Starting phenix.real_space_refine on Sat Sep 12 11:50:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lqo_63299/09_2026/9lqo_63299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lqo_63299/09_2026/9lqo_63299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lqo_63299/09_2026/9lqo_63299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lqo_63299/09_2026/9lqo_63299.map" model { file = "/net/cci-nas-00/data/ceres_data/9lqo_63299/09_2026/9lqo_63299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lqo_63299/09_2026/9lqo_63299.cif" } resolution = 3.0 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= 0.018 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 60 5.49 5 Mg 2 5.21 5 S 104 5.16 5 C 9468 2.51 5 N 2636 2.21 5 O 2953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 15225 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4368 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 25, 'TRANS': 518} Chain: "B" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2615 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 19, 'TRANS': 314} Chain breaks: 3 Chain: "C" Number of atoms: 4368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4368 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 25, 'TRANS': 518} Chain: "D" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2640 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain breaks: 2 Chain: "F" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 282 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "L" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 292 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "M" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2068 SG CYS A 727 24.980 97.438 62.037 1.00 49.09 S ATOM 2089 SG CYS A 730 22.195 99.520 64.043 1.00 31.70 S ATOM 9051 SG CYS C 727 78.613 57.816 59.281 1.00 33.96 S ATOM 9072 SG CYS C 730 81.261 55.566 61.162 1.00 23.76 S Time building chain proxies: 3.43, per 1000 atoms: 0.23 Number of scatterers: 15225 At special positions: 0 Unit cell: (104.475, 151.725, 103.425, 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 60 15.00 Mg 2 11.99 O 2953 8.00 N 2636 7.00 C 9468 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: 1.31 Conformation dependent library (CDL) restraints added in 674.7 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 727 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " Number of angles added : 4 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 21 sheets defined 36.8% alpha, 25.5% beta 28 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 510 removed outlier: 3.543A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 740 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 841 Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.759A pdb=" N GLU A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 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 908 Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.844A pdb=" N LYS A 938 " --> pdb=" O ASN A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 950 Processing helix chain 'A' and resid 958 through 975 Processing helix chain 'A' and resid 979 through 995 removed outlier: 4.782A pdb=" N MET A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1004 removed outlier: 3.887A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.822A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) 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 812 Processing helix chain 'C' and resid 822 through 841 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 873 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 908 Processing helix chain 'C' and resid 908 through 924 Processing helix chain 'C' and resid 924 through 929 Processing helix chain 'C' and resid 933 through 951 removed outlier: 4.045A pdb=" N VAL C 943 " --> pdb=" O THR C 939 " (cutoff:3.500A) Proline residue: C 944 - end of helix Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 958 through 975 Processing helix chain 'C' and resid 979 through 995 removed outlier: 4.816A pdb=" N MET C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1003 removed outlier: 4.045A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 3.749A 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 168 through 172 removed outlier: 3.551A 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: 3.565A pdb=" N GLU A 518 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP A 600 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 622 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET A 602 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL A 620 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 7.122A 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: 3.565A pdb=" N GLU A 518 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP A 600 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 622 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET A 602 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL A 620 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.035A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL B 8 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N PHE B 343 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 80 removed outlier: 3.628A pdb=" N HIS B 94 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.312A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 208 through 211 removed outlier: 4.317A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 262 through 267 removed outlier: 7.141A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 277 through 279 removed outlier: 3.500A pdb=" N GLN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 518 through 519 removed outlier: 7.281A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N MET C 602 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL C 620 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 7.281A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N MET C 602 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL C 620 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C 636 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 7 through 8 removed outlier: 6.280A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 58 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.234A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS D 115 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.086A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 142 through 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB8, first strand: chain 'D' and resid 208 through 211 removed outlier: 4.110A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 262 through 267 removed outlier: 3.570A pdb=" N THR D 266 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 277 through 279 Processing sheet with id=AC2, first strand: chain 'D' and resid 318 through 321 Processing sheet with id=AC3, first strand: chain 'D' and resid 318 through 321 660 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4152 1.33 - 1.45: 3009 1.45 - 1.57: 8255 1.57 - 1.69: 116 1.69 - 1.81: 160 Bond restraints: 15692 Sorted by residual: bond pdb=" C3' DC G 39 " pdb=" C2' DC G 39 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.46e+00 bond pdb=" C3' DT M 6 " pdb=" C2' DT M 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.79e+00 bond pdb=" C3' DG L 11 " pdb=" C2' DG L 11 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.78e+00 bond pdb=" C3' DG M 11 " pdb=" C2' DG M 11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.14e+00 bond pdb=" C ASP C 708 " pdb=" N GLU C 709 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.31e-02 5.83e+03 7.86e+00 ... (remaining 15687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 20911 1.63 - 3.27: 475 3.27 - 4.90: 51 4.90 - 6.53: 14 6.53 - 8.16: 7 Bond angle restraints: 21458 Sorted by residual: angle pdb=" O4' DT F 33 " pdb=" C4' DT F 33 " pdb=" C3' DT F 33 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.63e+01 angle pdb=" O4' DC F 30 " pdb=" C4' DC F 30 " pdb=" C3' DC F 30 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT F 31 " pdb=" C4 DT F 31 " pdb=" O4 DT F 31 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT L 6 " pdb=" C4 DT L 6 " pdb=" O4 DT L 6 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT G 42 " pdb=" C4 DT G 42 " pdb=" O4 DT G 42 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 21453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 8259 15.86 - 31.73: 630 31.73 - 47.59: 234 47.59 - 63.45: 152 63.45 - 79.31: 11 Dihedral angle restraints: 9286 sinusoidal: 4178 harmonic: 5108 Sorted by residual: 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 180.00 157.09 22.91 0 5.00e+00 4.00e-02 2.10e+01 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 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ARG C 558 " pdb=" C ARG C 558 " pdb=" N TYR C 559 " pdb=" CA TYR C 559 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 9283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2318 0.123 - 0.246: 14 0.246 - 0.368: 0 0.368 - 0.491: 0 0.491 - 0.614: 9 Chirality restraints: 2341 Sorted by residual: chirality pdb=" P DG G 45 " pdb=" OP1 DG G 45 " pdb=" OP2 DG G 45 " pdb=" O5' DG G 45 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.42e+00 chirality pdb=" P DG M 15 " pdb=" OP1 DG M 15 " pdb=" OP2 DG M 15 " pdb=" O5' DG M 15 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.97e+00 chirality pdb=" P DT L 12 " pdb=" OP1 DT L 12 " pdb=" OP2 DT L 12 " pdb=" O5' DT L 12 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.49e+00 ... (remaining 2338 not shown) Planarity restraints: 2554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 676 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ILE A 676 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE A 676 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 677 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 559 " -0.011 2.00e-02 2.50e+03 1.20e-02 2.89e+00 pdb=" CG TYR C 559 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR C 559 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 559 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 559 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 559 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 559 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 559 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 99 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " 0.021 5.00e-02 4.00e+02 ... (remaining 2551 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 11 2.58 - 3.16: 11850 3.16 - 3.74: 24200 3.74 - 4.32: 35718 4.32 - 4.90: 58466 Nonbonded interactions: 130245 Sorted by model distance: nonbonded pdb=" OD2 ASP A 600 " pdb="MG MG A1102 " model vdw 1.997 2.170 nonbonded pdb=" O3' DG F 34 " pdb="MG MG A1102 " model vdw 2.101 2.170 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A1102 " model vdw 2.192 2.170 nonbonded pdb=" OD1 ASP C 600 " pdb="MG MG C1102 " model vdw 2.200 2.170 nonbonded pdb=" OE1 GLU A 962 " pdb="MG MG A1102 " model vdw 2.265 2.170 ... (remaining 130240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 115 or resid 119 through 350)) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 32 through 45) } ncs_group { reference = chain 'L' selection = (chain 'M' and resid 1 through 14) } 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: 16.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.540 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.160 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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 0.043 15700 Z= 0.244 Angle : 0.590 8.165 21462 Z= 0.375 Chirality : 0.055 0.614 2341 Planarity : 0.004 0.037 2554 Dihedral : 15.152 79.313 5996 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.26 (0.21), residues: 1741 helix: 1.35 (0.22), residues: 552 sheet: -0.04 (0.30), residues: 312 loop : -0.46 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 977 TYR 0.030 0.001 TYR C 559 PHE 0.014 0.001 PHE C 557 TRP 0.010 0.001 TRP C 893 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.24 (15692) covalent geometry : angle 0.58811 / 0.38 (21458) hydrogen bonds : bond 0.15084 / 9.72 ( 695) hydrogen bonds : angle 8.23748 / 5.90 ( 1991) metal coordination : bond 0.01608 / 1.00 ( 8) metal coordination : angle 3.28344 / 1.78 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7708 (mtp180) REVERT: A 572 GLU cc_start: 0.6730 (mp0) cc_final: 0.6399 (mp0) REVERT: A 588 ASN cc_start: 0.7889 (p0) cc_final: 0.7617 (p0) REVERT: A 797 ASP cc_start: 0.6719 (t0) cc_final: 0.6417 (t0) REVERT: A 847 MET cc_start: 0.8488 (mtt) cc_final: 0.7798 (tpt) REVERT: A 856 LYS cc_start: 0.8277 (mtpt) cc_final: 0.8019 (mtmm) REVERT: A 900 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7552 (mmtp) REVERT: A 948 GLU cc_start: 0.7838 (tt0) cc_final: 0.7582 (mt-10) REVERT: B 5 MET cc_start: 0.7918 (tpt) cc_final: 0.6911 (mtt) REVERT: B 7 THR cc_start: 0.8247 (m) cc_final: 0.8041 (t) REVERT: B 128 ASP cc_start: 0.7303 (m-30) cc_final: 0.6895 (m-30) REVERT: B 214 ASP cc_start: 0.8335 (p0) cc_final: 0.7985 (p0) REVERT: C 588 ASN cc_start: 0.8078 (p0) cc_final: 0.7738 (p0) REVERT: C 632 GLU cc_start: 0.8017 (tt0) cc_final: 0.7436 (pt0) REVERT: C 667 THR cc_start: 0.8864 (m) cc_final: 0.8497 (p) REVERT: C 691 MET cc_start: 0.8698 (mtt) cc_final: 0.8183 (mtm) REVERT: C 765 TYR cc_start: 0.8724 (m-80) cc_final: 0.8517 (m-80) REVERT: C 827 LYS cc_start: 0.7658 (mttt) cc_final: 0.7191 (mtpt) REVERT: C 841 MET cc_start: 0.7913 (mmm) cc_final: 0.7687 (mmm) REVERT: C 907 CYS cc_start: 0.8037 (t) cc_final: 0.7688 (m) REVERT: C 973 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8146 (tttm) REVERT: D 5 MET cc_start: 0.7891 (ttm) cc_final: 0.7584 (tpp) REVERT: D 58 GLU cc_start: 0.8534 (tt0) cc_final: 0.8061 (tm-30) REVERT: D 106 LYS cc_start: 0.8404 (mttm) cc_final: 0.7610 (mtmt) REVERT: D 199 GLU cc_start: 0.7934 (mp0) cc_final: 0.7655 (mp0) REVERT: D 282 GLN cc_start: 0.7232 (tt0) cc_final: 0.6935 (tm-30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.5971 time to fit residues: 182.5156 Evaluate side-chains 193 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 809 GLN B 89 HIS B 94 HIS B 248 ASN B 267 ASN B 278 GLN B 282 GLN B 295 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.153939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.123014 restraints weight = 14958.180| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.73 r_work: 0.3163 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15700 Z= 0.194 Angle : 0.599 7.511 21462 Z= 0.321 Chirality : 0.046 0.172 2341 Planarity : 0.005 0.043 2554 Dihedral : 17.117 75.794 2558 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.94 % Allowed : 7.69 % Favored : 90.37 % 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: 0.37 (0.20), residues: 1741 helix: 1.51 (0.22), residues: 554 sheet: 0.15 (0.27), residues: 347 loop : -0.53 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 703 TYR 0.014 0.002 TYR C 757 PHE 0.017 0.002 PHE C 557 TRP 0.011 0.001 TRP C 893 HIS 0.006 0.001 HIS A 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (15692) covalent geometry : angle 0.59514 / 0.32 (21458) hydrogen bonds : bond 0.04516 / 3.07 ( 695) hydrogen bonds : angle 5.97429 / 4.22 ( 1991) metal coordination : bond 0.00731 / 0.48 ( 8) metal coordination : angle 4.82251 / 2.39 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 GLU cc_start: 0.6694 (mp0) cc_final: 0.6428 (mp0) REVERT: A 588 ASN cc_start: 0.7997 (p0) cc_final: 0.7682 (p0) REVERT: A 797 ASP cc_start: 0.6759 (t0) cc_final: 0.6414 (t0) REVERT: A 847 MET cc_start: 0.8511 (mtt) cc_final: 0.7722 (tpt) REVERT: A 856 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7747 (mtmm) REVERT: A 948 GLU cc_start: 0.7707 (tt0) cc_final: 0.7369 (mt-10) REVERT: B 5 MET cc_start: 0.8028 (tpt) cc_final: 0.7137 (mtt) REVERT: B 51 LYS cc_start: 0.7213 (mtmm) cc_final: 0.7005 (mtmp) REVERT: B 128 ASP cc_start: 0.7383 (m-30) cc_final: 0.7136 (m-30) REVERT: B 214 ASP cc_start: 0.8365 (p0) cc_final: 0.7935 (p0) REVERT: B 269 ASP cc_start: 0.7955 (m-30) cc_final: 0.6894 (p0) REVERT: B 279 LEU cc_start: 0.7823 (mt) cc_final: 0.7515 (mp) REVERT: C 508 LYS cc_start: 0.8073 (mmpt) cc_final: 0.7710 (mtmt) REVERT: C 529 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7716 (mtm110) REVERT: C 588 ASN cc_start: 0.8029 (p0) cc_final: 0.7543 (p0) REVERT: C 632 GLU cc_start: 0.8186 (tt0) cc_final: 0.7453 (pt0) REVERT: C 664 ASP cc_start: 0.8145 (t0) cc_final: 0.7553 (t70) REVERT: C 765 TYR cc_start: 0.8696 (m-80) cc_final: 0.8484 (m-80) REVERT: C 827 LYS cc_start: 0.7382 (mttt) cc_final: 0.6882 (mtpt) REVERT: C 877 GLU cc_start: 0.7018 (pt0) cc_final: 0.6099 (mm-30) REVERT: C 900 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8137 (mttp) REVERT: C 907 CYS cc_start: 0.8023 (t) cc_final: 0.7409 (m) REVERT: C 973 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8122 (tttm) REVERT: C 1001 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7729 (mptt) REVERT: D 5 MET cc_start: 0.7855 (ttm) cc_final: 0.7542 (tpp) REVERT: D 58 GLU cc_start: 0.8553 (tt0) cc_final: 0.7966 (tm-30) REVERT: D 199 GLU cc_start: 0.7886 (mp0) cc_final: 0.7529 (mp0) REVERT: D 282 GLN cc_start: 0.6916 (tt0) cc_final: 0.6487 (tm-30) outliers start: 30 outliers final: 9 residues processed: 213 average time/residue: 0.5941 time to fit residues: 139.8737 Evaluate side-chains 199 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 900 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 8 optimal weight: 0.0870 chunk 120 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1004 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.153009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122263 restraints weight = 15110.762| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.76 r_work: 0.3131 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15700 Z= 0.164 Angle : 0.552 6.996 21462 Z= 0.299 Chirality : 0.044 0.159 2341 Planarity : 0.004 0.051 2554 Dihedral : 17.206 70.488 2558 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.52 % Allowed : 9.11 % Favored : 88.36 % 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: 0.39 (0.20), residues: 1741 helix: 1.53 (0.22), residues: 560 sheet: 0.28 (0.28), residues: 346 loop : -0.59 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 756 TYR 0.015 0.001 TYR D 146 PHE 0.015 0.001 PHE C 557 TRP 0.010 0.001 TRP A 893 HIS 0.006 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (15692) covalent geometry : angle 0.54832 / 0.30 (21458) hydrogen bonds : bond 0.04154 / 2.79 ( 695) hydrogen bonds : angle 5.56028 / 3.91 ( 1991) metal coordination : bond 0.00626 / 0.40 ( 8) metal coordination : angle 4.81340 / 2.42 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 GLU cc_start: 0.6790 (mp0) cc_final: 0.6557 (mp0) REVERT: A 588 ASN cc_start: 0.7994 (p0) cc_final: 0.7685 (p0) REVERT: A 739 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6981 (mt0) REVERT: A 797 ASP cc_start: 0.6808 (t0) cc_final: 0.6551 (m-30) REVERT: A 847 MET cc_start: 0.8528 (mtt) cc_final: 0.7761 (tpt) REVERT: A 856 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7814 (mtmm) REVERT: B 51 LYS cc_start: 0.7236 (mtmm) cc_final: 0.7026 (mtmp) REVERT: B 128 ASP cc_start: 0.7396 (m-30) cc_final: 0.7175 (m-30) REVERT: B 214 ASP cc_start: 0.8390 (p0) cc_final: 0.7966 (p0) REVERT: B 282 GLN cc_start: 0.7199 (tt0) cc_final: 0.6995 (tt0) REVERT: C 508 LYS cc_start: 0.8063 (mmpt) cc_final: 0.7736 (mtmt) REVERT: C 588 ASN cc_start: 0.8037 (p0) cc_final: 0.7474 (p0) REVERT: C 632 GLU cc_start: 0.8194 (tt0) cc_final: 0.7445 (pt0) REVERT: C 664 ASP cc_start: 0.8190 (t0) cc_final: 0.7601 (t0) REVERT: C 755 GLN cc_start: 0.7824 (mt0) cc_final: 0.7566 (mt0) REVERT: C 765 TYR cc_start: 0.8744 (m-80) cc_final: 0.8539 (m-80) REVERT: C 768 SER cc_start: 0.8438 (m) cc_final: 0.8138 (p) REVERT: C 827 LYS cc_start: 0.7426 (mttt) cc_final: 0.6929 (mtpt) REVERT: C 877 GLU cc_start: 0.7046 (pt0) cc_final: 0.6120 (mm-30) REVERT: C 900 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8079 (mptt) REVERT: C 907 CYS cc_start: 0.8049 (t) cc_final: 0.7446 (m) REVERT: C 1001 LYS cc_start: 0.8076 (mmtp) cc_final: 0.7651 (mptt) REVERT: D 5 MET cc_start: 0.7917 (ttm) cc_final: 0.7608 (tpp) REVERT: D 58 GLU cc_start: 0.8575 (tt0) cc_final: 0.7985 (tm-30) REVERT: D 199 GLU cc_start: 0.7898 (mp0) cc_final: 0.7536 (mp0) REVERT: D 282 GLN cc_start: 0.6920 (tt0) cc_final: 0.6492 (tm-30) outliers start: 39 outliers final: 16 residues processed: 219 average time/residue: 0.5747 time to fit residues: 139.4441 Evaluate side-chains 205 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 119 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 852 ASN B 33 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120498 restraints weight = 15178.668| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.75 r_work: 0.3164 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15700 Z= 0.131 Angle : 0.522 7.089 21462 Z= 0.283 Chirality : 0.043 0.156 2341 Planarity : 0.004 0.076 2554 Dihedral : 17.170 71.902 2558 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.91 % Allowed : 9.57 % Favored : 87.52 % 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: 0.45 (0.20), residues: 1741 helix: 1.63 (0.22), residues: 562 sheet: 0.31 (0.27), residues: 348 loop : -0.61 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 529 TYR 0.014 0.001 TYR C 707 PHE 0.013 0.001 PHE C 557 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 0.00287 / 0.13 (15692) covalent geometry : angle 0.51795 / 0.28 (21458) hydrogen bonds : bond 0.03700 / 2.50 ( 695) hydrogen bonds : angle 5.34981 / 3.75 ( 1991) metal coordination : bond 0.00517 / 0.33 ( 8) metal coordination : angle 4.55879 / 2.29 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7603 (mtp180) REVERT: A 572 GLU cc_start: 0.6754 (mp0) cc_final: 0.6435 (mp0) REVERT: A 588 ASN cc_start: 0.7884 (p0) cc_final: 0.7578 (p0) REVERT: A 658 MET cc_start: 0.8802 (mtm) cc_final: 0.8469 (mtp) REVERT: A 739 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.6919 (mt0) REVERT: A 752 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: A 797 ASP cc_start: 0.6649 (t0) cc_final: 0.6429 (m-30) REVERT: A 847 MET cc_start: 0.8504 (mtt) cc_final: 0.7716 (tpt) REVERT: A 856 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7736 (mtmm) REVERT: B 49 ASP cc_start: 0.7989 (p0) cc_final: 0.7780 (p0) REVERT: B 51 LYS cc_start: 0.7222 (mtmm) cc_final: 0.6869 (mtmp) REVERT: B 128 ASP cc_start: 0.7352 (m-30) cc_final: 0.7151 (m-30) REVERT: B 214 ASP cc_start: 0.8338 (p0) cc_final: 0.7939 (p0) REVERT: B 282 GLN cc_start: 0.7176 (tt0) cc_final: 0.6960 (tt0) REVERT: C 508 LYS cc_start: 0.8027 (mmpt) cc_final: 0.7677 (mtmt) REVERT: C 573 ASP cc_start: 0.8260 (m-30) cc_final: 0.8023 (m-30) REVERT: C 588 ASN cc_start: 0.8000 (p0) cc_final: 0.7474 (p0) REVERT: C 632 GLU cc_start: 0.8199 (tt0) cc_final: 0.7415 (pt0) REVERT: C 664 ASP cc_start: 0.8169 (t0) cc_final: 0.7546 (t0) REVERT: C 755 GLN cc_start: 0.7782 (mt0) cc_final: 0.7502 (mt0) REVERT: C 765 TYR cc_start: 0.8708 (m-80) cc_final: 0.8480 (m-80) REVERT: C 768 SER cc_start: 0.8429 (m) cc_final: 0.8144 (p) REVERT: C 803 GLU cc_start: 0.7612 (tp30) cc_final: 0.7411 (tp30) REVERT: C 827 LYS cc_start: 0.7398 (mttt) cc_final: 0.6895 (mtpt) REVERT: C 877 GLU cc_start: 0.7013 (pt0) cc_final: 0.6110 (mm-30) REVERT: C 900 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8100 (mttp) REVERT: C 907 CYS cc_start: 0.8013 (t) cc_final: 0.7414 (m) REVERT: C 1001 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7589 (mptt) REVERT: D 1 MET cc_start: 0.8011 (mtp) cc_final: 0.7685 (mtm) REVERT: D 5 MET cc_start: 0.7883 (ttm) cc_final: 0.7572 (tpp) REVERT: D 58 GLU cc_start: 0.8540 (tt0) cc_final: 0.7941 (tm-30) REVERT: D 199 GLU cc_start: 0.7871 (mp0) cc_final: 0.7495 (mp0) REVERT: D 282 GLN cc_start: 0.6858 (tt0) cc_final: 0.6412 (tm-30) outliers start: 45 outliers final: 19 residues processed: 217 average time/residue: 0.5885 time to fit residues: 141.5222 Evaluate side-chains 201 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 981 CYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 128 optimal weight: 0.0670 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.154621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124291 restraints weight = 15001.087| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.67 r_work: 0.3139 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15700 Z= 0.153 Angle : 0.533 7.353 21462 Z= 0.288 Chirality : 0.044 0.160 2341 Planarity : 0.004 0.059 2554 Dihedral : 17.238 71.827 2558 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.10 % Allowed : 10.02 % Favored : 86.88 % 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: 0.45 (0.20), residues: 1741 helix: 1.63 (0.22), residues: 562 sheet: 0.34 (0.27), residues: 352 loop : -0.62 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 529 TYR 0.019 0.001 TYR C 707 PHE 0.013 0.001 PHE C 557 TRP 0.009 0.001 TRP A 893 HIS 0.006 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15692) covalent geometry : angle 0.52899 / 0.29 (21458) hydrogen bonds : bond 0.03786 / 2.54 ( 695) hydrogen bonds : angle 5.27953 / 3.70 ( 1991) metal coordination : bond 0.00642 / 0.40 ( 8) metal coordination : angle 4.55335 / 2.26 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7622 (mtp180) REVERT: A 572 GLU cc_start: 0.6813 (mp0) cc_final: 0.6520 (mp0) REVERT: A 588 ASN cc_start: 0.7887 (p0) cc_final: 0.7597 (p0) REVERT: A 658 MET cc_start: 0.8796 (mtm) cc_final: 0.8515 (mtp) REVERT: A 739 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6968 (mt0) REVERT: A 797 ASP cc_start: 0.6732 (t0) cc_final: 0.6510 (m-30) REVERT: A 847 MET cc_start: 0.8524 (mtt) cc_final: 0.7756 (tpt) REVERT: A 856 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7795 (mtmm) REVERT: B 51 LYS cc_start: 0.7260 (mtmm) cc_final: 0.7043 (mtmp) REVERT: B 214 ASP cc_start: 0.8382 (p0) cc_final: 0.7993 (p0) REVERT: B 282 GLN cc_start: 0.7254 (tt0) cc_final: 0.7053 (tt0) REVERT: C 573 ASP cc_start: 0.8281 (m-30) cc_final: 0.8030 (m-30) REVERT: C 588 ASN cc_start: 0.8013 (p0) cc_final: 0.7440 (p0) REVERT: C 632 GLU cc_start: 0.8147 (tt0) cc_final: 0.7403 (pt0) REVERT: C 664 ASP cc_start: 0.8197 (t0) cc_final: 0.7584 (t0) REVERT: C 755 GLN cc_start: 0.7804 (mt0) cc_final: 0.7520 (mt0) REVERT: C 765 TYR cc_start: 0.8740 (m-80) cc_final: 0.8507 (m-80) REVERT: C 768 SER cc_start: 0.8474 (m) cc_final: 0.8206 (p) REVERT: C 827 LYS cc_start: 0.7428 (mttt) cc_final: 0.6924 (mtpt) REVERT: C 877 GLU cc_start: 0.7077 (pt0) cc_final: 0.6173 (mm-30) REVERT: C 900 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8093 (mptt) REVERT: C 907 CYS cc_start: 0.8049 (t) cc_final: 0.7472 (m) REVERT: C 1001 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7664 (mptt) REVERT: D 1 MET cc_start: 0.8076 (mtp) cc_final: 0.7773 (mtm) REVERT: D 5 MET cc_start: 0.7940 (ttm) cc_final: 0.7639 (tpp) REVERT: D 127 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7805 (ttmm) REVERT: D 199 GLU cc_start: 0.7899 (mp0) cc_final: 0.7527 (mp0) REVERT: D 282 GLN cc_start: 0.6885 (tt0) cc_final: 0.6488 (tm-30) outliers start: 48 outliers final: 29 residues processed: 215 average time/residue: 0.5854 time to fit residues: 139.2382 Evaluate side-chains 206 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 981 CYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 143 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124901 restraints weight = 14938.739| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.65 r_work: 0.3125 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15700 Z= 0.145 Angle : 0.525 7.374 21462 Z= 0.283 Chirality : 0.043 0.158 2341 Planarity : 0.004 0.049 2554 Dihedral : 17.259 71.912 2558 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.04 % Allowed : 10.73 % Favored : 86.23 % 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: 0.48 (0.20), residues: 1741 helix: 1.61 (0.22), residues: 566 sheet: 0.36 (0.27), residues: 352 loop : -0.58 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 529 TYR 0.014 0.001 TYR C 757 PHE 0.013 0.001 PHE C 557 TRP 0.010 0.001 TRP A 893 HIS 0.006 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (15692) covalent geometry : angle 0.52111 / 0.28 (21458) hydrogen bonds : bond 0.03685 / 2.47 ( 695) hydrogen bonds : angle 5.21169 / 3.65 ( 1991) metal coordination : bond 0.00568 / 0.36 ( 8) metal coordination : angle 4.41540 / 2.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7657 (mtp180) REVERT: A 572 GLU cc_start: 0.6834 (mp0) cc_final: 0.6568 (mp0) REVERT: A 588 ASN cc_start: 0.7884 (p0) cc_final: 0.7596 (p0) REVERT: A 658 MET cc_start: 0.8768 (mtm) cc_final: 0.8519 (mtp) REVERT: A 739 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.6952 (mt0) REVERT: A 752 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: A 847 MET cc_start: 0.8537 (mtt) cc_final: 0.7779 (tpt) REVERT: A 856 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7813 (mtmm) REVERT: A 934 ASN cc_start: 0.8112 (t0) cc_final: 0.7466 (m-40) REVERT: B 51 LYS cc_start: 0.7299 (mtmm) cc_final: 0.7074 (mtmp) REVERT: B 214 ASP cc_start: 0.8394 (p0) cc_final: 0.8019 (p0) REVERT: B 282 GLN cc_start: 0.7226 (tt0) cc_final: 0.7012 (tt0) REVERT: C 573 ASP cc_start: 0.8285 (m-30) cc_final: 0.8025 (m-30) REVERT: C 588 ASN cc_start: 0.7972 (p0) cc_final: 0.7397 (p0) REVERT: C 632 GLU cc_start: 0.8100 (tt0) cc_final: 0.7419 (pt0) REVERT: C 664 ASP cc_start: 0.8218 (t0) cc_final: 0.7638 (t0) REVERT: C 765 TYR cc_start: 0.8745 (m-80) cc_final: 0.8515 (m-80) REVERT: C 768 SER cc_start: 0.8494 (m) cc_final: 0.8235 (p) REVERT: C 827 LYS cc_start: 0.7449 (mttt) cc_final: 0.6950 (mtpt) REVERT: C 877 GLU cc_start: 0.7112 (pt0) cc_final: 0.6220 (mm-30) REVERT: C 900 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8111 (mptt) REVERT: C 907 CYS cc_start: 0.8041 (t) cc_final: 0.7481 (m) REVERT: C 1001 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7665 (mptt) REVERT: D 1 MET cc_start: 0.8065 (mtp) cc_final: 0.7847 (mtm) REVERT: D 5 MET cc_start: 0.7945 (ttm) cc_final: 0.7653 (tpp) REVERT: D 127 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7812 (ttmm) REVERT: D 282 GLN cc_start: 0.6883 (tt0) cc_final: 0.6490 (tm-30) outliers start: 47 outliers final: 26 residues processed: 207 average time/residue: 0.5891 time to fit residues: 134.6129 Evaluate side-chains 204 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 981 CYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 107 optimal weight: 0.9990 chunk 54 optimal weight: 0.0060 chunk 48 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN C 739 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.154263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123464 restraints weight = 14873.237| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.68 r_work: 0.3132 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 0.026 15700 Z= 0.131 Angle : 0.512 7.209 21462 Z= 0.277 Chirality : 0.043 0.157 2341 Planarity : 0.004 0.043 2554 Dihedral : 17.226 71.790 2558 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.59 % Allowed : 11.57 % Favored : 85.84 % 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: 0.51 (0.20), residues: 1741 helix: 1.65 (0.22), residues: 566 sheet: 0.36 (0.27), residues: 352 loop : -0.57 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 529 TYR 0.014 0.001 TYR C 928 PHE 0.012 0.001 PHE C 557 TRP 0.011 0.001 TRP A 893 HIS 0.004 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15692) covalent geometry : angle 0.50898 / 0.28 (21458) hydrogen bonds : bond 0.03571 / 2.40 ( 695) hydrogen bonds : angle 5.15373 / 3.60 ( 1991) metal coordination : bond 0.00547 / 0.34 ( 8) metal coordination : angle 4.29120 / 2.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7632 (mtp180) REVERT: A 572 GLU cc_start: 0.6805 (mp0) cc_final: 0.6547 (mp0) REVERT: A 588 ASN cc_start: 0.7835 (p0) cc_final: 0.7569 (p0) REVERT: A 658 MET cc_start: 0.8761 (mtm) cc_final: 0.8526 (mtp) REVERT: A 739 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6897 (mt0) REVERT: A 847 MET cc_start: 0.8543 (mtt) cc_final: 0.7780 (tpt) REVERT: A 856 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7805 (mtmm) REVERT: A 900 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7410 (mttp) REVERT: A 934 ASN cc_start: 0.8091 (t0) cc_final: 0.7394 (m-40) REVERT: B 1 MET cc_start: 0.8287 (mpp) cc_final: 0.7892 (mtt) REVERT: B 51 LYS cc_start: 0.7251 (mtmm) cc_final: 0.7023 (mtmp) REVERT: B 214 ASP cc_start: 0.8360 (p0) cc_final: 0.8014 (p0) REVERT: C 573 ASP cc_start: 0.8245 (m-30) cc_final: 0.7994 (m-30) REVERT: C 588 ASN cc_start: 0.7923 (p0) cc_final: 0.7352 (p0) REVERT: C 632 GLU cc_start: 0.8092 (tt0) cc_final: 0.7402 (pt0) REVERT: C 664 ASP cc_start: 0.8205 (t0) cc_final: 0.7622 (t0) REVERT: C 765 TYR cc_start: 0.8714 (m-80) cc_final: 0.8481 (m-80) REVERT: C 768 SER cc_start: 0.8508 (m) cc_final: 0.8264 (p) REVERT: C 827 LYS cc_start: 0.7417 (mttt) cc_final: 0.6916 (mtpt) REVERT: C 877 GLU cc_start: 0.7070 (pt0) cc_final: 0.6181 (mm-30) REVERT: C 907 CYS cc_start: 0.8036 (t) cc_final: 0.7484 (m) REVERT: C 1001 LYS cc_start: 0.8076 (mmtp) cc_final: 0.7653 (mptt) REVERT: D 1 MET cc_start: 0.8045 (mtp) cc_final: 0.7834 (mtm) REVERT: D 5 MET cc_start: 0.7933 (ttm) cc_final: 0.7582 (tpp) REVERT: D 127 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7772 (ttmm) REVERT: D 282 GLN cc_start: 0.6871 (tt0) cc_final: 0.6438 (tm-30) outliers start: 40 outliers final: 20 residues processed: 198 average time/residue: 0.6117 time to fit residues: 133.8967 Evaluate side-chains 189 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 981 CYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 153 optimal weight: 0.0000 chunk 175 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 GLN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.152722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121323 restraints weight = 15031.315| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.76 r_work: 0.3120 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15700 Z= 0.136 Angle : 0.515 7.032 21462 Z= 0.278 Chirality : 0.043 0.157 2341 Planarity : 0.004 0.042 2554 Dihedral : 17.239 71.645 2558 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.65 % Allowed : 11.89 % Favored : 85.46 % 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: 0.51 (0.20), residues: 1741 helix: 1.61 (0.22), residues: 570 sheet: 0.35 (0.27), residues: 352 loop : -0.53 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 529 TYR 0.018 0.001 TYR C 707 PHE 0.012 0.001 PHE C 557 TRP 0.011 0.001 TRP A 893 HIS 0.005 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (15692) covalent geometry : angle 0.51187 / 0.28 (21458) hydrogen bonds : bond 0.03575 / 2.41 ( 695) hydrogen bonds : angle 5.12968 / 3.59 ( 1991) metal coordination : bond 0.00557 / 0.35 ( 8) metal coordination : angle 4.28736 / 2.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7630 (mtp180) REVERT: A 572 GLU cc_start: 0.6824 (mp0) cc_final: 0.6557 (mp0) REVERT: A 588 ASN cc_start: 0.7819 (p0) cc_final: 0.7567 (p0) REVERT: A 658 MET cc_start: 0.8755 (mtm) cc_final: 0.8527 (mtp) REVERT: A 739 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6858 (mt0) REVERT: A 752 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: A 847 MET cc_start: 0.8547 (mtt) cc_final: 0.7772 (tpt) REVERT: A 856 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7792 (mtmm) REVERT: A 900 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7372 (mttp) REVERT: A 934 ASN cc_start: 0.8100 (t0) cc_final: 0.7402 (m-40) REVERT: B 1 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7916 (mtt) REVERT: B 51 LYS cc_start: 0.7224 (mtmm) cc_final: 0.6996 (mtmp) REVERT: B 214 ASP cc_start: 0.8373 (p0) cc_final: 0.8025 (p0) REVERT: C 573 ASP cc_start: 0.8239 (m-30) cc_final: 0.7974 (m-30) REVERT: C 588 ASN cc_start: 0.7907 (p0) cc_final: 0.7322 (p0) REVERT: C 632 GLU cc_start: 0.8100 (tt0) cc_final: 0.7394 (pt0) REVERT: C 645 LYS cc_start: 0.8465 (mmtp) cc_final: 0.8244 (mttt) REVERT: C 664 ASP cc_start: 0.8201 (t0) cc_final: 0.7613 (t0) REVERT: C 765 TYR cc_start: 0.8720 (m-80) cc_final: 0.8498 (m-80) REVERT: C 768 SER cc_start: 0.8506 (m) cc_final: 0.8253 (p) REVERT: C 827 LYS cc_start: 0.7420 (mttt) cc_final: 0.6919 (mtpt) REVERT: C 877 GLU cc_start: 0.7059 (pt0) cc_final: 0.6172 (mm-30) REVERT: C 907 CYS cc_start: 0.8025 (t) cc_final: 0.7473 (m) REVERT: C 1001 LYS cc_start: 0.8070 (mmtp) cc_final: 0.7643 (mptt) REVERT: D 5 MET cc_start: 0.7948 (ttm) cc_final: 0.7599 (tpp) REVERT: D 127 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7754 (ttmm) REVERT: D 282 GLN cc_start: 0.6881 (tt0) cc_final: 0.6434 (tm-30) outliers start: 41 outliers final: 22 residues processed: 195 average time/residue: 0.5981 time to fit residues: 128.8473 Evaluate side-chains 192 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 981 CYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 108 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 167 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 176 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120597 restraints weight = 15094.724| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.73 r_work: 0.3152 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15700 Z= 0.122 Angle : 0.506 7.723 21462 Z= 0.274 Chirality : 0.042 0.155 2341 Planarity : 0.004 0.042 2554 Dihedral : 17.214 72.162 2558 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.39 % Allowed : 12.28 % Favored : 85.33 % 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: 0.54 (0.20), residues: 1741 helix: 1.65 (0.22), residues: 570 sheet: 0.35 (0.27), residues: 352 loop : -0.52 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 529 TYR 0.014 0.001 TYR C 928 PHE 0.011 0.001 PHE C 557 TRP 0.011 0.001 TRP A 829 HIS 0.004 0.001 HIS C 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15692) covalent geometry : angle 0.50296 / 0.27 (21458) hydrogen bonds : bond 0.03474 / 2.34 ( 695) hydrogen bonds : angle 5.09221 / 3.56 ( 1991) metal coordination : bond 0.00505 / 0.32 ( 8) metal coordination : angle 4.11962 / 2.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7608 (mtp180) REVERT: A 572 GLU cc_start: 0.6757 (mp0) cc_final: 0.6490 (mp0) REVERT: A 588 ASN cc_start: 0.7785 (p0) cc_final: 0.7547 (p0) REVERT: A 658 MET cc_start: 0.8738 (mtm) cc_final: 0.8509 (mtp) REVERT: A 739 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6818 (mt0) REVERT: A 752 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: A 847 MET cc_start: 0.8510 (mtt) cc_final: 0.7734 (tpt) REVERT: A 856 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7754 (mtmm) REVERT: A 900 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7368 (mttp) REVERT: A 934 ASN cc_start: 0.8084 (t0) cc_final: 0.7420 (m-40) REVERT: B 1 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7923 (mtt) REVERT: B 51 LYS cc_start: 0.7218 (mtmm) cc_final: 0.6986 (mtmp) REVERT: B 214 ASP cc_start: 0.8345 (p0) cc_final: 0.8015 (p0) REVERT: C 573 ASP cc_start: 0.8206 (m-30) cc_final: 0.7925 (m-30) REVERT: C 588 ASN cc_start: 0.7893 (p0) cc_final: 0.7300 (p0) REVERT: C 632 GLU cc_start: 0.8086 (tt0) cc_final: 0.7401 (pt0) REVERT: C 645 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8219 (mttt) REVERT: C 664 ASP cc_start: 0.8198 (t0) cc_final: 0.7603 (t0) REVERT: C 765 TYR cc_start: 0.8698 (m-80) cc_final: 0.8482 (m-80) REVERT: C 768 SER cc_start: 0.8499 (m) cc_final: 0.8243 (p) REVERT: C 827 LYS cc_start: 0.7402 (mttt) cc_final: 0.6899 (mtpt) REVERT: C 877 GLU cc_start: 0.7005 (pt0) cc_final: 0.6113 (mm-30) REVERT: C 907 CYS cc_start: 0.7968 (t) cc_final: 0.7427 (m) REVERT: C 1001 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7555 (mptt) REVERT: D 5 MET cc_start: 0.7908 (ttm) cc_final: 0.7552 (tpp) REVERT: D 127 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7726 (ttmm) REVERT: D 282 GLN cc_start: 0.6849 (tt0) cc_final: 0.6401 (tm-30) outliers start: 37 outliers final: 22 residues processed: 198 average time/residue: 0.5736 time to fit residues: 125.6561 Evaluate side-chains 194 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 981 CYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 144 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 67 optimal weight: 0.0010 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 157 optimal weight: 0.7980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.154099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123111 restraints weight = 15092.424| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.75 r_work: 0.3187 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15700 Z= 0.114 Angle : 0.500 7.677 21462 Z= 0.270 Chirality : 0.042 0.152 2341 Planarity : 0.004 0.042 2554 Dihedral : 17.172 73.038 2558 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.00 % Allowed : 13.06 % Favored : 84.94 % 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: 0.61 (0.20), residues: 1741 helix: 1.72 (0.22), residues: 570 sheet: 0.38 (0.27), residues: 352 loop : -0.49 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 529 TYR 0.013 0.001 TYR C 707 PHE 0.011 0.001 PHE C 557 TRP 0.015 0.001 TRP A 829 HIS 0.004 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15692) covalent geometry : angle 0.49703 / 0.27 (21458) hydrogen bonds : bond 0.03364 / 2.27 ( 695) hydrogen bonds : angle 5.02459 / 3.51 ( 1991) metal coordination : bond 0.00449 / 0.29 ( 8) metal coordination : angle 4.03150 / 1.99 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7628 (mtp180) REVERT: A 572 GLU cc_start: 0.6759 (mp0) cc_final: 0.6498 (mp0) REVERT: A 588 ASN cc_start: 0.7714 (p0) cc_final: 0.7507 (p0) REVERT: A 658 MET cc_start: 0.8725 (mtm) cc_final: 0.8507 (mtp) REVERT: A 739 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6816 (mt0) REVERT: A 752 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: A 847 MET cc_start: 0.8512 (mtt) cc_final: 0.7735 (tpt) REVERT: A 856 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7753 (mtmm) REVERT: A 900 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7391 (mttp) REVERT: A 934 ASN cc_start: 0.8060 (t0) cc_final: 0.7401 (m-40) REVERT: B 1 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: B 51 LYS cc_start: 0.7255 (mtmm) cc_final: 0.6872 (mtmp) REVERT: C 573 ASP cc_start: 0.8216 (m-30) cc_final: 0.7960 (m-30) REVERT: C 588 ASN cc_start: 0.7875 (p0) cc_final: 0.7338 (p0) REVERT: C 632 GLU cc_start: 0.8066 (tt0) cc_final: 0.7435 (pt0) REVERT: C 645 LYS cc_start: 0.8456 (mmtp) cc_final: 0.8246 (mttt) REVERT: C 664 ASP cc_start: 0.8181 (t0) cc_final: 0.7596 (t0) REVERT: C 765 TYR cc_start: 0.8683 (m-80) cc_final: 0.8424 (m-80) REVERT: C 768 SER cc_start: 0.8511 (m) cc_final: 0.8265 (p) REVERT: C 827 LYS cc_start: 0.7417 (mttt) cc_final: 0.6919 (mtpt) REVERT: C 877 GLU cc_start: 0.7021 (pt0) cc_final: 0.6125 (mm-30) REVERT: C 907 CYS cc_start: 0.7969 (t) cc_final: 0.7446 (m) REVERT: C 1001 LYS cc_start: 0.8037 (mmtp) cc_final: 0.7611 (mptt) REVERT: D 5 MET cc_start: 0.7921 (ttm) cc_final: 0.7574 (tpp) REVERT: D 58 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: D 127 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7724 (ttmm) REVERT: D 282 GLN cc_start: 0.6846 (tt0) cc_final: 0.6436 (tm-30) outliers start: 31 outliers final: 17 residues processed: 198 average time/residue: 0.5626 time to fit residues: 123.5148 Evaluate side-chains 197 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 981 CYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 100 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.155737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125060 restraints weight = 14922.626| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.67 r_work: 0.3157 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15700 Z= 0.120 Angle : 0.506 7.100 21462 Z= 0.274 Chirality : 0.042 0.153 2341 Planarity : 0.004 0.042 2554 Dihedral : 17.171 73.344 2558 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.81 % Allowed : 13.51 % Favored : 84.68 % 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: 0.63 (0.20), residues: 1741 helix: 1.74 (0.22), residues: 570 sheet: 0.40 (0.27), residues: 352 loop : -0.49 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 529 TYR 0.013 0.001 TYR C 928 PHE 0.011 0.001 PHE C 557 TRP 0.018 0.001 TRP A 829 HIS 0.004 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15692) covalent geometry : angle 0.50268 / 0.27 (21458) hydrogen bonds : bond 0.03373 / 2.27 ( 695) hydrogen bonds : angle 5.02309 / 3.52 ( 1991) metal coordination : bond 0.00477 / 0.31 ( 8) metal coordination : angle 4.00149 / 1.96 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5697.86 seconds wall clock time: 98 minutes 3.83 seconds (5883.83 seconds total)