Starting phenix.real_space_refine on Tue Dec 31 13:54:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ryz_24749/12_2024/7ryz_24749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryz_24749/12_2024/7ryz_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_24749/12_2024/7ryz_24749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryz_24749/12_2024/7ryz_24749.map" model { file = "/net/cci-nas-00/data/ceres_data/7ryz_24749/12_2024/7ryz_24749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryz_24749/12_2024/7ryz_24749.cif" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.41, per 1000 atoms: 0.60 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: 3.86 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.73 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: 5.31 Time building geometry restraints manager: 4.45 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: 0.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.460 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.230 ------------------------------------------------------------------------------- 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 16094 Z= 0.475 Angle : 0.980 13.680 21754 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 : 4.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.003 TRP A1032 HIS 0.004 0.002 HIS C1092 PHE 0.021 0.002 PHE D 574 TYR 0.021 0.002 TYR C1135 ARG 0.010 0.001 ARG A 599 *********************** 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 : 1.753 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: 0.8603 (mt) REVERT: A 434 LYS cc_start: 0.8915 (tptt) cc_final: 0.8454 (tmmt) REVERT: A 435 HIS cc_start: 0.7819 (t-90) cc_final: 0.7581 (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: 0.7098 (mmmt) REVERT: A 537 SER cc_start: 0.9256 (p) cc_final: 0.8485 (t) REVERT: A 585 MET cc_start: 0.8203 (mmt) cc_final: 0.7775 (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: 0.8807 (p) REVERT: A 637 GLU cc_start: 0.8190 (tt0) cc_final: 0.7628 (tp30) REVERT: A 642 GLN cc_start: 0.7326 (tt0) cc_final: 0.7006 (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: 0.8458 (mt) REVERT: A 1016 ASN cc_start: 0.8338 (m-40) cc_final: 0.7754 (t0) REVERT: A 1022 PHE cc_start: 0.8235 (m-10) cc_final: 0.7150 (m-10) REVERT: A 1131 SER cc_start: 0.9290 (m) cc_final: 0.9085 (p) REVERT: A 1141 VAL cc_start: 0.8890 (t) cc_final: 0.8673 (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: 0.8286 (m) REVERT: B 407 MET cc_start: 0.8413 (mtp) cc_final: 0.8051 (mtp) REVERT: B 408 MET cc_start: 0.7183 (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: 0.8760 (pt) REVERT: B 504 ILE cc_start: 0.8946 (pt) cc_final: 0.8634 (pt) REVERT: B 505 LYS cc_start: 0.7833 (tmtm) cc_final: 0.7252 (tptp) REVERT: B 506 LYS cc_start: 0.7906 (ttmp) cc_final: 0.7573 (mtpt) REVERT: B 509 LYS cc_start: 0.7725 (pmtt) cc_final: 0.7174 (tppt) REVERT: B 637 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7854 (tm-30) REVERT: B 670 MET cc_start: 0.8816 (mtp) cc_final: 0.8317 (mtp) REVERT: B 761 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7689 (pttt) REVERT: B 807 MET cc_start: 0.9199 (mmm) cc_final: 0.8657 (mmt) REVERT: C 399 THR cc_start: 0.8006 (t) cc_final: 0.7792 (t) REVERT: C 408 MET cc_start: 0.6750 (tpp) cc_final: 0.6242 (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: 0.7308 (t-170) REVERT: C 537 SER cc_start: 0.9218 (p) cc_final: 0.8410 (t) REVERT: C 540 LEU cc_start: 0.9181 (tt) cc_final: 0.8969 (mm) REVERT: C 585 MET cc_start: 0.8451 (mmt) cc_final: 0.7885 (mmt) REVERT: C 591 ILE cc_start: 0.8350 (mp) cc_final: 0.7969 (mt) REVERT: C 626 VAL cc_start: 0.9100 (t) cc_final: 0.8779 (p) REVERT: C 637 GLU cc_start: 0.8316 (tt0) cc_final: 0.7421 (mp0) REVERT: C 709 ASN cc_start: 0.8712 (t0) cc_final: 0.8139 (t0) REVERT: C 710 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8540 (mt-10) REVERT: C 714 GLN cc_start: 0.7352 (mt0) cc_final: 0.6352 (tp40) REVERT: C 720 THR cc_start: 0.8071 (p) cc_final: 0.7010 (p) REVERT: C 728 ASP cc_start: 0.7544 (t70) cc_final: 0.6763 (t70) REVERT: C 1016 ASN cc_start: 0.8676 (m-40) cc_final: 0.8331 (t0) REVERT: C 1022 PHE cc_start: 0.8333 (m-10) cc_final: 0.7397 (m-10) REVERT: C 1175 LEU cc_start: 0.9327 (mt) cc_final: 0.9043 (mt) REVERT: C 1219 CYS cc_start: 0.8562 (m) cc_final: 0.7983 (m) REVERT: D 408 MET cc_start: 0.7245 (mmm) cc_final: 0.6945 (mmm) REVERT: D 418 ASN cc_start: 0.6580 (m-40) cc_final: 0.4628 (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: 0.8662 (mt) REVERT: D 509 LYS cc_start: 0.7906 (pmtt) cc_final: 0.7510 (tppt) REVERT: D 569 ASN cc_start: 0.5652 (m-40) cc_final: 0.5202 (m-40) REVERT: D 590 ASP cc_start: 0.7646 (p0) cc_final: 0.7371 (m-30) REVERT: D 591 ILE cc_start: 0.8505 (pt) cc_final: 0.8279 (pt) REVERT: D 710 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8115 (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: 0.8693 (mmt) outliers start: 4 outliers final: 2 residues processed: 655 average time/residue: 0.2971 time to fit residues: 280.4400 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 : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 60 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16094 Z= 0.176 Angle : 0.590 6.500 21754 Z= 0.315 Chirality : 0.041 0.152 2442 Planarity : 0.005 0.047 2682 Dihedral : 7.233 88.395 2198 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 1990 helix: -0.67 (0.14), residues: 1082 sheet: -1.69 (0.36), residues: 174 loop : -1.77 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 766 HIS 0.005 0.001 HIS A1181 PHE 0.016 0.001 PHE C 574 TYR 0.021 0.002 TYR A 732 ARG 0.005 0.001 ARG C 453 *********************** 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 503 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 501 time to evaluate : 1.785 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: A 434 LYS cc_start: 0.8855 (tptt) cc_final: 0.8494 (tmmt) REVERT: A 504 ILE cc_start: 0.8811 (tp) cc_final: 0.8419 (tp) REVERT: A 580 SER cc_start: 0.9088 (t) cc_final: 0.8885 (t) REVERT: A 585 MET cc_start: 0.8428 (mmt) cc_final: 0.7747 (mmt) REVERT: A 589 CYS cc_start: 0.7029 (t) cc_final: 0.6547 (t) REVERT: A 591 ILE cc_start: 0.8236 (mp) cc_final: 0.7863 (pt) REVERT: A 619 ASN cc_start: 0.8676 (t0) cc_final: 0.8361 (t0) REVERT: A 637 GLU cc_start: 0.8085 (tt0) cc_final: 0.7725 (tp30) REVERT: A 661 ARG cc_start: 0.8404 (ptm-80) cc_final: 0.8138 (ttp80) REVERT: A 708 MET cc_start: 0.8227 (mpp) cc_final: 0.7190 (mtt) REVERT: A 805 LEU cc_start: 0.8932 (mt) cc_final: 0.8428 (tt) REVERT: A 1022 PHE cc_start: 0.8480 (m-10) cc_final: 0.8179 (m-10) REVERT: A 1169 PHE cc_start: 0.8168 (m-80) cc_final: 0.7929 (m-80) REVERT: A 1170 THR cc_start: 0.8611 (p) cc_final: 0.8341 (t) REVERT: A 1175 LEU cc_start: 0.9350 (mt) cc_final: 0.8886 (tp) REVERT: A 1219 CYS cc_start: 0.8862 (m) cc_final: 0.8464 (m) REVERT: B 407 MET cc_start: 0.8209 (mtp) cc_final: 0.7912 (mtp) REVERT: B 414 MET cc_start: 0.6893 (ttm) cc_final: 0.6647 (ttp) REVERT: B 503 MET cc_start: 0.8920 (tmm) cc_final: 0.8593 (tmm) REVERT: B 542 LEU cc_start: 0.8651 (mt) cc_final: 0.8372 (mp) REVERT: B 633 ILE cc_start: 0.8786 (pt) cc_final: 0.8050 (pt) REVERT: B 637 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7879 (tm-30) REVERT: B 638 ASP cc_start: 0.7211 (m-30) cc_final: 0.6945 (t0) REVERT: B 761 LYS cc_start: 0.8506 (mtpp) cc_final: 0.7683 (mtmm) REVERT: C 434 LYS cc_start: 0.8938 (tptt) cc_final: 0.8595 (tmmt) REVERT: C 504 ILE cc_start: 0.8757 (tp) cc_final: 0.8401 (tp) REVERT: C 585 MET cc_start: 0.8529 (mmt) cc_final: 0.7775 (mmt) REVERT: C 589 CYS cc_start: 0.7517 (t) cc_final: 0.7242 (t) REVERT: C 591 ILE cc_start: 0.8228 (mp) cc_final: 0.7865 (pt) REVERT: C 611 ILE cc_start: 0.9401 (mm) cc_final: 0.9165 (mm) REVERT: C 637 GLU cc_start: 0.8168 (tt0) cc_final: 0.7488 (mp0) REVERT: C 720 THR cc_start: 0.8418 (p) cc_final: 0.6890 (p) REVERT: C 732 TYR cc_start: 0.8374 (m-10) cc_final: 0.8050 (m-10) REVERT: C 755 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7473 (tm-30) REVERT: C 756 GLN cc_start: 0.8604 (tt0) cc_final: 0.8162 (tt0) REVERT: C 770 LYS cc_start: 0.6402 (mppt) cc_final: 0.5750 (pttt) REVERT: C 808 LEU cc_start: 0.8705 (mt) cc_final: 0.8440 (mm) REVERT: C 1022 PHE cc_start: 0.8559 (m-10) cc_final: 0.8321 (m-10) REVERT: C 1169 PHE cc_start: 0.8251 (m-80) cc_final: 0.7858 (m-80) REVERT: C 1172 LEU cc_start: 0.9219 (mm) cc_final: 0.8992 (tp) REVERT: C 1211 CYS cc_start: 0.9024 (p) cc_final: 0.8586 (p) REVERT: C 1219 CYS cc_start: 0.8716 (m) cc_final: 0.8245 (m) REVERT: D 408 MET cc_start: 0.7100 (mmm) cc_final: 0.6857 (mmm) REVERT: D 411 ASN cc_start: 0.7302 (t0) cc_final: 0.7056 (t0) REVERT: D 418 ASN cc_start: 0.6669 (m-40) cc_final: 0.5300 (p0) REVERT: D 432 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8544 (tp) REVERT: D 442 LEU cc_start: 0.8053 (mt) cc_final: 0.7706 (mm) REVERT: D 503 MET cc_start: 0.8682 (tmm) cc_final: 0.8462 (tmm) REVERT: D 590 ASP cc_start: 0.7592 (p0) cc_final: 0.7266 (m-30) REVERT: D 597 SER cc_start: 0.8747 (p) cc_final: 0.8188 (m) REVERT: D 670 MET cc_start: 0.8300 (mtm) cc_final: 0.7972 (mtp) REVERT: D 710 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8304 (mt-10) REVERT: D 815 CYS cc_start: 0.7282 (m) cc_final: 0.6935 (t) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.2651 time to fit residues: 199.6416 Evaluate side-chains 321 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 151 optimal weight: 0.0170 chunk 123 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN 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 586 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16094 Z= 0.260 Angle : 0.614 7.297 21754 Z= 0.326 Chirality : 0.042 0.160 2442 Planarity : 0.004 0.056 2682 Dihedral : 6.799 88.815 2198 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 1990 helix: 0.47 (0.15), residues: 1082 sheet: -1.46 (0.39), residues: 156 loop : -1.61 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C1032 HIS 0.005 0.001 HIS C1181 PHE 0.018 0.002 PHE C 623 TYR 0.022 0.002 TYR A 732 ARG 0.005 0.000 ARG A 545 *********************** 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 427 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 426 time to evaluate : 1.736 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 434 LYS cc_start: 0.8855 (tptt) cc_final: 0.8533 (tmmt) REVERT: A 585 MET cc_start: 0.8481 (mmt) cc_final: 0.7883 (mmt) REVERT: A 589 CYS cc_start: 0.7339 (t) cc_final: 0.6684 (t) REVERT: A 591 ILE cc_start: 0.8199 (mp) cc_final: 0.7884 (pt) REVERT: A 619 ASN cc_start: 0.8737 (t0) cc_final: 0.8420 (t0) REVERT: A 656 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8340 (ttmt) REVERT: A 805 LEU cc_start: 0.8990 (mt) cc_final: 0.8437 (tt) REVERT: A 1022 PHE cc_start: 0.8531 (m-10) cc_final: 0.8196 (m-10) REVERT: A 1143 PHE cc_start: 0.8323 (p90) cc_final: 0.7911 (p90) REVERT: A 1169 PHE cc_start: 0.8119 (m-80) cc_final: 0.7762 (m-80) REVERT: A 1175 LEU cc_start: 0.9273 (mt) cc_final: 0.8999 (tp) REVERT: A 1219 CYS cc_start: 0.8785 (m) cc_final: 0.8245 (m) REVERT: B 407 MET cc_start: 0.8108 (mtp) cc_final: 0.7745 (mtp) REVERT: B 503 MET cc_start: 0.8954 (tmm) cc_final: 0.8573 (tmm) REVERT: B 504 ILE cc_start: 0.9215 (pt) cc_final: 0.8854 (pt) REVERT: B 546 PHE cc_start: 0.6407 (m-10) cc_final: 0.5854 (m-80) REVERT: B 637 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7942 (tm-30) REVERT: B 657 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7603 (tp30) REVERT: B 721 MET cc_start: 0.8804 (ptt) cc_final: 0.8157 (ppp) REVERT: B 761 LYS cc_start: 0.8678 (mtpp) cc_final: 0.7883 (mtmm) REVERT: B 764 ASN cc_start: 0.9073 (t0) cc_final: 0.8810 (t0) REVERT: C 434 LYS cc_start: 0.8913 (tptt) cc_final: 0.8555 (tmmt) REVERT: C 585 MET cc_start: 0.8632 (mmt) cc_final: 0.7937 (mmt) REVERT: C 619 ASN cc_start: 0.8618 (t0) cc_final: 0.8393 (t0) REVERT: C 637 GLU cc_start: 0.8189 (tt0) cc_final: 0.7401 (mp0) REVERT: C 647 TYR cc_start: 0.5587 (m-80) cc_final: 0.5208 (m-80) REVERT: C 755 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7478 (tm-30) REVERT: C 756 GLN cc_start: 0.8661 (tt0) cc_final: 0.8194 (tt0) REVERT: C 808 LEU cc_start: 0.8720 (mt) cc_final: 0.8475 (mm) REVERT: C 815 CYS cc_start: 0.7298 (m) cc_final: 0.6994 (t) REVERT: C 1022 PHE cc_start: 0.8647 (m-10) cc_final: 0.8438 (m-10) REVERT: C 1169 PHE cc_start: 0.8258 (m-80) cc_final: 0.7829 (m-80) REVERT: C 1182 MET cc_start: 0.8191 (mmt) cc_final: 0.7950 (mmt) REVERT: C 1211 CYS cc_start: 0.9129 (p) cc_final: 0.8741 (p) REVERT: C 1219 CYS cc_start: 0.8767 (m) cc_final: 0.8288 (m) REVERT: D 411 ASN cc_start: 0.7251 (t0) cc_final: 0.6940 (t0) REVERT: D 418 ASN cc_start: 0.6683 (m-40) cc_final: 0.5363 (p0) REVERT: D 432 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8554 (tp) REVERT: D 456 ASP cc_start: 0.6863 (m-30) cc_final: 0.6635 (m-30) REVERT: D 479 LEU cc_start: 0.8635 (mt) cc_final: 0.8252 (mp) REVERT: D 503 MET cc_start: 0.8751 (tmm) cc_final: 0.8290 (tmm) REVERT: D 569 ASN cc_start: 0.5680 (m-40) cc_final: 0.5446 (m110) REVERT: D 590 ASP cc_start: 0.7669 (p0) cc_final: 0.7143 (m-30) REVERT: D 591 ILE cc_start: 0.8389 (pt) cc_final: 0.8126 (pt) REVERT: D 670 MET cc_start: 0.8356 (mtm) cc_final: 0.8139 (ttm) REVERT: D 721 MET cc_start: 0.8103 (ppp) cc_final: 0.7741 (ppp) REVERT: D 815 CYS cc_start: 0.7365 (m) cc_final: 0.7060 (t) outliers start: 1 outliers final: 0 residues processed: 426 average time/residue: 0.2424 time to fit residues: 159.4782 Evaluate side-chains 300 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16094 Z= 0.190 Angle : 0.556 6.415 21754 Z= 0.292 Chirality : 0.040 0.144 2442 Planarity : 0.004 0.053 2682 Dihedral : 6.175 85.737 2198 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 1990 helix: 1.06 (0.16), residues: 1092 sheet: -1.41 (0.39), residues: 166 loop : -1.51 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1032 HIS 0.005 0.001 HIS C1181 PHE 0.020 0.001 PHE A1143 TYR 0.023 0.001 TYR A 732 ARG 0.002 0.000 ARG A 545 *********************** 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 431 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 430 time to evaluate : 1.806 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: A 434 LYS cc_start: 0.8835 (tptt) cc_final: 0.8503 (tmmt) REVERT: A 585 MET cc_start: 0.8563 (mmt) cc_final: 0.7805 (mmt) REVERT: A 589 CYS cc_start: 0.7199 (t) cc_final: 0.6497 (t) REVERT: A 591 ILE cc_start: 0.8230 (mp) cc_final: 0.7941 (pt) REVERT: A 619 ASN cc_start: 0.8693 (t0) cc_final: 0.8413 (t0) REVERT: A 637 GLU cc_start: 0.8100 (tt0) cc_final: 0.7728 (tp30) REVERT: A 805 LEU cc_start: 0.8999 (mt) cc_final: 0.8501 (tt) REVERT: A 1169 PHE cc_start: 0.8034 (m-80) cc_final: 0.7786 (m-80) REVERT: A 1219 CYS cc_start: 0.8692 (m) cc_final: 0.8239 (m) REVERT: B 407 MET cc_start: 0.7983 (mtp) cc_final: 0.7668 (mtp) REVERT: B 425 CYS cc_start: 0.8183 (m) cc_final: 0.7973 (m) REVERT: B 503 MET cc_start: 0.9033 (tmm) cc_final: 0.8592 (tmm) REVERT: B 504 ILE cc_start: 0.9204 (pt) cc_final: 0.8747 (pt) REVERT: B 542 LEU cc_start: 0.8444 (mp) cc_final: 0.8194 (mt) REVERT: B 546 PHE cc_start: 0.6374 (m-10) cc_final: 0.5828 (m-80) REVERT: B 637 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7936 (tm-30) REVERT: B 657 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7601 (tp30) REVERT: B 670 MET cc_start: 0.8314 (mtm) cc_final: 0.8083 (ttm) REVERT: B 693 VAL cc_start: 0.8719 (t) cc_final: 0.8495 (t) REVERT: B 720 THR cc_start: 0.8061 (p) cc_final: 0.7824 (p) REVERT: B 721 MET cc_start: 0.8811 (ptt) cc_final: 0.8151 (ppp) REVERT: B 761 LYS cc_start: 0.8648 (mtpp) cc_final: 0.7902 (mtmm) REVERT: B 764 ASN cc_start: 0.9028 (t0) cc_final: 0.8806 (t0) REVERT: C 434 LYS cc_start: 0.8896 (tptt) cc_final: 0.8589 (tmmt) REVERT: C 585 MET cc_start: 0.8570 (mmt) cc_final: 0.7763 (mmt) REVERT: C 619 ASN cc_start: 0.8592 (t0) cc_final: 0.8291 (t0) REVERT: C 637 GLU cc_start: 0.8182 (tt0) cc_final: 0.7378 (mp0) REVERT: C 647 TYR cc_start: 0.5351 (m-80) cc_final: 0.4847 (m-80) REVERT: C 734 ILE cc_start: 0.9045 (mt) cc_final: 0.8838 (mt) REVERT: C 755 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7491 (tm-30) REVERT: C 756 GLN cc_start: 0.8692 (tt0) cc_final: 0.8251 (tt0) REVERT: C 770 LYS cc_start: 0.7092 (mptt) cc_final: 0.6347 (pttt) REVERT: C 808 LEU cc_start: 0.8692 (mt) cc_final: 0.8464 (mm) REVERT: C 815 CYS cc_start: 0.7273 (m) cc_final: 0.6967 (t) REVERT: C 1022 PHE cc_start: 0.8618 (m-10) cc_final: 0.8415 (m-10) REVERT: C 1169 PHE cc_start: 0.8215 (m-80) cc_final: 0.7739 (m-80) REVERT: C 1211 CYS cc_start: 0.8963 (p) cc_final: 0.8564 (p) REVERT: C 1219 CYS cc_start: 0.8786 (m) cc_final: 0.8391 (m) REVERT: C 1224 SER cc_start: 0.8897 (t) cc_final: 0.8617 (p) REVERT: D 411 ASN cc_start: 0.7362 (t0) cc_final: 0.7079 (t0) REVERT: D 418 ASN cc_start: 0.6652 (m-40) cc_final: 0.5065 (p0) REVERT: D 432 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8469 (tp) REVERT: D 456 ASP cc_start: 0.6824 (m-30) cc_final: 0.6597 (m-30) REVERT: D 479 LEU cc_start: 0.8592 (mt) cc_final: 0.8381 (mt) REVERT: D 503 MET cc_start: 0.8797 (tmm) cc_final: 0.8315 (tmm) REVERT: D 569 ASN cc_start: 0.5612 (m-40) cc_final: 0.5389 (m110) REVERT: D 590 ASP cc_start: 0.7636 (p0) cc_final: 0.7136 (m-30) REVERT: D 591 ILE cc_start: 0.8384 (pt) cc_final: 0.8126 (pt) REVERT: D 597 SER cc_start: 0.8680 (p) cc_final: 0.8054 (m) REVERT: D 693 VAL cc_start: 0.8722 (t) cc_final: 0.8507 (t) REVERT: D 708 MET cc_start: 0.8539 (mmp) cc_final: 0.8267 (mmp) REVERT: D 765 LYS cc_start: 0.8237 (ptmm) cc_final: 0.7931 (ttpt) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.2434 time to fit residues: 162.1637 Evaluate side-chains 315 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16094 Z= 0.181 Angle : 0.552 10.420 21754 Z= 0.289 Chirality : 0.041 0.170 2442 Planarity : 0.004 0.052 2682 Dihedral : 5.628 82.961 2198 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1990 helix: 1.31 (0.16), residues: 1088 sheet: -1.08 (0.41), residues: 146 loop : -1.37 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1204 HIS 0.005 0.001 HIS C1181 PHE 0.039 0.001 PHE A1022 TYR 0.022 0.001 TYR A 732 ARG 0.003 0.000 ARG A 545 *********************** 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 417 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 415 time to evaluate : 1.765 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: A 431 GLU cc_start: 0.8180 (mp0) cc_final: 0.7801 (mp0) REVERT: A 434 LYS cc_start: 0.8834 (tptt) cc_final: 0.8555 (tmmt) REVERT: A 585 MET cc_start: 0.8540 (mmt) cc_final: 0.7718 (mmt) REVERT: A 589 CYS cc_start: 0.7219 (t) cc_final: 0.6569 (t) REVERT: A 591 ILE cc_start: 0.8242 (mp) cc_final: 0.7909 (pt) REVERT: A 619 ASN cc_start: 0.8693 (t0) cc_final: 0.8361 (t0) REVERT: A 805 LEU cc_start: 0.8967 (mt) cc_final: 0.8518 (tt) REVERT: A 1022 PHE cc_start: 0.8291 (m-80) cc_final: 0.7093 (m-80) REVERT: A 1034 GLN cc_start: 0.8646 (pm20) cc_final: 0.8370 (pm20) REVERT: A 1169 PHE cc_start: 0.8013 (m-80) cc_final: 0.7742 (m-80) REVERT: A 1181 HIS cc_start: 0.8835 (m90) cc_final: 0.8444 (m90) REVERT: A 1219 CYS cc_start: 0.8757 (m) cc_final: 0.8134 (m) REVERT: B 407 MET cc_start: 0.7856 (mtp) cc_final: 0.7525 (mtp) REVERT: B 425 CYS cc_start: 0.8062 (m) cc_final: 0.7827 (m) REVERT: B 479 LEU cc_start: 0.8738 (tp) cc_final: 0.8366 (mt) REVERT: B 503 MET cc_start: 0.9052 (tmm) cc_final: 0.8587 (tmm) REVERT: B 504 ILE cc_start: 0.9226 (pt) cc_final: 0.8778 (pt) REVERT: B 542 LEU cc_start: 0.8425 (mp) cc_final: 0.8189 (mp) REVERT: B 546 PHE cc_start: 0.6342 (m-10) cc_final: 0.5733 (m-80) REVERT: B 585 MET cc_start: 0.8845 (mmm) cc_final: 0.8380 (mmm) REVERT: B 637 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7897 (tm-30) REVERT: B 657 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7600 (tp30) REVERT: B 693 VAL cc_start: 0.8705 (t) cc_final: 0.8456 (t) REVERT: B 720 THR cc_start: 0.8040 (p) cc_final: 0.7742 (p) REVERT: B 721 MET cc_start: 0.8789 (ptt) cc_final: 0.8188 (ppp) REVERT: B 761 LYS cc_start: 0.8652 (mtpp) cc_final: 0.7956 (mtmm) REVERT: B 764 ASN cc_start: 0.9028 (t0) cc_final: 0.8780 (t0) REVERT: C 434 LYS cc_start: 0.8883 (tptt) cc_final: 0.8622 (tmmt) REVERT: C 504 ILE cc_start: 0.8901 (tp) cc_final: 0.8594 (tp) REVERT: C 585 MET cc_start: 0.8549 (mmt) cc_final: 0.7788 (mmt) REVERT: C 619 ASN cc_start: 0.8623 (t0) cc_final: 0.8340 (t0) REVERT: C 637 GLU cc_start: 0.8165 (tt0) cc_final: 0.7439 (mp0) REVERT: C 647 TYR cc_start: 0.5310 (m-80) cc_final: 0.4520 (m-80) REVERT: C 815 CYS cc_start: 0.7230 (m) cc_final: 0.6972 (t) REVERT: C 1099 CYS cc_start: 0.5092 (m) cc_final: 0.4584 (m) REVERT: C 1143 PHE cc_start: 0.8804 (p90) cc_final: 0.8510 (p90) REVERT: C 1169 PHE cc_start: 0.8074 (m-80) cc_final: 0.7680 (m-80) REVERT: C 1219 CYS cc_start: 0.8639 (m) cc_final: 0.8270 (m) REVERT: D 418 ASN cc_start: 0.6656 (m-40) cc_final: 0.5093 (p0) REVERT: D 456 ASP cc_start: 0.6798 (m-30) cc_final: 0.6570 (m-30) REVERT: D 503 MET cc_start: 0.8854 (tmm) cc_final: 0.8378 (tmm) REVERT: D 569 ASN cc_start: 0.5838 (m-40) cc_final: 0.5618 (m110) REVERT: D 585 MET cc_start: 0.8909 (mmm) cc_final: 0.8248 (mmm) REVERT: D 590 ASP cc_start: 0.7665 (p0) cc_final: 0.7151 (m-30) REVERT: D 591 ILE cc_start: 0.8366 (pt) cc_final: 0.8105 (pt) REVERT: D 597 SER cc_start: 0.8682 (p) cc_final: 0.8011 (m) REVERT: D 693 VAL cc_start: 0.8742 (t) cc_final: 0.8479 (t) REVERT: D 709 ASN cc_start: 0.9330 (OUTLIER) cc_final: 0.8883 (t0) REVERT: D 721 MET cc_start: 0.8021 (ppp) cc_final: 0.7685 (ppp) REVERT: D 765 LYS cc_start: 0.8242 (ptmm) cc_final: 0.7994 (ttpt) outliers start: 2 outliers final: 0 residues processed: 416 average time/residue: 0.2369 time to fit residues: 153.3885 Evaluate side-chains 321 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1186 GLN D 619 ASN D 709 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16094 Z= 0.214 Angle : 0.580 8.746 21754 Z= 0.304 Chirality : 0.042 0.212 2442 Planarity : 0.004 0.050 2682 Dihedral : 5.454 84.004 2198 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1990 helix: 1.34 (0.16), residues: 1086 sheet: -1.30 (0.40), residues: 156 loop : -1.21 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1204 HIS 0.006 0.001 HIS C1181 PHE 0.044 0.002 PHE A1022 TYR 0.021 0.002 TYR A 732 ARG 0.003 0.000 ARG A 545 *********************** 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 407 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.816 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 431 GLU cc_start: 0.8147 (mp0) cc_final: 0.7767 (mp0) REVERT: A 434 LYS cc_start: 0.8799 (tptt) cc_final: 0.8537 (tmmt) REVERT: A 585 MET cc_start: 0.8596 (mmt) cc_final: 0.7808 (mmt) REVERT: A 589 CYS cc_start: 0.7346 (t) cc_final: 0.6706 (t) REVERT: A 591 ILE cc_start: 0.8226 (mp) cc_final: 0.7933 (pt) REVERT: A 619 ASN cc_start: 0.8639 (t0) cc_final: 0.8248 (t0) REVERT: A 770 LYS cc_start: 0.6836 (mptt) cc_final: 0.6566 (mppt) REVERT: A 805 LEU cc_start: 0.9024 (mt) cc_final: 0.8519 (tt) REVERT: A 1034 GLN cc_start: 0.8634 (pm20) cc_final: 0.8352 (pm20) REVERT: A 1143 PHE cc_start: 0.8246 (p90) cc_final: 0.7954 (p90) REVERT: A 1169 PHE cc_start: 0.7974 (m-80) cc_final: 0.7752 (m-80) REVERT: A 1219 CYS cc_start: 0.8795 (m) cc_final: 0.8415 (m) REVERT: B 407 MET cc_start: 0.7760 (mtp) cc_final: 0.7544 (mtp) REVERT: B 425 CYS cc_start: 0.7984 (m) cc_final: 0.7782 (m) REVERT: B 479 LEU cc_start: 0.8777 (tp) cc_final: 0.8362 (mt) REVERT: B 503 MET cc_start: 0.9052 (tmm) cc_final: 0.8630 (tmm) REVERT: B 504 ILE cc_start: 0.9248 (pt) cc_final: 0.8826 (pt) REVERT: B 546 PHE cc_start: 0.6479 (m-10) cc_final: 0.5952 (m-80) REVERT: B 637 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7777 (tm-30) REVERT: B 657 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 670 MET cc_start: 0.8570 (mtp) cc_final: 0.8030 (mtt) REVERT: B 693 VAL cc_start: 0.8734 (t) cc_final: 0.8328 (t) REVERT: B 721 MET cc_start: 0.8789 (ptt) cc_final: 0.8209 (ppp) REVERT: B 761 LYS cc_start: 0.8686 (mtpp) cc_final: 0.7957 (mtmm) REVERT: B 764 ASN cc_start: 0.9077 (t0) cc_final: 0.8657 (t0) REVERT: C 434 LYS cc_start: 0.8830 (tptt) cc_final: 0.8584 (tmmt) REVERT: C 508 GLN cc_start: 0.5656 (mm110) cc_final: 0.5320 (pp30) REVERT: C 585 MET cc_start: 0.8554 (mmt) cc_final: 0.7825 (mmt) REVERT: C 619 ASN cc_start: 0.8599 (t0) cc_final: 0.8196 (t0) REVERT: C 734 ILE cc_start: 0.9052 (mt) cc_final: 0.8844 (mt) REVERT: C 815 CYS cc_start: 0.7269 (m) cc_final: 0.6982 (t) REVERT: C 1022 PHE cc_start: 0.8315 (m-80) cc_final: 0.7116 (m-80) REVERT: C 1028 LEU cc_start: 0.8824 (mp) cc_final: 0.8618 (mp) REVERT: C 1122 LYS cc_start: 0.7929 (mttp) cc_final: 0.7532 (mmtp) REVERT: C 1143 PHE cc_start: 0.8553 (p90) cc_final: 0.7959 (p90) REVERT: C 1169 PHE cc_start: 0.8075 (m-80) cc_final: 0.7683 (m-80) REVERT: C 1219 CYS cc_start: 0.8619 (m) cc_final: 0.8120 (m) REVERT: D 456 ASP cc_start: 0.6831 (m-30) cc_final: 0.6593 (m-30) REVERT: D 479 LEU cc_start: 0.8534 (mt) cc_final: 0.8242 (mt) REVERT: D 503 MET cc_start: 0.8944 (tmm) cc_final: 0.8456 (tmm) REVERT: D 569 ASN cc_start: 0.6012 (m-40) cc_final: 0.5777 (m110) REVERT: D 597 SER cc_start: 0.8731 (p) cc_final: 0.8068 (m) REVERT: D 693 VAL cc_start: 0.8818 (t) cc_final: 0.8430 (t) REVERT: D 765 LYS cc_start: 0.8267 (ptmm) cc_final: 0.8043 (ttpt) REVERT: D 803 LEU cc_start: 0.9426 (mt) cc_final: 0.9183 (mm) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.2441 time to fit residues: 154.0130 Evaluate side-chains 305 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 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** ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1186 GLN D 619 ASN D 709 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16094 Z= 0.219 Angle : 0.586 8.588 21754 Z= 0.308 Chirality : 0.042 0.261 2442 Planarity : 0.004 0.045 2682 Dihedral : 5.407 83.805 2198 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1990 helix: 1.39 (0.16), residues: 1086 sheet: -1.07 (0.42), residues: 148 loop : -1.23 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1204 HIS 0.006 0.001 HIS A1181 PHE 0.049 0.002 PHE C1022 TYR 0.017 0.002 TYR B 732 ARG 0.004 0.000 ARG B 715 *********************** 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 396 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.759 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: A 431 GLU cc_start: 0.8167 (mp0) cc_final: 0.7856 (mp0) REVERT: A 434 LYS cc_start: 0.8793 (tptt) cc_final: 0.8546 (tmmt) REVERT: A 585 MET cc_start: 0.8605 (mmt) cc_final: 0.7731 (mmt) REVERT: A 589 CYS cc_start: 0.7288 (t) cc_final: 0.6611 (t) REVERT: A 591 ILE cc_start: 0.8243 (mp) cc_final: 0.7963 (pt) REVERT: A 619 ASN cc_start: 0.8646 (t0) cc_final: 0.8264 (t0) REVERT: A 770 LYS cc_start: 0.6746 (mptt) cc_final: 0.6399 (mppt) REVERT: A 805 LEU cc_start: 0.9067 (mt) cc_final: 0.8588 (tt) REVERT: A 1034 GLN cc_start: 0.8611 (pm20) cc_final: 0.8308 (pm20) REVERT: A 1169 PHE cc_start: 0.8051 (m-80) cc_final: 0.7777 (m-80) REVERT: A 1212 LEU cc_start: 0.8400 (tp) cc_final: 0.8142 (tp) REVERT: A 1219 CYS cc_start: 0.8770 (m) cc_final: 0.8302 (m) REVERT: B 432 ILE cc_start: 0.9013 (mm) cc_final: 0.8793 (mm) REVERT: B 479 LEU cc_start: 0.8753 (tp) cc_final: 0.8259 (mt) REVERT: B 503 MET cc_start: 0.9081 (tmm) cc_final: 0.8609 (tmm) REVERT: B 504 ILE cc_start: 0.9291 (pt) cc_final: 0.8882 (pt) REVERT: B 542 LEU cc_start: 0.8398 (mp) cc_final: 0.8142 (pp) REVERT: B 543 VAL cc_start: 0.8173 (t) cc_final: 0.7649 (t) REVERT: B 546 PHE cc_start: 0.6614 (m-10) cc_final: 0.5983 (m-80) REVERT: B 585 MET cc_start: 0.8883 (mmm) cc_final: 0.8358 (mmm) REVERT: B 657 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7672 (mm-30) REVERT: B 670 MET cc_start: 0.8573 (mtp) cc_final: 0.7940 (mtt) REVERT: B 721 MET cc_start: 0.8690 (ptt) cc_final: 0.8213 (ppp) REVERT: B 760 ASP cc_start: 0.8258 (m-30) cc_final: 0.7957 (m-30) REVERT: B 761 LYS cc_start: 0.8705 (mtpp) cc_final: 0.7990 (mtmm) REVERT: C 434 LYS cc_start: 0.8807 (tptt) cc_final: 0.8589 (tmmt) REVERT: C 508 GLN cc_start: 0.5687 (mm110) cc_final: 0.5343 (pp30) REVERT: C 585 MET cc_start: 0.8551 (mmt) cc_final: 0.7915 (mmt) REVERT: C 613 ILE cc_start: 0.9341 (mt) cc_final: 0.8901 (mt) REVERT: C 619 ASN cc_start: 0.8606 (t0) cc_final: 0.8234 (t0) REVERT: C 1143 PHE cc_start: 0.8064 (p90) cc_final: 0.7824 (p90) REVERT: C 1169 PHE cc_start: 0.8060 (m-80) cc_final: 0.7654 (m-80) REVERT: C 1219 CYS cc_start: 0.8646 (m) cc_final: 0.8330 (m) REVERT: D 456 ASP cc_start: 0.6799 (m-30) cc_final: 0.6553 (m-30) REVERT: D 479 LEU cc_start: 0.8582 (mt) cc_final: 0.8369 (mt) REVERT: D 503 MET cc_start: 0.8968 (tmm) cc_final: 0.8474 (tmm) REVERT: D 546 PHE cc_start: 0.6950 (m-80) cc_final: 0.6657 (m-80) REVERT: D 590 ASP cc_start: 0.7610 (p0) cc_final: 0.7029 (m-30) REVERT: D 591 ILE cc_start: 0.8340 (pt) cc_final: 0.8025 (pt) REVERT: D 597 SER cc_start: 0.8638 (p) cc_final: 0.8021 (m) REVERT: D 671 TRP cc_start: 0.8248 (t-100) cc_final: 0.7153 (t-100) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.2555 time to fit residues: 156.4337 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 : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 HIS A1186 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 HIS C1186 GLN D 619 ASN D 709 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16094 Z= 0.169 Angle : 0.565 8.779 21754 Z= 0.294 Chirality : 0.041 0.297 2442 Planarity : 0.004 0.043 2682 Dihedral : 5.238 80.216 2198 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1990 helix: 1.47 (0.16), residues: 1092 sheet: -0.73 (0.44), residues: 128 loop : -1.15 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1032 HIS 0.007 0.001 HIS A1181 PHE 0.023 0.001 PHE D 546 TYR 0.015 0.001 TYR C 424 ARG 0.003 0.000 ARG B 715 *********************** 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 406 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8175 (mp0) cc_final: 0.7839 (mp0) REVERT: A 434 LYS cc_start: 0.8768 (tptt) cc_final: 0.8540 (tmmt) REVERT: A 585 MET cc_start: 0.8533 (mmt) cc_final: 0.7713 (mmt) REVERT: A 589 CYS cc_start: 0.7134 (t) cc_final: 0.6501 (t) REVERT: A 591 ILE cc_start: 0.8233 (mp) cc_final: 0.7909 (pt) REVERT: A 619 ASN cc_start: 0.8613 (t0) cc_final: 0.8192 (t0) REVERT: A 637 GLU cc_start: 0.8007 (tt0) cc_final: 0.7382 (mp0) REVERT: A 647 TYR cc_start: 0.5079 (m-80) cc_final: 0.4863 (m-80) REVERT: A 661 ARG cc_start: 0.8400 (ptm-80) cc_final: 0.8028 (tmt170) REVERT: A 770 LYS cc_start: 0.6829 (mptt) cc_final: 0.6504 (mppt) REVERT: A 805 LEU cc_start: 0.9028 (mt) cc_final: 0.8507 (tt) REVERT: A 1034 GLN cc_start: 0.8623 (pm20) cc_final: 0.8347 (pm20) REVERT: A 1169 PHE cc_start: 0.8012 (m-80) cc_final: 0.7755 (m-80) REVERT: A 1219 CYS cc_start: 0.8741 (m) cc_final: 0.8401 (m) REVERT: B 432 ILE cc_start: 0.8975 (mm) cc_final: 0.8771 (mm) REVERT: B 503 MET cc_start: 0.9065 (tmm) cc_final: 0.8577 (tmm) REVERT: B 504 ILE cc_start: 0.9282 (pt) cc_final: 0.8896 (pt) REVERT: B 542 LEU cc_start: 0.8382 (mp) cc_final: 0.8124 (pp) REVERT: B 543 VAL cc_start: 0.8254 (t) cc_final: 0.7752 (t) REVERT: B 546 PHE cc_start: 0.6541 (m-10) cc_final: 0.5902 (m-80) REVERT: B 585 MET cc_start: 0.8867 (mmm) cc_final: 0.8403 (mmm) REVERT: B 637 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7800 (tm-30) REVERT: B 657 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 670 MET cc_start: 0.8563 (mtp) cc_final: 0.8122 (mtt) REVERT: B 693 VAL cc_start: 0.8757 (t) cc_final: 0.8380 (t) REVERT: B 721 MET cc_start: 0.8674 (ptt) cc_final: 0.8279 (ppp) REVERT: B 760 ASP cc_start: 0.8240 (m-30) cc_final: 0.7922 (m-30) REVERT: B 761 LYS cc_start: 0.8683 (mtpp) cc_final: 0.7997 (mtmm) REVERT: B 764 ASN cc_start: 0.9070 (t0) cc_final: 0.8825 (t0) REVERT: C 585 MET cc_start: 0.8546 (mmt) cc_final: 0.7705 (mmt) REVERT: C 619 ASN cc_start: 0.8561 (t0) cc_final: 0.8177 (t0) REVERT: C 1022 PHE cc_start: 0.8495 (m-10) cc_final: 0.8260 (m-10) REVERT: C 1169 PHE cc_start: 0.8059 (m-80) cc_final: 0.7627 (m-80) REVERT: C 1212 LEU cc_start: 0.8437 (tp) cc_final: 0.8215 (tp) REVERT: C 1219 CYS cc_start: 0.8695 (m) cc_final: 0.8244 (m) REVERT: D 456 ASP cc_start: 0.6732 (m-30) cc_final: 0.6507 (m-30) REVERT: D 479 LEU cc_start: 0.8574 (mt) cc_final: 0.8350 (mt) REVERT: D 503 MET cc_start: 0.8969 (tmm) cc_final: 0.8518 (tmm) REVERT: D 543 VAL cc_start: 0.8183 (t) cc_final: 0.7714 (m) REVERT: D 546 PHE cc_start: 0.6955 (m-80) cc_final: 0.6563 (m-80) REVERT: D 569 ASN cc_start: 0.5821 (m-40) cc_final: 0.5574 (m110) REVERT: D 585 MET cc_start: 0.8809 (mmm) cc_final: 0.8173 (mmm) REVERT: D 590 ASP cc_start: 0.7615 (p0) cc_final: 0.7087 (m-30) REVERT: D 591 ILE cc_start: 0.8346 (pt) cc_final: 0.8058 (pt) REVERT: D 597 SER cc_start: 0.8580 (p) cc_final: 0.8062 (p) REVERT: D 693 VAL cc_start: 0.8800 (t) cc_final: 0.8407 (t) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.2492 time to fit residues: 156.8854 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 : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 162 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN B 619 ASN ** B 709 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16094 Z= 0.183 Angle : 0.578 8.414 21754 Z= 0.300 Chirality : 0.042 0.303 2442 Planarity : 0.004 0.044 2682 Dihedral : 5.187 80.015 2198 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1990 helix: 1.47 (0.16), residues: 1090 sheet: -0.77 (0.39), residues: 166 loop : -1.11 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1032 HIS 0.006 0.001 HIS A1181 PHE 0.022 0.001 PHE B 814 TYR 0.014 0.001 TYR C 424 ARG 0.002 0.000 ARG A 545 *********************** 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 395 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8191 (mp0) cc_final: 0.7871 (mp0) REVERT: A 434 LYS cc_start: 0.8764 (tptt) cc_final: 0.8557 (tmmt) REVERT: A 585 MET cc_start: 0.8537 (mmt) cc_final: 0.7710 (mmt) REVERT: A 589 CYS cc_start: 0.7221 (t) cc_final: 0.6525 (t) REVERT: A 591 ILE cc_start: 0.8183 (mp) cc_final: 0.7909 (pt) REVERT: A 619 ASN cc_start: 0.8657 (t0) cc_final: 0.8270 (t0) REVERT: A 637 GLU cc_start: 0.8005 (tt0) cc_final: 0.7374 (mp0) REVERT: A 770 LYS cc_start: 0.6794 (mptt) cc_final: 0.6443 (mppt) REVERT: A 805 LEU cc_start: 0.9081 (mt) cc_final: 0.8575 (tt) REVERT: A 1022 PHE cc_start: 0.8467 (m-80) cc_final: 0.8219 (m-80) REVERT: A 1034 GLN cc_start: 0.8619 (pm20) cc_final: 0.8337 (pm20) REVERT: A 1169 PHE cc_start: 0.8040 (m-80) cc_final: 0.7818 (m-80) REVERT: A 1212 LEU cc_start: 0.8318 (tp) cc_final: 0.8116 (tp) REVERT: A 1219 CYS cc_start: 0.8780 (m) cc_final: 0.8351 (m) REVERT: B 503 MET cc_start: 0.9066 (tmm) cc_final: 0.8552 (tmm) REVERT: B 504 ILE cc_start: 0.9280 (pt) cc_final: 0.8921 (pt) REVERT: B 542 LEU cc_start: 0.8359 (mp) cc_final: 0.8119 (pp) REVERT: B 543 VAL cc_start: 0.8249 (t) cc_final: 0.7744 (t) REVERT: B 546 PHE cc_start: 0.6615 (m-10) cc_final: 0.5976 (m-80) REVERT: B 585 MET cc_start: 0.8901 (mmm) cc_final: 0.8422 (mmm) REVERT: B 657 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 693 VAL cc_start: 0.8776 (t) cc_final: 0.8401 (t) REVERT: B 721 MET cc_start: 0.8643 (ptt) cc_final: 0.8300 (ppp) REVERT: B 761 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8001 (mtmm) REVERT: C 503 MET cc_start: 0.7831 (tpp) cc_final: 0.7529 (mmm) REVERT: C 585 MET cc_start: 0.8582 (mmt) cc_final: 0.7714 (mmt) REVERT: C 619 ASN cc_start: 0.8573 (t0) cc_final: 0.8203 (t0) REVERT: C 637 GLU cc_start: 0.8244 (tt0) cc_final: 0.7859 (tp30) REVERT: C 732 TYR cc_start: 0.8410 (m-10) cc_final: 0.8089 (m-10) REVERT: C 1169 PHE cc_start: 0.8044 (m-80) cc_final: 0.7741 (m-80) REVERT: C 1219 CYS cc_start: 0.8651 (m) cc_final: 0.8151 (m) REVERT: C 1224 SER cc_start: 0.8837 (t) cc_final: 0.8546 (p) REVERT: D 456 ASP cc_start: 0.6726 (m-30) cc_final: 0.6502 (m-30) REVERT: D 479 LEU cc_start: 0.8583 (mt) cc_final: 0.8243 (mp) REVERT: D 503 MET cc_start: 0.9056 (tmm) cc_final: 0.8514 (tmm) REVERT: D 546 PHE cc_start: 0.6959 (m-80) cc_final: 0.6407 (m-80) REVERT: D 585 MET cc_start: 0.8760 (mmm) cc_final: 0.8358 (mmm) REVERT: D 590 ASP cc_start: 0.7607 (p0) cc_final: 0.7113 (m-30) REVERT: D 591 ILE cc_start: 0.8332 (pt) cc_final: 0.8005 (pt) REVERT: D 597 SER cc_start: 0.8638 (p) cc_final: 0.8339 (p) REVERT: D 693 VAL cc_start: 0.8830 (t) cc_final: 0.8491 (t) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2369 time to fit residues: 146.4347 Evaluate side-chains 296 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16094 Z= 0.178 Angle : 0.579 8.997 21754 Z= 0.301 Chirality : 0.041 0.301 2442 Planarity : 0.004 0.045 2682 Dihedral : 5.065 79.457 2198 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.14 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 : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1990 helix: 1.57 (0.16), residues: 1074 sheet: -0.53 (0.38), residues: 188 loop : -0.99 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1032 HIS 0.008 0.001 HIS A1181 PHE 0.020 0.001 PHE D 546 TYR 0.017 0.001 TYR A 424 ARG 0.002 0.000 ARG D 715 ********************** 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 397 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8195 (mp0) cc_final: 0.7856 (mp0) REVERT: A 585 MET cc_start: 0.8540 (mmt) cc_final: 0.7688 (mmt) REVERT: A 589 CYS cc_start: 0.7202 (t) cc_final: 0.6635 (t) REVERT: A 591 ILE cc_start: 0.8268 (mp) cc_final: 0.7963 (pt) REVERT: A 619 ASN cc_start: 0.8654 (t0) cc_final: 0.8252 (t0) REVERT: A 637 GLU cc_start: 0.7952 (tt0) cc_final: 0.7293 (mp0) REVERT: A 661 ARG cc_start: 0.8415 (ptt90) cc_final: 0.8042 (tmt170) REVERT: A 768 TYR cc_start: 0.7401 (m-80) cc_final: 0.6950 (m-80) REVERT: A 805 LEU cc_start: 0.9121 (mt) cc_final: 0.8634 (tt) REVERT: A 1034 GLN cc_start: 0.8610 (pm20) cc_final: 0.8320 (pm20) REVERT: A 1219 CYS cc_start: 0.8760 (m) cc_final: 0.8404 (m) REVERT: B 503 MET cc_start: 0.9075 (tmm) cc_final: 0.8570 (tmm) REVERT: B 504 ILE cc_start: 0.9268 (pt) cc_final: 0.8973 (pt) REVERT: B 543 VAL cc_start: 0.8254 (t) cc_final: 0.7781 (t) REVERT: B 546 PHE cc_start: 0.6611 (m-10) cc_final: 0.5999 (m-80) REVERT: B 585 MET cc_start: 0.8907 (mmm) cc_final: 0.8415 (mmm) REVERT: B 657 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7640 (mm-30) REVERT: B 693 VAL cc_start: 0.8760 (t) cc_final: 0.8434 (t) REVERT: B 721 MET cc_start: 0.8663 (ptt) cc_final: 0.8367 (ppp) REVERT: B 761 LYS cc_start: 0.8660 (mtpp) cc_final: 0.7978 (mtmm) REVERT: B 764 ASN cc_start: 0.9044 (t0) cc_final: 0.8735 (t0) REVERT: C 504 ILE cc_start: 0.8489 (tp) cc_final: 0.8054 (tp) REVERT: C 585 MET cc_start: 0.8534 (mmt) cc_final: 0.7686 (mmt) REVERT: C 619 ASN cc_start: 0.8570 (t0) cc_final: 0.8186 (t0) REVERT: C 637 GLU cc_start: 0.8266 (tt0) cc_final: 0.7844 (tp30) REVERT: C 732 TYR cc_start: 0.8349 (m-10) cc_final: 0.8060 (m-10) REVERT: C 1169 PHE cc_start: 0.7973 (m-80) cc_final: 0.7637 (m-80) REVERT: C 1219 CYS cc_start: 0.8686 (m) cc_final: 0.8213 (m) REVERT: D 445 VAL cc_start: 0.8264 (p) cc_final: 0.7006 (p) REVERT: D 456 ASP cc_start: 0.6707 (m-30) cc_final: 0.6490 (m-30) REVERT: D 479 LEU cc_start: 0.8524 (mt) cc_final: 0.8252 (mt) REVERT: D 503 MET cc_start: 0.8982 (tmm) cc_final: 0.8487 (tmm) REVERT: D 585 MET cc_start: 0.8732 (mmm) cc_final: 0.8339 (mmm) REVERT: D 590 ASP cc_start: 0.7615 (p0) cc_final: 0.7141 (m-30) REVERT: D 591 ILE cc_start: 0.8341 (pt) cc_final: 0.8007 (pt) REVERT: D 597 SER cc_start: 0.8564 (p) cc_final: 0.8232 (p) REVERT: D 693 VAL cc_start: 0.8799 (t) cc_final: 0.8436 (t) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.2457 time to fit residues: 152.0399 Evaluate side-chains 292 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 158 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 709 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083002 restraints weight = 45247.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083511 restraints weight = 32941.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.083818 restraints weight = 26033.240| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16094 Z= 0.178 Angle : 0.584 7.686 21754 Z= 0.302 Chirality : 0.041 0.213 2442 Planarity : 0.004 0.053 2682 Dihedral : 5.060 79.516 2198 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 1990 helix: 1.60 (0.16), residues: 1074 sheet: -0.66 (0.39), residues: 170 loop : -1.03 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1032 HIS 0.006 0.001 HIS C1181 PHE 0.043 0.002 PHE C1022 TYR 0.017 0.001 TYR A 424 ARG 0.002 0.000 ARG D 715 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3712.42 seconds wall clock time: 68 minutes 51.16 seconds (4131.16 seconds total)