Starting phenix.real_space_refine on Sat Sep 12 14:45:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lr0_63311/09_2026/9lr0_63311.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lr0_63311/09_2026/9lr0_63311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lr0_63311/09_2026/9lr0_63311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lr0_63311/09_2026/9lr0_63311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lr0_63311/09_2026/9lr0_63311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lr0_63311/09_2026/9lr0_63311.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.094 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 102 5.49 5 Mg 3 5.21 5 S 104 5.16 5 C 9891 2.51 5 N 2800 2.21 5 O 3214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16116 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4389 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 25, 'TRANS': 520} Chain: "B" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2630 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 19, 'TRANS': 315} Chain breaks: 2 Chain: "C" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4379 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 25, 'TRANS': 519} Chain: "D" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2622 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 18, 'TRANS': 315} Chain breaks: 2 Chain: "I" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "J" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "x" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 581 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "M" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 292 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "y" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "L" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 727 77.713 96.497 43.426 1.00 56.57 S ATOM 2095 SG CYS A 730 80.177 98.257 41.023 1.00 66.69 S ATOM 9093 SG CYS C 727 26.817 53.177 46.060 1.00 59.03 S ATOM 9114 SG CYS C 730 24.137 51.072 44.165 1.00 60.31 S Time building chain proxies: 3.52, per 1000 atoms: 0.22 Number of scatterers: 16116 At special positions: 0 Unit cell: (104.384, 149.12, 106.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 104 16.00 P 102 15.00 Mg 3 11.99 O 3214 8.00 N 2800 7.00 C 9891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.94 Conformation dependent library (CDL) restraints added in 535.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " Number of angles added : 4 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 21 sheets defined 36.1% alpha, 24.0% beta 49 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.555A pdb=" N ILE A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.012A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.592A pdb=" N LEU A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.979A pdb=" N ALA A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 735 through 739 removed outlier: 3.565A pdb=" N GLN A 739 " --> pdb=" O GLU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 822 through 842 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 868 Processing helix chain 'A' and resid 872 through 895 Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 923 removed outlier: 5.028A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 953 through 957 removed outlier: 3.913A pdb=" N ALA A 957 " --> pdb=" O GLY A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.582A pdb=" N LYS A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1001 through 1005 removed outlier: 3.735A pdb=" N ALA A1005 " --> pdb=" O PHE A1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.657A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 479 through 493 Processing helix chain 'C' and resid 499 through 511 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 Processing helix chain 'C' and resid 822 through 841 removed outlier: 3.705A pdb=" N GLN C 830 " --> pdb=" O ARG C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 removed outlier: 3.830A pdb=" N GLU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 923 removed outlier: 5.135A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.573A pdb=" N SER C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 996 Processing helix chain 'C' and resid 996 through 1003 removed outlier: 3.834A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 163 through 167 removed outlier: 3.867A pdb=" N ARG D 167 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.578A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 4.016A pdb=" N MET A 691 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 519 removed outlier: 4.016A pdb=" N MET A 691 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.943A pdb=" N SER B 2 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 4 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 340 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.943A pdb=" N SER B 2 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 4 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 340 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.396A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.434A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.559A pdb=" N CYS B 78 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 146 removed outlier: 3.691A pdb=" N MET B 152 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.899A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 262 through 266 Processing sheet with id=AB4, first strand: chain 'B' and resid 277 through 279 Processing sheet with id=AB5, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.870A pdb=" N MET C 691 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 555 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.870A pdb=" N MET C 691 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.369A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER D 2 " --> pdb=" O ARG D 343 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE D 339 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL D 8 " --> pdb=" O PHE D 337 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N PHE D 337 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.412A pdb=" N MET D 110 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N THR D 125 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL D 112 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG D 123 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.260A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET D 152 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 145 " --> pdb=" O MET D 152 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE D 156 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC2, first strand: chain 'D' and resid 204 through 211 removed outlier: 7.676A pdb=" N LEU D 204 " --> pdb=" O SER D 223 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER D 223 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE D 206 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY D 221 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 262 through 265 637 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 119 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4718 1.34 - 1.46: 3307 1.46 - 1.58: 8303 1.58 - 1.69: 198 1.69 - 1.81: 160 Bond restraints: 16686 Sorted by residual: bond pdb=" C GLN A 908 " pdb=" N TYR A 909 " ideal model delta sigma weight residual 1.335 1.286 0.049 1.31e-02 5.83e+03 1.40e+01 bond pdb=" C TYR A 548 " pdb=" N PRO A 549 " ideal model delta sigma weight residual 1.332 1.286 0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" C3' DA I 22 " pdb=" C2' DA I 22 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC x 35 " pdb=" C2' DC x 35 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG I 23 " pdb=" C2' DG I 23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 16681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 21983 1.56 - 3.11: 863 3.11 - 4.67: 114 4.67 - 6.23: 14 6.23 - 7.78: 3 Bond angle restraints: 22977 Sorted by residual: angle pdb=" O4' DT y 42 " pdb=" C4' DT y 42 " pdb=" C3' DT y 42 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N3 DT x 52 " pdb=" C4 DT x 52 " pdb=" O4 DT x 52 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT x 42 " pdb=" C4 DT x 42 " pdb=" O4 DT x 42 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT y 31 " pdb=" C4 DT y 31 " pdb=" O4 DT y 31 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 26 " pdb=" C4 DT I 26 " pdb=" O4 DT I 26 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 22972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 9287 35.41 - 70.82: 471 70.82 - 106.23: 11 106.23 - 141.64: 4 141.64 - 177.05: 8 Dihedral angle restraints: 9781 sinusoidal: 4665 harmonic: 5116 Sorted by residual: dihedral pdb=" CA GLN C 520 " pdb=" C GLN C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" C4' DC J 20 " pdb=" C3' DC J 20 " pdb=" O3' DC J 20 " pdb=" P DA J 21 " ideal model delta sinusoidal sigma weight residual 220.00 42.95 177.05 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 9778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2482 0.123 - 0.246: 24 0.246 - 0.369: 0 0.369 - 0.491: 0 0.491 - 0.614: 3 Chirality restraints: 2509 Sorted by residual: chirality pdb=" P DT y 48 " pdb=" OP1 DT y 48 " pdb=" OP2 DT y 48 " pdb=" O5' DT y 48 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" P DA y 49 " pdb=" OP1 DA y 49 " pdb=" OP2 DA y 49 " pdb=" O5' DA y 49 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.12e+00 chirality pdb=" P DT y 47 " pdb=" OP1 DT y 47 " pdb=" OP2 DT y 47 " pdb=" O5' DT y 47 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 2506 not shown) Planarity restraints: 2601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 520 " -0.052 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO C 521 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 340 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C TYR B 340 " 0.048 2.00e-02 2.50e+03 pdb=" O TYR B 340 " -0.018 2.00e-02 2.50e+03 pdb=" N THR B 341 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 317 " 0.017 2.00e-02 2.50e+03 1.54e-02 5.94e+00 pdb=" CG TRP D 317 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP D 317 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 317 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 317 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 317 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 317 " 0.003 2.00e-02 2.50e+03 ... (remaining 2598 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 46 2.62 - 3.19: 13487 3.19 - 3.76: 25768 3.76 - 4.33: 36236 4.33 - 4.90: 58574 Nonbonded interactions: 134111 Sorted by model distance: nonbonded pdb=" OP2 DC x 46 " pdb="MG MG C1102 " model vdw 2.046 2.170 nonbonded pdb=" O3' DT I 27 " pdb="MG MG I 101 " model vdw 2.144 2.170 nonbonded pdb=" OD2 ASP C 708 " pdb="MG MG I 101 " model vdw 2.208 2.170 nonbonded pdb=" CB ASN C 473 " pdb=" SD MET C1003 " model vdw 2.252 3.800 nonbonded pdb=" O ASN C1004 " pdb=" OD1 ASN C1004 " model vdw 2.309 3.040 ... (remaining 134106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 461 through 1005 or resid 1101 through 1102)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 241 or resid 246 through 344)) selection = (chain 'D' and resid 1 through 344) } ncs_group { reference = chain 'L' selection = (chain 'M' and resid 1 through 12) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.450 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.004 0.049 16694 Z= 0.306 Angle : 0.672 7.784 22981 Z= 0.481 Chirality : 0.048 0.614 2509 Planarity : 0.004 0.077 2601 Dihedral : 18.445 177.045 6485 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1744 helix: 1.33 (0.22), residues: 564 sheet: -0.93 (0.30), residues: 325 loop : -1.09 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 927 TYR 0.020 0.001 TYR A 559 PHE 0.018 0.001 PHE A 936 TRP 0.040 0.002 TRP D 317 HIS 0.012 0.001 HIS D 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.31 (16686) covalent geometry : angle 0.67184 / 0.48 (22977) hydrogen bonds : bond 0.15344 / 9.91 ( 719) hydrogen bonds : angle 7.43120 / 5.14 ( 2026) metal coordination : bond 0.00908 / 0.73 ( 8) metal coordination : angle 1.71083 / 0.75 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 633 HIS cc_start: 0.6850 (t70) cc_final: 0.6617 (t-90) REVERT: B 188 GLU cc_start: 0.8350 (tt0) cc_final: 0.8015 (pt0) REVERT: B 191 CYS cc_start: 0.7909 (p) cc_final: 0.7693 (p) REVERT: B 223 SER cc_start: 0.8719 (m) cc_final: 0.8348 (t) REVERT: C 858 MET cc_start: 0.8501 (mmm) cc_final: 0.8276 (mmm) REVERT: D 114 CYS cc_start: 0.8319 (t) cc_final: 0.8104 (p) REVERT: D 189 PHE cc_start: 0.6719 (m-10) cc_final: 0.6404 (m-10) REVERT: D 199 GLU cc_start: 0.7585 (mp0) cc_final: 0.7211 (mp0) REVERT: D 291 SER cc_start: 0.9372 (t) cc_final: 0.9109 (m) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1167 time to fit residues: 46.0452 Evaluate side-chains 170 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 HIS A 744 HIS ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 267 ASN D 222 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119463 restraints weight = 24110.653| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.95 r_work: 0.3386 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16694 Z= 0.130 Angle : 0.572 7.945 22981 Z= 0.320 Chirality : 0.046 0.373 2509 Planarity : 0.004 0.055 2601 Dihedral : 21.789 178.680 3030 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.96 % Allowed : 6.62 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1744 helix: 1.58 (0.22), residues: 565 sheet: -0.62 (0.30), residues: 320 loop : -1.04 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 123 TYR 0.011 0.001 TYR C 757 PHE 0.013 0.001 PHE D 48 TRP 0.011 0.001 TRP D 317 HIS 0.011 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (16686) covalent geometry : angle 0.57141 / 0.32 (22977) hydrogen bonds : bond 0.04410 / 2.88 ( 719) hydrogen bonds : angle 5.73921 / 4.01 ( 2026) metal coordination : bond 0.00641 / 0.47 ( 8) metal coordination : angle 2.07302 / 0.92 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 584 ASP cc_start: 0.7576 (p0) cc_final: 0.7204 (p0) REVERT: A 600 ASP cc_start: 0.8433 (p0) cc_final: 0.8187 (p0) REVERT: A 633 HIS cc_start: 0.6831 (t70) cc_final: 0.6626 (t-90) REVERT: A 848 MET cc_start: 0.8022 (mtt) cc_final: 0.7585 (mtt) REVERT: B 143 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: B 191 CYS cc_start: 0.7968 (p) cc_final: 0.7712 (p) REVERT: B 223 SER cc_start: 0.8848 (m) cc_final: 0.8460 (t) REVERT: B 270 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7563 (mp0) REVERT: B 302 MET cc_start: 0.7179 (mtp) cc_final: 0.6951 (mtp) REVERT: C 858 MET cc_start: 0.8455 (mmm) cc_final: 0.8253 (mmm) REVERT: D 189 PHE cc_start: 0.6829 (m-10) cc_final: 0.6556 (m-10) REVERT: D 291 SER cc_start: 0.9110 (t) cc_final: 0.8797 (m) outliers start: 15 outliers final: 10 residues processed: 194 average time/residue: 0.1171 time to fit residues: 34.6365 Evaluate side-chains 173 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain D residue 12 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 122 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118818 restraints weight = 24348.665| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.97 r_work: 0.3382 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16694 Z= 0.121 Angle : 0.542 6.695 22981 Z= 0.303 Chirality : 0.045 0.380 2509 Planarity : 0.004 0.047 2601 Dihedral : 21.836 178.476 3030 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.16 % Allowed : 8.03 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1744 helix: 1.66 (0.22), residues: 566 sheet: -0.50 (0.30), residues: 324 loop : -1.00 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 828 TYR 0.011 0.001 TYR C 757 PHE 0.018 0.001 PHE C 911 TRP 0.009 0.001 TRP B 317 HIS 0.006 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (16686) covalent geometry : angle 0.54158 / 0.30 (22977) hydrogen bonds : bond 0.03934 / 2.57 ( 719) hydrogen bonds : angle 5.28913 / 3.70 ( 2026) metal coordination : bond 0.00731 / 0.52 ( 8) metal coordination : angle 2.16332 / 0.88 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 584 ASP cc_start: 0.7537 (p0) cc_final: 0.7175 (p0) REVERT: A 848 MET cc_start: 0.8038 (mtt) cc_final: 0.7755 (mtt) REVERT: B 143 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: B 191 CYS cc_start: 0.8072 (p) cc_final: 0.7813 (p) REVERT: B 223 SER cc_start: 0.8901 (m) cc_final: 0.8516 (t) REVERT: B 270 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7425 (mp0) REVERT: B 334 ASP cc_start: 0.8048 (p0) cc_final: 0.7766 (p0) REVERT: C 657 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8731 (pp) REVERT: C 858 MET cc_start: 0.8540 (mmm) cc_final: 0.8315 (mmm) REVERT: D 159 ARG cc_start: 0.8450 (mtp85) cc_final: 0.7934 (mtt-85) REVERT: D 189 PHE cc_start: 0.6867 (m-10) cc_final: 0.6590 (m-10) REVERT: D 232 ASN cc_start: 0.7779 (p0) cc_final: 0.6666 (m-40) REVERT: D 291 SER cc_start: 0.9113 (t) cc_final: 0.8838 (m) outliers start: 18 outliers final: 7 residues processed: 191 average time/residue: 0.1204 time to fit residues: 35.0078 Evaluate side-chains 170 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 694 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 162 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 0.0000 chunk 82 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS B 89 HIS B 278 GLN B 313 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115517 restraints weight = 24251.076| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.96 r_work: 0.3339 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16694 Z= 0.156 Angle : 0.562 6.716 22981 Z= 0.311 Chirality : 0.046 0.376 2509 Planarity : 0.004 0.048 2601 Dihedral : 21.929 178.681 3030 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.41 % Allowed : 9.25 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1744 helix: 1.66 (0.22), residues: 566 sheet: -0.50 (0.29), residues: 329 loop : -0.99 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 828 TYR 0.014 0.001 TYR A 725 PHE 0.015 0.001 PHE C 924 TRP 0.011 0.001 TRP B 317 HIS 0.014 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (16686) covalent geometry : angle 0.56097 / 0.31 (22977) hydrogen bonds : bond 0.03997 / 2.61 ( 719) hydrogen bonds : angle 5.12293 / 3.58 ( 2026) metal coordination : bond 0.01332 / 0.91 ( 8) metal coordination : angle 2.38285 / 0.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 584 ASP cc_start: 0.7557 (p0) cc_final: 0.7235 (p0) REVERT: A 586 TYR cc_start: 0.7425 (p90) cc_final: 0.6892 (p90) REVERT: A 848 MET cc_start: 0.8060 (mtt) cc_final: 0.7757 (mtt) REVERT: B 143 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: B 191 CYS cc_start: 0.8008 (p) cc_final: 0.7779 (p) REVERT: B 223 SER cc_start: 0.8981 (m) cc_final: 0.8653 (t) REVERT: B 270 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7420 (mp0) REVERT: B 334 ASP cc_start: 0.8099 (p0) cc_final: 0.7790 (p0) REVERT: C 657 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8749 (pp) REVERT: C 858 MET cc_start: 0.8598 (mmm) cc_final: 0.8243 (mmm) REVERT: C 897 CYS cc_start: 0.9019 (t) cc_final: 0.8703 (t) REVERT: D 189 PHE cc_start: 0.6901 (m-10) cc_final: 0.6635 (m-10) REVERT: D 232 ASN cc_start: 0.7836 (p0) cc_final: 0.6716 (m-40) REVERT: D 291 SER cc_start: 0.9112 (t) cc_final: 0.8868 (m) outliers start: 22 outliers final: 12 residues processed: 184 average time/residue: 0.1227 time to fit residues: 34.0128 Evaluate side-chains 170 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 78 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 24 optimal weight: 5.9990 chunk 153 optimal weight: 0.0470 chunk 111 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 112 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS B 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118647 restraints weight = 24072.773| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.96 r_work: 0.3379 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16694 Z= 0.110 Angle : 0.524 6.787 22981 Z= 0.293 Chirality : 0.044 0.374 2509 Planarity : 0.004 0.042 2601 Dihedral : 21.804 179.726 3030 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.41 % Allowed : 10.03 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1744 helix: 1.78 (0.22), residues: 568 sheet: -0.42 (0.29), residues: 329 loop : -0.88 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 828 TYR 0.011 0.001 TYR A 757 PHE 0.014 0.001 PHE C 911 TRP 0.011 0.001 TRP A 893 HIS 0.005 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.11 (16686) covalent geometry : angle 0.52289 / 0.29 (22977) hydrogen bonds : bond 0.03572 / 2.33 ( 719) hydrogen bonds : angle 4.92268 / 3.44 ( 2026) metal coordination : bond 0.00531 / 0.38 ( 8) metal coordination : angle 2.78098 / 1.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 584 ASP cc_start: 0.7525 (p0) cc_final: 0.7198 (p0) REVERT: A 586 TYR cc_start: 0.7408 (p90) cc_final: 0.6874 (p90) REVERT: A 848 MET cc_start: 0.8051 (mtt) cc_final: 0.7549 (mtt) REVERT: B 143 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8217 (m-30) REVERT: B 191 CYS cc_start: 0.8169 (p) cc_final: 0.7958 (p) REVERT: B 223 SER cc_start: 0.8927 (m) cc_final: 0.8587 (t) REVERT: B 270 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7384 (mp0) REVERT: B 285 MET cc_start: 0.9300 (mmm) cc_final: 0.8857 (mmt) REVERT: C 657 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8713 (pp) REVERT: C 858 MET cc_start: 0.8542 (mmm) cc_final: 0.8332 (mmm) REVERT: C 897 CYS cc_start: 0.8980 (t) cc_final: 0.8665 (t) REVERT: D 189 PHE cc_start: 0.6900 (m-10) cc_final: 0.6657 (m-10) REVERT: D 232 ASN cc_start: 0.7745 (p0) cc_final: 0.6678 (m-40) REVERT: D 291 SER cc_start: 0.9077 (t) cc_final: 0.8843 (m) outliers start: 22 outliers final: 15 residues processed: 183 average time/residue: 0.1201 time to fit residues: 33.3291 Evaluate side-chains 174 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 627 MET Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 12 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 41 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 180 optimal weight: 20.0000 chunk 87 optimal weight: 0.1980 chunk 178 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS A 665 HIS B 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114699 restraints weight = 24117.252| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.96 r_work: 0.3321 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16694 Z= 0.172 Angle : 0.567 6.751 22981 Z= 0.313 Chirality : 0.046 0.374 2509 Planarity : 0.004 0.049 2601 Dihedral : 21.906 179.010 3030 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.93 % Allowed : 10.67 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1744 helix: 1.72 (0.22), residues: 566 sheet: -0.47 (0.29), residues: 331 loop : -0.91 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 828 TYR 0.014 0.001 TYR A 725 PHE 0.015 0.002 PHE C 924 TRP 0.011 0.001 TRP B 317 HIS 0.005 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (16686) covalent geometry : angle 0.56646 / 0.31 (22977) hydrogen bonds : bond 0.04016 / 2.62 ( 719) hydrogen bonds : angle 4.94250 / 3.45 ( 2026) metal coordination : bond 0.01478 / 1.00 ( 8) metal coordination : angle 2.34970 / 0.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 584 ASP cc_start: 0.7485 (p0) cc_final: 0.7124 (p0) REVERT: A 586 TYR cc_start: 0.7421 (p90) cc_final: 0.6910 (p90) REVERT: A 633 HIS cc_start: 0.7007 (t-90) cc_final: 0.6644 (t-90) REVERT: A 661 ASP cc_start: 0.8357 (t0) cc_final: 0.8139 (t0) REVERT: A 848 MET cc_start: 0.7976 (mtt) cc_final: 0.7593 (mtt) REVERT: A 877 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7913 (mt-10) REVERT: B 143 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: B 191 CYS cc_start: 0.8226 (p) cc_final: 0.8012 (p) REVERT: B 223 SER cc_start: 0.8997 (m) cc_final: 0.8677 (t) REVERT: B 270 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7380 (mp0) REVERT: B 285 MET cc_start: 0.9313 (mmm) cc_final: 0.8961 (mmt) REVERT: B 334 ASP cc_start: 0.8140 (p0) cc_final: 0.7917 (p0) REVERT: B 343 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7778 (ttp80) REVERT: C 657 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8721 (pp) REVERT: C 897 CYS cc_start: 0.8986 (t) cc_final: 0.8653 (t) REVERT: D 189 PHE cc_start: 0.6919 (m-10) cc_final: 0.6667 (m-10) REVERT: D 232 ASN cc_start: 0.7801 (p0) cc_final: 0.6698 (m-40) REVERT: D 291 SER cc_start: 0.9070 (t) cc_final: 0.8839 (m) outliers start: 30 outliers final: 16 residues processed: 189 average time/residue: 0.1208 time to fit residues: 34.6162 Evaluate side-chains 176 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 627 MET Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 78 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 123 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS A 665 HIS A 830 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115391 restraints weight = 24100.902| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.97 r_work: 0.3332 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16694 Z= 0.143 Angle : 0.554 8.314 22981 Z= 0.306 Chirality : 0.045 0.374 2509 Planarity : 0.004 0.044 2601 Dihedral : 21.866 179.535 3030 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.67 % Allowed : 11.31 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1744 helix: 1.71 (0.22), residues: 567 sheet: -0.46 (0.29), residues: 329 loop : -0.91 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 828 TYR 0.012 0.001 TYR C 725 PHE 0.014 0.001 PHE A 936 TRP 0.010 0.001 TRP A 893 HIS 0.004 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (16686) covalent geometry : angle 0.55294 / 0.31 (22977) hydrogen bonds : bond 0.03778 / 2.47 ( 719) hydrogen bonds : angle 4.89596 / 3.42 ( 2026) metal coordination : bond 0.01134 / 0.77 ( 8) metal coordination : angle 2.67642 / 1.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 584 ASP cc_start: 0.7480 (p0) cc_final: 0.7099 (p0) REVERT: A 586 TYR cc_start: 0.7437 (p90) cc_final: 0.6923 (p90) REVERT: A 661 ASP cc_start: 0.8362 (t0) cc_final: 0.8131 (t0) REVERT: A 848 MET cc_start: 0.7914 (mtt) cc_final: 0.7519 (mtt) REVERT: A 877 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7898 (mt-10) REVERT: B 143 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: B 191 CYS cc_start: 0.8237 (p) cc_final: 0.8027 (p) REVERT: B 223 SER cc_start: 0.9015 (m) cc_final: 0.8707 (t) REVERT: B 270 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7411 (mp0) REVERT: B 285 MET cc_start: 0.9312 (mmm) cc_final: 0.9020 (mmt) REVERT: B 334 ASP cc_start: 0.8128 (p0) cc_final: 0.7906 (p0) REVERT: C 657 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8725 (pp) REVERT: C 858 MET cc_start: 0.8703 (mmm) cc_final: 0.8399 (mmm) REVERT: C 897 CYS cc_start: 0.9004 (t) cc_final: 0.8660 (t) REVERT: D 189 PHE cc_start: 0.6921 (m-10) cc_final: 0.6669 (m-10) REVERT: D 232 ASN cc_start: 0.7709 (p0) cc_final: 0.6680 (m-40) REVERT: D 291 SER cc_start: 0.9067 (t) cc_final: 0.8832 (m) outliers start: 26 outliers final: 17 residues processed: 187 average time/residue: 0.1232 time to fit residues: 35.1546 Evaluate side-chains 179 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 627 MET Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 156 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 HIS A 830 GLN B 89 HIS C 665 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112020 restraints weight = 24317.331| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.95 r_work: 0.3274 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16694 Z= 0.215 Angle : 0.610 7.444 22981 Z= 0.333 Chirality : 0.048 0.377 2509 Planarity : 0.004 0.050 2601 Dihedral : 22.005 179.184 3030 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.86 % Allowed : 10.99 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1744 helix: 1.53 (0.22), residues: 567 sheet: -0.58 (0.29), residues: 331 loop : -0.97 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 828 TYR 0.018 0.002 TYR A 559 PHE 0.017 0.002 PHE C 924 TRP 0.017 0.002 TRP B 317 HIS 0.006 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (16686) covalent geometry : angle 0.60974 / 0.33 (22977) hydrogen bonds : bond 0.04345 / 2.84 ( 719) hydrogen bonds : angle 5.02086 / 3.51 ( 2026) metal coordination : bond 0.01691 / 1.12 ( 8) metal coordination : angle 2.33169 / 1.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.606 Fit side-chains REVERT: A 584 ASP cc_start: 0.7505 (p0) cc_final: 0.7124 (p0) REVERT: A 586 TYR cc_start: 0.7483 (p90) cc_final: 0.7018 (p90) REVERT: A 633 HIS cc_start: 0.7072 (t-90) cc_final: 0.6791 (t-90) REVERT: A 661 ASP cc_start: 0.8389 (t0) cc_final: 0.8180 (t0) REVERT: A 877 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7930 (mt-10) REVERT: B 143 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: B 223 SER cc_start: 0.9081 (m) cc_final: 0.8807 (t) REVERT: B 265 GLN cc_start: 0.8418 (tp40) cc_final: 0.7960 (tp-100) REVERT: B 270 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7452 (mp0) REVERT: B 285 MET cc_start: 0.9309 (mmm) cc_final: 0.9067 (mmt) REVERT: B 334 ASP cc_start: 0.8079 (p0) cc_final: 0.7754 (p0) REVERT: B 343 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7838 (ttp80) REVERT: C 657 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8688 (pp) REVERT: C 858 MET cc_start: 0.8636 (mmm) cc_final: 0.8284 (mmm) REVERT: C 897 CYS cc_start: 0.9043 (t) cc_final: 0.8721 (t) REVERT: D 189 PHE cc_start: 0.6939 (m-10) cc_final: 0.6723 (m-10) REVERT: D 232 ASN cc_start: 0.7890 (p0) cc_final: 0.6747 (m-40) REVERT: D 291 SER cc_start: 0.9101 (t) cc_final: 0.8874 (m) outliers start: 29 outliers final: 20 residues processed: 179 average time/residue: 0.1201 time to fit residues: 32.9047 Evaluate side-chains 174 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 627 MET Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 15 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 830 GLN B 89 HIS C 665 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114183 restraints weight = 24168.978| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.96 r_work: 0.3305 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16694 Z= 0.151 Angle : 0.566 7.633 22981 Z= 0.312 Chirality : 0.046 0.375 2509 Planarity : 0.004 0.044 2601 Dihedral : 21.905 179.812 3030 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.67 % Allowed : 11.63 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1744 helix: 1.60 (0.22), residues: 567 sheet: -0.55 (0.29), residues: 331 loop : -0.92 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 828 TYR 0.012 0.001 TYR C 805 PHE 0.016 0.001 PHE A 936 TRP 0.012 0.001 TRP A 893 HIS 0.004 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (16686) covalent geometry : angle 0.56489 / 0.31 (22977) hydrogen bonds : bond 0.03857 / 2.51 ( 719) hydrogen bonds : angle 4.92579 / 3.44 ( 2026) metal coordination : bond 0.01127 / 0.75 ( 8) metal coordination : angle 2.78007 / 1.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 584 ASP cc_start: 0.7541 (p0) cc_final: 0.7162 (p0) REVERT: A 586 TYR cc_start: 0.7428 (p90) cc_final: 0.6959 (p90) REVERT: A 633 HIS cc_start: 0.7112 (t-90) cc_final: 0.6782 (t-90) REVERT: A 661 ASP cc_start: 0.8354 (t0) cc_final: 0.8128 (t0) REVERT: A 848 MET cc_start: 0.8069 (mtt) cc_final: 0.7703 (mtt) REVERT: B 143 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: B 223 SER cc_start: 0.9066 (m) cc_final: 0.8780 (t) REVERT: B 265 GLN cc_start: 0.8449 (tp40) cc_final: 0.7990 (tp-100) REVERT: B 270 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7431 (mp0) REVERT: B 285 MET cc_start: 0.9308 (mmm) cc_final: 0.9052 (mmt) REVERT: B 334 ASP cc_start: 0.8098 (p0) cc_final: 0.7777 (p0) REVERT: B 343 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7848 (ttp80) REVERT: C 657 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8717 (pp) REVERT: C 858 MET cc_start: 0.8650 (mmm) cc_final: 0.8342 (mmm) REVERT: C 897 CYS cc_start: 0.9031 (t) cc_final: 0.8709 (t) REVERT: D 189 PHE cc_start: 0.6951 (m-10) cc_final: 0.6722 (m-10) REVERT: D 232 ASN cc_start: 0.7849 (p0) cc_final: 0.6718 (m-40) REVERT: D 291 SER cc_start: 0.9068 (t) cc_final: 0.8840 (m) outliers start: 26 outliers final: 18 residues processed: 177 average time/residue: 0.1192 time to fit residues: 32.2249 Evaluate side-chains 176 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 12 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 830 GLN B 89 HIS C 665 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114072 restraints weight = 24113.169| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.95 r_work: 0.3313 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16694 Z= 0.152 Angle : 0.566 7.413 22981 Z= 0.311 Chirality : 0.046 0.375 2509 Planarity : 0.004 0.048 2601 Dihedral : 21.871 179.644 3030 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.29 % Allowed : 11.95 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1744 helix: 1.56 (0.22), residues: 573 sheet: -0.49 (0.29), residues: 331 loop : -0.92 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 828 TYR 0.012 0.001 TYR C 725 PHE 0.018 0.002 PHE A 936 TRP 0.011 0.001 TRP A 893 HIS 0.004 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16686) covalent geometry : angle 0.56479 / 0.31 (22977) hydrogen bonds : bond 0.03868 / 2.52 ( 719) hydrogen bonds : angle 4.88486 / 3.41 ( 2026) metal coordination : bond 0.01238 / 0.82 ( 8) metal coordination : angle 2.52546 / 1.13 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 584 ASP cc_start: 0.7521 (p0) cc_final: 0.7116 (p0) REVERT: A 586 TYR cc_start: 0.7414 (p90) cc_final: 0.6960 (p90) REVERT: A 633 HIS cc_start: 0.7105 (t-90) cc_final: 0.6801 (t-90) REVERT: A 661 ASP cc_start: 0.8335 (t0) cc_final: 0.8093 (t0) REVERT: A 848 MET cc_start: 0.8073 (mtt) cc_final: 0.7696 (mtt) REVERT: B 143 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8316 (m-30) REVERT: B 223 SER cc_start: 0.9050 (m) cc_final: 0.8753 (t) REVERT: B 265 GLN cc_start: 0.8451 (tp40) cc_final: 0.7972 (tp-100) REVERT: B 270 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7395 (mp0) REVERT: B 285 MET cc_start: 0.9311 (mmm) cc_final: 0.9062 (mmt) REVERT: B 334 ASP cc_start: 0.8098 (p0) cc_final: 0.7786 (p0) REVERT: B 343 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7817 (ttp80) REVERT: C 657 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8713 (pp) REVERT: C 858 MET cc_start: 0.8650 (mmm) cc_final: 0.8337 (mmm) REVERT: C 897 CYS cc_start: 0.9021 (t) cc_final: 0.8675 (t) REVERT: D 189 PHE cc_start: 0.6969 (m-10) cc_final: 0.6738 (m-10) REVERT: D 232 ASN cc_start: 0.7780 (p0) cc_final: 0.6694 (m-40) REVERT: D 291 SER cc_start: 0.9056 (t) cc_final: 0.8832 (m) outliers start: 20 outliers final: 18 residues processed: 173 average time/residue: 0.1173 time to fit residues: 30.7099 Evaluate side-chains 178 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 125 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 830 GLN B 89 HIS C 665 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116546 restraints weight = 24063.064| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.95 r_work: 0.3346 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16694 Z= 0.121 Angle : 0.542 7.392 22981 Z= 0.300 Chirality : 0.045 0.372 2509 Planarity : 0.004 0.044 2601 Dihedral : 21.743 179.097 3030 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.22 % Allowed : 12.02 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1744 helix: 1.64 (0.22), residues: 574 sheet: -0.36 (0.29), residues: 329 loop : -0.86 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 828 TYR 0.012 0.001 TYR C 757 PHE 0.019 0.001 PHE B 187 TRP 0.013 0.001 TRP A 893 HIS 0.004 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (16686) covalent geometry : angle 0.54038 / 0.30 (22977) hydrogen bonds : bond 0.03590 / 2.34 ( 719) hydrogen bonds : angle 4.75927 / 3.32 ( 2026) metal coordination : bond 0.00867 / 0.59 ( 8) metal coordination : angle 2.88991 / 1.30 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3432.85 seconds wall clock time: 59 minutes 44.97 seconds (3584.97 seconds total)