1172 LEU cc_start: 0.9152 (mm) cc_final: 0.8862 (mm) REVERT: A 1219 CYS cc_start: 0.8753 (m) cc_final: 0.8319 (m) REVERT: B 407 MET cc_start: 0.7683 (mtp) cc_final: 0.7314 (mtp) REVERT: B 479 LEU cc_start: 0.8631 (tp) cc_final: 0.8352 (mt) REVERT: B 503 MET cc_start: 0.8958 (tmm) cc_final: 0.8718 (tmm) REVERT: B 504 ILE cc_start: 0.9229 (pt) cc_final: 0.8758 (pt) REVERT: B 542 LEU cc_start: 0.8449 (mp) cc_final: 0.7947 (pp) REVERT: B 543 VAL cc_start: 0.8183 (t) cc_final: 0.7637 (t) REVERT: B 546 PHE cc_start: 0.6236 (m-10) cc_final: 0.5260 (m-80) REVERT: B 585 MET cc_start: 0.8755 (mmm) cc_final: 0.8389 (mmm) REVERT: B 637 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7715 (tm-30) REVERT: B 657 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 670 MET cc_start: 0.8489 (mtp) cc_final: 0.8104 (mtt) REVERT: B 693 VAL cc_start: 0.8698 (t) cc_final: 0.8464 (t) REVERT: B 721 MET cc_start: 0.8645 (ptt) cc_final: 0.8295 (ppp) REVERT: B 760 ASP cc_start: 0.8217 (m-30) cc_final: 0.7955 (m-30) REVERT: B 761 LYS cc_start: 0.8635 (mtpp) cc_final: 0.7941 (mtmm) REVERT: C 418 ASN cc_start: 0.7327 (p0) cc_final: 0.6927 (m-40) REVERT: C 434 LYS cc_start: 0.8819 (tptt) cc_final: 0.8591 (tmmt) REVERT: C 508 GLN cc_start: 0.5495 (mm110) cc_final: 0.5293 (mm-40) REVERT: C 585 MET cc_start: 0.8503 (mmt) cc_final: 0.7650 (mmt) REVERT: C 619 ASN cc_start: 0.8725 (t0) cc_final: 0.8401 (t0) REVERT: C 637 GLU cc_start: 0.8098 (tt0) cc_final: 0.7376 (mp0) REVERT: C 647 TYR cc_start: 0.5043 (m-80) cc_final: 0.4616 (m-80) REVERT: C 661 ARG cc_start: 0.8307 (ptm-80) cc_final: 0.7853 (tmt170) REVERT: C 719 ASP cc_start: 0.7599 (t0) cc_final: 0.7358 (t0) REVERT: C 734 ILE cc_start: 0.9021 (mt) cc_final: 0.8802 (mt) REVERT: C 770 LYS cc_start: 0.6999 (mptt) cc_final: 0.6272 (pttt) REVERT: C 1172 LEU cc_start: 0.9168 (mm) cc_final: 0.8842 (tp) REVERT: C 1182 MET cc_start: 0.7727 (mmt) cc_final: 0.7205 (mmt) REVERT: C 1219 CYS cc_start: 0.8837 (m) cc_final: 0.8495 (m) REVERT: C 1224 SER cc_start: 0.8987 (t) cc_final: 0.8605 (p) REVERT: D 411 ASN cc_start: 0.7341 (t0) cc_final: 0.7011 (t0) REVERT: D 418 ASN cc_start: 0.6567 (m-40) cc_final: 0.4991 (p0) REVERT: D 456 ASP cc_start: 0.6782 (m-30) cc_final: 0.6564 (m-30) REVERT: D 503 MET cc_start: 0.8884 (tmm) cc_final: 0.8527 (tmm) REVERT: D 543 VAL cc_start: 0.8085 (t) cc_final: 0.7870 (t) REVERT: D 569 ASN cc_start: 0.5711 (m-40) cc_final: 0.5477 (m110) REVERT: D 590 ASP cc_start: 0.7599 (p0) cc_final: 0.7051 (m-30) REVERT: D 591 ILE cc_start: 0.8465 (pt) cc_final: 0.8178 (pt) REVERT: D 597 SER cc_start: 0.8707 (p) cc_final: 0.8295 (p) REVERT: D 693 VAL cc_start: 0.8776 (t) cc_final: 0.8517 (t) REVERT: D 709 ASN cc_start: 0.9399 (OUTLIER) cc_final: 0.9043 (t0) REVERT: D 765 LYS cc_start: 0.8196 (ptmm) cc_final: 0.7922 (ttpt) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.0996 time to fit residues: 67.3899 Evaluate side-chains 307 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 91 optimal weight: 0.0010 chunk 7 optimal weight: 5.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 GLN ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1186 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083332 restraints weight = 44574.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084300 restraints weight = 29875.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084558 restraints weight = 22101.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085028 restraints weight = 20780.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085081 restraints weight = 19760.014| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16100 Z= 0.110 Angle : 0.543 7.173 21766 Z= 0.283 Chirality : 0.041 0.290 2442 Planarity : 0.004 0.053 2682 Dihedral : 5.358 89.429 2198 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1990 helix: 1.46 (0.16), residues: 1090 sheet: -0.83 (0.40), residues: 150 loop : -1.16 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 715 TYR 0.015 0.001 TYR A 732 PHE 0.043 0.001 PHE A1022 TRP 0.013 0.001 TRP A1032 HIS 0.005 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00242 (16094) covalent geometry : angle 0.54302 (21754) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.60003 ( 12) hydrogen bonds : bond 0.03268 ( 850) hydrogen bonds : angle 4.08960 ( 2496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8788 (tptt) cc_final: 0.8336 (pptt) REVERT: A 519 ASP cc_start: 0.8333 (m-30) cc_final: 0.7798 (t0) REVERT: A 585 MET cc_start: 0.8515 (mmt) cc_final: 0.7661 (mmt) REVERT: A 619 ASN cc_start: 0.8561 (t0) cc_final: 0.7986 (t0) REVERT: A 637 GLU cc_start: 0.8064 (tt0) cc_final: 0.7698 (tp30) REVERT: A 645 ILE cc_start: 0.8586 (mm) cc_final: 0.8243 (mt) REVERT: A 661 ARG cc_start: 0.8321 (ptm-80) cc_final: 0.7920 (tmt170) REVERT: A 805 LEU cc_start: 0.8974 (mt) cc_final: 0.8490 (tt) REVERT: A 1022 PHE cc_start: 0.8066 (m-80) cc_final: 0.6750 (m-80) REVERT: A 1169 PHE cc_start: 0.7953 (m-80) cc_final: 0.7719 (m-80) REVERT: A 1172 LEU cc_start: 0.9267 (mm) cc_final: 0.8916 (tp) REVERT: A 1219 CYS cc_start: 0.8734 (m) cc_final: 0.8229 (m) REVERT: B 407 MET cc_start: 0.7596 (mtp) cc_final: 0.7245 (mtp) REVERT: B 479 LEU cc_start: 0.8622 (tp) cc_final: 0.8378 (mt) REVERT: B 503 MET cc_start: 0.9035 (tmm) cc_final: 0.8628 (tmm) REVERT: B 504 ILE cc_start: 0.9309 (pt) cc_final: 0.8952 (pt) REVERT: B 542 LEU cc_start: 0.8453 (mp) cc_final: 0.8198 (pp) REVERT: B 543 VAL cc_start: 0.8205 (t) cc_final: 0.7653 (t) REVERT: B 546 PHE cc_start: 0.6305 (m-10) cc_final: 0.5751 (m-80) REVERT: B 585 MET cc_start: 0.8872 (mmm) cc_final: 0.8419 (mmm) REVERT: B 637 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7726 (tm-30) REVERT: B 657 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7494 (mm-30) REVERT: B 670 MET cc_start: 0.8489 (mtp) cc_final: 0.8236 (mtp) REVERT: B 693 VAL cc_start: 0.8758 (t) cc_final: 0.8413 (t) REVERT: B 760 ASP cc_start: 0.8197 (m-30) cc_final: 0.7945 (m-30) REVERT: B 761 LYS cc_start: 0.8620 (mtpp) cc_final: 0.7940 (mtmm) REVERT: C 418 ASN cc_start: 0.7390 (p0) cc_final: 0.7020 (m-40) REVERT: C 585 MET cc_start: 0.8537 (mmt) cc_final: 0.7728 (mmt) REVERT: C 637 GLU cc_start: 0.8089 (tt0) cc_final: 0.7375 (mp0) REVERT: C 661 ARG cc_start: 0.8288 (ptm-80) cc_final: 0.7836 (tmt170) REVERT: C 734 ILE cc_start: 0.8998 (mt) cc_final: 0.8796 (mt) REVERT: C 768 TYR cc_start: 0.7094 (m-80) cc_final: 0.6804 (m-80) REVERT: C 1022 PHE cc_start: 0.8039 (m-80) cc_final: 0.7625 (m-80) REVERT: C 1095 ILE cc_start: 0.8191 (pt) cc_final: 0.7964 (pt) REVERT: C 1097 TYR cc_start: 0.7179 (m-10) cc_final: 0.6932 (m-10) REVERT: C 1172 LEU cc_start: 0.9214 (mm) cc_final: 0.8957 (tp) REVERT: C 1182 MET cc_start: 0.7828 (mmt) cc_final: 0.7251 (mmp) REVERT: C 1219 CYS cc_start: 0.8729 (m) cc_final: 0.8338 (m) REVERT: D 456 ASP cc_start: 0.6729 (m-30) cc_final: 0.6528 (m-30) REVERT: D 503 MET cc_start: 0.9049 (tmm) cc_final: 0.8724 (tmm) REVERT: D 543 VAL cc_start: 0.8129 (t) cc_final: 0.7884 (t) REVERT: D 569 ASN cc_start: 0.5802 (m-40) cc_final: 0.5557 (m110) REVERT: D 585 MET cc_start: 0.8695 (mmm) cc_final: 0.8156 (mmm) REVERT: D 590 ASP cc_start: 0.7602 (p0) cc_final: 0.7113 (m-30) REVERT: D 591 ILE cc_start: 0.8455 (pt) cc_final: 0.8176 (pt) REVERT: D 597 SER cc_start: 0.8733 (p) cc_final: 0.8154 (p) REVERT: D 693 VAL cc_start: 0.8919 (t) cc_final: 0.8580 (t) REVERT: D 803 LEU cc_start: 0.9368 (mt) cc_final: 0.9165 (mm) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.0977 time to fit residues: 61.7199 Evaluate side-chains 302 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 68 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081514 restraints weight = 44495.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083324 restraints weight = 27645.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083500 restraints weight = 19441.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.083895 restraints weight = 19278.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084009 restraints weight = 18131.686| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16100 Z= 0.120 Angle : 0.553 8.557 21766 Z= 0.288 Chirality : 0.041 0.300 2442 Planarity : 0.004 0.054 2682 Dihedral : 5.275 88.831 2198 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1990 helix: 1.52 (0.16), residues: 1092 sheet: -0.67 (0.43), residues: 128 loop : -1.03 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.017 0.001 TYR C 424 PHE 0.042 0.001 PHE A1022 TRP 0.012 0.001 TRP A1032 HIS 0.005 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00270 (16094) covalent geometry : angle 0.55353 (21754) SS BOND : bond 0.00113 ( 6) SS BOND : angle 0.47248 ( 12) hydrogen bonds : bond 0.03257 ( 850) hydrogen bonds : angle 4.11398 ( 2496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7133 (tpp) cc_final: 0.6801 (tpt) REVERT: A 585 MET cc_start: 0.8546 (mmt) cc_final: 0.7708 (mmt) REVERT: A 637 GLU cc_start: 0.8055 (tt0) cc_final: 0.7674 (tp30) REVERT: A 645 ILE cc_start: 0.8547 (mm) cc_final: 0.8201 (mt) REVERT: A 661 ARG cc_start: 0.8314 (ptm-80) cc_final: 0.7912 (tmt170) REVERT: A 770 LYS cc_start: 0.6794 (mptt) cc_final: 0.6522 (mppt) REVERT: A 805 LEU cc_start: 0.9055 (mt) cc_final: 0.8520 (tt) REVERT: A 1022 PHE cc_start: 0.8046 (m-80) cc_final: 0.6808 (m-80) REVERT: A 1169 PHE cc_start: 0.7954 (m-80) cc_final: 0.7730 (m-80) REVERT: A 1172 LEU cc_start: 0.9257 (mm) cc_final: 0.8941 (tp) REVERT: A 1219 CYS cc_start: 0.8772 (m) cc_final: 0.8147 (m) REVERT: B 407 MET cc_start: 0.7672 (mtp) cc_final: 0.7339 (mtp) REVERT: B 479 LEU cc_start: 0.8644 (tp) cc_final: 0.8399 (mt) REVERT: B 503 MET cc_start: 0.9043 (tmm) cc_final: 0.8623 (tmm) REVERT: B 504 ILE cc_start: 0.9215 (pt) cc_final: 0.8987 (pt) REVERT: B 546 PHE cc_start: 0.6455 (m-10) cc_final: 0.5964 (m-80) REVERT: B 637 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7739 (tm-30) REVERT: B 657 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7529 (mm-30) REVERT: B 693 VAL cc_start: 0.8796 (t) cc_final: 0.8386 (t) REVERT: B 760 ASP cc_start: 0.8137 (m-30) cc_final: 0.7861 (m-30) REVERT: B 761 LYS cc_start: 0.8616 (mtpp) cc_final: 0.7931 (mtmm) REVERT: C 431 GLU cc_start: 0.8330 (mp0) cc_final: 0.7898 (mp0) REVERT: C 585 MET cc_start: 0.8484 (mmt) cc_final: 0.7569 (mmt) REVERT: C 619 ASN cc_start: 0.8591 (t0) cc_final: 0.8362 (t0) REVERT: C 661 ARG cc_start: 0.8245 (ptm-80) cc_final: 0.7861 (tmt170) REVERT: C 768 TYR cc_start: 0.7195 (m-80) cc_final: 0.6985 (m-80) REVERT: C 1022 PHE cc_start: 0.8045 (m-80) cc_final: 0.6961 (m-80) REVERT: C 1172 LEU cc_start: 0.9201 (mm) cc_final: 0.8912 (tp) REVERT: C 1219 CYS cc_start: 0.8717 (m) cc_final: 0.8298 (m) REVERT: C 1224 SER cc_start: 0.8979 (t) cc_final: 0.8603 (p) REVERT: D 411 ASN cc_start: 0.7413 (t0) cc_final: 0.7165 (t0) REVERT: D 456 ASP cc_start: 0.6830 (m-30) cc_final: 0.6618 (m-30) REVERT: D 503 MET cc_start: 0.9009 (tmm) cc_final: 0.8638 (tmm) REVERT: D 543 VAL cc_start: 0.8108 (t) cc_final: 0.7576 (t) REVERT: D 590 ASP cc_start: 0.7565 (p0) cc_final: 0.7178 (m-30) REVERT: D 591 ILE cc_start: 0.8435 (pt) cc_final: 0.8123 (pt) REVERT: D 597 SER cc_start: 0.8675 (p) cc_final: 0.8280 (p) REVERT: D 693 VAL cc_start: 0.8916 (t) cc_final: 0.8563 (t) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1012 time to fit residues: 62.9878 Evaluate side-chains 303 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 110 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 128 optimal weight: 0.0570 chunk 178 optimal weight: 0.5980 chunk 184 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.083401 restraints weight = 44618.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084350 restraints weight = 31536.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085081 restraints weight = 22875.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085402 restraints weight = 19795.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085471 restraints weight = 19721.547| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16100 Z= 0.109 Angle : 0.556 8.848 21766 Z= 0.287 Chirality : 0.041 0.292 2442 Planarity : 0.004 0.052 2682 Dihedral : 5.123 88.516 2198 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1990 helix: 1.59 (0.16), residues: 1094 sheet: -0.34 (0.38), residues: 168 loop : -0.96 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 715 TYR 0.016 0.001 TYR C 424 PHE 0.036 0.001 PHE A1022 TRP 0.013 0.001 TRP C1032 HIS 0.005 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00246 (16094) covalent geometry : angle 0.55583 (21754) SS BOND : bond 0.00101 ( 6) SS BOND : angle 0.79402 ( 12) hydrogen bonds : bond 0.03185 ( 850) hydrogen bonds : angle 4.05239 ( 2496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.8512 (mmt) cc_final: 0.7673 (mmt) REVERT: A 637 GLU cc_start: 0.7975 (tt0) cc_final: 0.7385 (mp0) REVERT: A 661 ARG cc_start: 0.8326 (ptm-80) cc_final: 0.8021 (ttp80) REVERT: A 805 LEU cc_start: 0.9119 (mt) cc_final: 0.8606 (tt) REVERT: A 1022 PHE cc_start: 0.7990 (m-80) cc_final: 0.6806 (m-80) REVERT: A 1172 LEU cc_start: 0.9263 (mm) cc_final: 0.8941 (tp) REVERT: A 1219 CYS cc_start: 0.8759 (m) cc_final: 0.8139 (m) REVERT: B 407 MET cc_start: 0.7514 (mtp) cc_final: 0.7165 (mtp) REVERT: B 479 LEU cc_start: 0.8679 (tp) cc_final: 0.8317 (mp) REVERT: B 503 MET cc_start: 0.9038 (tmm) cc_final: 0.8661 (tmm) REVERT: B 542 LEU cc_start: 0.8415 (mp) cc_final: 0.8114 (pp) REVERT: B 543 VAL cc_start: 0.8180 (t) cc_final: 0.7723 (t) REVERT: B 546 PHE cc_start: 0.6418 (m-10) cc_final: 0.5501 (m-80) REVERT: B 585 MET cc_start: 0.8593 (mmm) cc_final: 0.8295 (mmm) REVERT: B 637 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7733 (tm-30) REVERT: B 657 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7531 (mm-30) REVERT: B 670 MET cc_start: 0.8622 (mtp) cc_final: 0.7828 (ptp) REVERT: B 693 VAL cc_start: 0.8784 (t) cc_final: 0.8375 (t) REVERT: B 760 ASP cc_start: 0.8141 (m-30) cc_final: 0.7824 (m-30) REVERT: B 761 LYS cc_start: 0.8594 (mtpp) cc_final: 0.7888 (mtmm) REVERT: C 431 GLU cc_start: 0.8342 (mp0) cc_final: 0.7887 (mp0) REVERT: C 508 GLN cc_start: 0.5650 (mm110) cc_final: 0.5380 (pp30) REVERT: C 585 MET cc_start: 0.8491 (mmt) cc_final: 0.7633 (mmt) REVERT: C 661 ARG cc_start: 0.8276 (ptm-80) cc_final: 0.7886 (tmt170) REVERT: C 1022 PHE cc_start: 0.8032 (m-80) cc_final: 0.7016 (m-80) REVERT: C 1172 LEU cc_start: 0.9159 (mm) cc_final: 0.8937 (tp) REVERT: C 1182 MET cc_start: 0.7829 (mmt) cc_final: 0.7283 (mmp) REVERT: C 1219 CYS cc_start: 0.8702 (m) cc_final: 0.8131 (m) REVERT: C 1224 SER cc_start: 0.8859 (t) cc_final: 0.8459 (p) REVERT: D 456 ASP cc_start: 0.6897 (m-30) cc_final: 0.6669 (m-30) REVERT: D 479 LEU cc_start: 0.8542 (mt) cc_final: 0.8326 (mt) REVERT: D 503 MET cc_start: 0.9016 (tmm) cc_final: 0.8597 (tmm) REVERT: D 543 VAL cc_start: 0.7954 (t) cc_final: 0.7719 (t) REVERT: D 585 MET cc_start: 0.8608 (mmm) cc_final: 0.8278 (mmm) REVERT: D 590 ASP cc_start: 0.7518 (p0) cc_final: 0.7154 (m-30) REVERT: D 591 ILE cc_start: 0.8436 (pt) cc_final: 0.8161 (pt) REVERT: D 597 SER cc_start: 0.8654 (p) cc_final: 0.8289 (p) REVERT: D 693 VAL cc_start: 0.8899 (t) cc_final: 0.8547 (t) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.1040 time to fit residues: 65.9006 Evaluate side-chains 311 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 52 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 45 optimal weight: 0.0030 chunk 91 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 133 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 overall best weight: 0.5308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1186 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.083149 restraints weight = 44812.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084203 restraints weight = 30346.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084793 restraints weight = 22754.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.085311 restraints weight = 21972.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085382 restraints weight = 19761.033| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16100 Z= 0.111 Angle : 0.561 8.673 21766 Z= 0.291 Chirality : 0.041 0.302 2442 Planarity : 0.004 0.053 2682 Dihedral : 5.072 88.413 2198 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1990 helix: 1.62 (0.16), residues: 1094 sheet: -0.15 (0.37), residues: 166 loop : -0.91 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1038 TYR 0.016 0.001 TYR C 424 PHE 0.034 0.001 PHE A1022 TRP 0.013 0.001 TRP C1032 HIS 0.005 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00249 (16094) covalent geometry : angle 0.56093 (21754) SS BOND : bond 0.00094 ( 6) SS BOND : angle 0.58167 ( 12) hydrogen bonds : bond 0.03187 ( 850) hydrogen bonds : angle 4.01470 ( 2496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7036 (tpp) cc_final: 0.6697 (tpt) REVERT: A 585 MET cc_start: 0.8495 (mmt) cc_final: 0.7672 (mmt) REVERT: A 637 GLU cc_start: 0.7835 (tt0) cc_final: 0.7371 (mp0) REVERT: A 661 ARG cc_start: 0.8311 (ptm-80) cc_final: 0.7935 (tmt170) REVERT: A 770 LYS cc_start: 0.6792 (mptt) cc_final: 0.6466 (mppt) REVERT: A 805 LEU cc_start: 0.9103 (mt) cc_final: 0.8602 (tt) REVERT: A 1022 PHE cc_start: 0.7981 (m-80) cc_final: 0.6954 (m-80) REVERT: A 1122 LYS cc_start: 0.7552 (mmtm) cc_final: 0.7316 (mmmt) REVERT: A 1172 LEU cc_start: 0.9231 (mm) cc_final: 0.8917 (tp) REVERT: A 1175 LEU cc_start: 0.9204 (mt) cc_final: 0.8970 (tp) REVERT: A 1219 CYS cc_start: 0.8781 (m) cc_final: 0.8170 (m) REVERT: B 407 MET cc_start: 0.7523 (mtp) cc_final: 0.7174 (mtp) REVERT: B 479 LEU cc_start: 0.8719 (tp) cc_final: 0.8424 (mp) REVERT: B 503 MET cc_start: 0.9017 (tmm) cc_final: 0.8629 (tmm) REVERT: B 504 ILE cc_start: 0.9156 (pt) cc_final: 0.8911 (pt) REVERT: B 542 LEU cc_start: 0.8433 (mp) cc_final: 0.8166 (pp) REVERT: B 543 VAL cc_start: 0.8191 (t) cc_final: 0.7722 (t) REVERT: B 546 PHE cc_start: 0.6494 (m-10) cc_final: 0.5618 (m-80) REVERT: B 585 MET cc_start: 0.8650 (mmm) cc_final: 0.8080 (mmm) REVERT: B 637 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7737 (tm-30) REVERT: B 657 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 670 MET cc_start: 0.8612 (mtp) cc_final: 0.7824 (ptp) REVERT: B 693 VAL cc_start: 0.8710 (t) cc_final: 0.8309 (t) REVERT: B 760 ASP cc_start: 0.8145 (m-30) cc_final: 0.7819 (m-30) REVERT: B 761 LYS cc_start: 0.8570 (mtpp) cc_final: 0.7867 (mtmm) REVERT: B 764 ASN cc_start: 0.9043 (t0) cc_final: 0.8831 (t0) REVERT: C 431 GLU cc_start: 0.8277 (mp0) cc_final: 0.7838 (mp0) REVERT: C 585 MET cc_start: 0.8485 (mmt) cc_final: 0.7610 (mmt) REVERT: C 637 GLU cc_start: 0.8112 (tt0) cc_final: 0.7687 (tp30) REVERT: C 661 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.7858 (tmt170) REVERT: C 734 ILE cc_start: 0.9061 (mt) cc_final: 0.8859 (mt) REVERT: C 805 LEU cc_start: 0.9018 (mt) cc_final: 0.8487 (tt) REVERT: C 1022 PHE cc_start: 0.8062 (m-80) cc_final: 0.7040 (m-80) REVERT: C 1182 MET cc_start: 0.7764 (mmt) cc_final: 0.7212 (mmt) REVERT: C 1219 CYS cc_start: 0.8662 (m) cc_final: 0.8121 (m) REVERT: D 411 ASN cc_start: 0.7635 (t0) cc_final: 0.7430 (t0) REVERT: D 456 ASP cc_start: 0.6833 (m-30) cc_final: 0.6579 (m-30) REVERT: D 479 LEU cc_start: 0.8545 (mt) cc_final: 0.8340 (mt) REVERT: D 503 MET cc_start: 0.8994 (tmm) cc_final: 0.8572 (tmm) REVERT: D 543 VAL cc_start: 0.8016 (t) cc_final: 0.7790 (t) REVERT: D 585 MET cc_start: 0.8564 (mmm) cc_final: 0.8170 (mmm) REVERT: D 590 ASP cc_start: 0.7560 (p0) cc_final: 0.7202 (m-30) REVERT: D 591 ILE cc_start: 0.8452 (pt) cc_final: 0.8183 (pt) REVERT: D 597 SER cc_start: 0.8677 (p) cc_final: 0.8303 (p) REVERT: D 693 VAL cc_start: 0.8900 (t) cc_final: 0.8553 (t) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.0978 time to fit residues: 60.7530 Evaluate side-chains 297 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 3 optimal weight: 3.9990 chunk 117 optimal weight: 0.0770 chunk 161 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 178 optimal weight: 0.6980 chunk 176 optimal weight: 0.0370 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.105785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083625 restraints weight = 44878.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084615 restraints weight = 30846.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085258 restraints weight = 23124.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085467 restraints weight = 21776.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085623 restraints weight = 20192.957| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16100 Z= 0.110 Angle : 0.567 8.196 21766 Z= 0.292 Chirality : 0.041 0.308 2442 Planarity : 0.004 0.052 2682 Dihedral : 5.042 88.395 2198 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1990 helix: 1.65 (0.16), residues: 1094 sheet: -0.29 (0.39), residues: 150 loop : -0.92 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1038 TYR 0.017 0.001 TYR A 424 PHE 0.037 0.001 PHE A1022 TRP 0.014 0.001 TRP A1032 HIS 0.005 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00247 (16094) covalent geometry : angle 0.56654 (21754) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.79682 ( 12) hydrogen bonds : bond 0.03203 ( 850) hydrogen bonds : angle 4.02379 ( 2496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.8491 (mmt) cc_final: 0.7658 (mmt) REVERT: A 637 GLU cc_start: 0.7811 (tt0) cc_final: 0.7273 (mp0) REVERT: A 661 ARG cc_start: 0.8291 (ptm-80) cc_final: 0.7909 (tmt170) REVERT: A 770 LYS cc_start: 0.6766 (mptt) cc_final: 0.6493 (mppt) REVERT: A 805 LEU cc_start: 0.9097 (mt) cc_final: 0.8589 (tt) REVERT: A 1022 PHE cc_start: 0.7916 (m-80) cc_final: 0.7584 (m-80) REVERT: A 1024 THR cc_start: 0.8608 (m) cc_final: 0.8357 (p) REVERT: A 1122 LYS cc_start: 0.7547 (mmtm) cc_final: 0.7317 (mmmt) REVERT: A 1219 CYS cc_start: 0.8675 (m) cc_final: 0.8216 (m) REVERT: B 407 MET cc_start: 0.7383 (mtp) cc_final: 0.7089 (mtp) REVERT: B 418 ASN cc_start: 0.6517 (m-40) cc_final: 0.4945 (p0) REVERT: B 479 LEU cc_start: 0.8674 (tp) cc_final: 0.8410 (mp) REVERT: B 503 MET cc_start: 0.8943 (tmm) cc_final: 0.8610 (tmm) REVERT: B 542 LEU cc_start: 0.8401 (mp) cc_final: 0.8136 (pp) REVERT: B 543 VAL cc_start: 0.8189 (t) cc_final: 0.7727 (t) REVERT: B 546 PHE cc_start: 0.6576 (m-10) cc_final: 0.5696 (m-80) REVERT: B 637 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7749 (tm-30) REVERT: B 657 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7510 (mm-30) REVERT: B 693 VAL cc_start: 0.8770 (t) cc_final: 0.8210 (t) REVERT: B 760 ASP cc_start: 0.8047 (m-30) cc_final: 0.7740 (m-30) REVERT: B 761 LYS cc_start: 0.8548 (mtpp) cc_final: 0.7840 (mtmm) REVERT: B 764 ASN cc_start: 0.9033 (t0) cc_final: 0.8806 (t0) REVERT: C 431 GLU cc_start: 0.8250 (mp0) cc_final: 0.7835 (mp0) REVERT: C 637 GLU cc_start: 0.8064 (tt0) cc_final: 0.7675 (tp30) REVERT: C 661 ARG cc_start: 0.8216 (ptm-80) cc_final: 0.7836 (tmt170) REVERT: C 770 LYS cc_start: 0.6669 (mptt) cc_final: 0.5794 (pttt) REVERT: C 805 LEU cc_start: 0.8988 (mt) cc_final: 0.8457 (tt) REVERT: C 1022 PHE cc_start: 0.8000 (m-80) cc_final: 0.7027 (m-80) REVERT: C 1024 THR cc_start: 0.8674 (m) cc_final: 0.8446 (p) REVERT: C 1172 LEU cc_start: 0.9205 (mm) cc_final: 0.8774 (tt) REVERT: C 1182 MET cc_start: 0.7814 (mmt) cc_final: 0.7291 (mmt) REVERT: C 1219 CYS cc_start: 0.8711 (m) cc_final: 0.8169 (m) REVERT: D 456 ASP cc_start: 0.6939 (m-30) cc_final: 0.6732 (m-30) REVERT: D 503 MET cc_start: 0.8990 (tmm) cc_final: 0.8577 (tmm) REVERT: D 543 VAL cc_start: 0.8029 (t) cc_final: 0.7805 (m) REVERT: D 585 MET cc_start: 0.8496 (mmm) cc_final: 0.8162 (mmm) REVERT: D 590 ASP cc_start: 0.7586 (p0) cc_final: 0.7254 (m-30) REVERT: D 591 ILE cc_start: 0.8466 (pt) cc_final: 0.8193 (pt) REVERT: D 597 SER cc_start: 0.8691 (p) cc_final: 0.8374 (p) REVERT: D 693 VAL cc_start: 0.8882 (t) cc_final: 0.8544 (t) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.1002 time to fit residues: 60.2587 Evaluate side-chains 295 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.105313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.083399 restraints weight = 44567.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084391 restraints weight = 30055.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085068 restraints weight = 22544.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085505 restraints weight = 21632.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085629 restraints weight = 19570.049| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16100 Z= 0.116 Angle : 0.570 7.961 21766 Z= 0.294 Chirality : 0.041 0.312 2442 Planarity : 0.004 0.052 2682 Dihedral : 5.051 88.823 2198 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1990 helix: 1.63 (0.16), residues: 1106 sheet: -0.20 (0.39), residues: 150 loop : -0.99 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1038 TYR 0.017 0.001 TYR A 424 PHE 0.038 0.001 PHE A1022 TRP 0.015 0.001 TRP A1032 HIS 0.007 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00263 (16094) covalent geometry : angle 0.56950 (21754) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.75131 ( 12) hydrogen bonds : bond 0.03252 ( 850) hydrogen bonds : angle 4.01942 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.63 seconds wall clock time: 45 minutes 26.38 seconds (2726.38 seconds total)