Starting phenix.real_space_refine on Mon Sep 14 09:58:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v38_21029/09_2026/6v38_21029.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v38_21029/09_2026/6v38_21029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6v38_21029/09_2026/6v38_21029.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v38_21029/09_2026/6v38_21029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v38_21029/09_2026/6v38_21029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v38_21029/09_2026/6v38_21029.map" model { file = "/net/cci-nas-00/data/ceres_data/6v38_21029/09_2026/6v38_21029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v38_21029/09_2026/6v38_21029.cif" } resolution = 3.8 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= -0.002 sd= 0.007 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 Ca 8 9.91 5 P 28 5.49 5 Mg 4 5.21 5 S 180 5.16 5 C 19108 2.51 5 N 4564 2.21 5 O 5260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.16s 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: 29152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6979 Classifications: {'peptide': 874} Link IDs: {'PTRANS': 27, 'TRANS': 846} Chain breaks: 5 Chain: "B" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6979 Classifications: {'peptide': 874} Link IDs: {'PTRANS': 27, 'TRANS': 846} Chain breaks: 5 Chain: "C" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6979 Classifications: {'peptide': 874} Link IDs: {'PTRANS': 27, 'TRANS': 846} Chain breaks: 5 Chain: "D" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6979 Classifications: {'peptide': 874} Link IDs: {'PTRANS': 27, 'TRANS': 846} Chain breaks: 5 Chain: "A" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 309 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 8} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 5, 'POV:plan-3': 3, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 374 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 10} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-3': 3, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 7} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-1': 5, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 278 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 7} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-1': 4, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 6.63, per 1000 atoms: 0.23 Number of scatterers: 29152 At special positions: 0 Unit cell: (144.3, 144.3, 127.4, 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) Ca 8 19.99 S 180 16.00 P 28 15.00 Mg 4 11.99 O 5260 8.00 N 4564 7.00 C 19108 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: 2.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 20 sheets defined 53.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 22 through 48 removed outlier: 4.307A pdb=" N LEU A 26 " --> pdb=" O TRP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 94 through 106 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 150 through 171 removed outlier: 3.849A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 200 removed outlier: 3.770A pdb=" N ASP A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Proline residue: A 191 - end of helix removed outlier: 3.966A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.481A pdb=" N PHE A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 326 removed outlier: 4.014A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.779A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 463 through 472 removed outlier: 4.140A pdb=" N ALA A 467 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS A 468 " --> pdb=" O HIS A 464 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 472 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.029A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 549 through 555 removed outlier: 4.237A pdb=" N GLU A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.755A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.626A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 759 through 768 removed outlier: 4.211A pdb=" N GLU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 884 through 891 removed outlier: 5.022A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 918 through 920 No H-bonds generated for 'chain 'A' and resid 918 through 920' Processing helix chain 'A' and resid 921 through 930 removed outlier: 4.444A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 4.411A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'A' and resid 1019 through 1022 Processing helix chain 'B' and resid 22 through 48 removed outlier: 4.306A pdb=" N LEU B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 94 through 106 Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 150 through 171 removed outlier: 3.850A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 200 removed outlier: 3.769A pdb=" N ASP B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Proline residue: B 191 - end of helix removed outlier: 3.965A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 4.480A pdb=" N PHE B 208 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 259 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 326 removed outlier: 4.014A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 removed outlier: 3.779A pdb=" N ASP B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 434 through 451 Processing helix chain 'B' and resid 463 through 472 removed outlier: 4.140A pdb=" N ALA B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 472 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 502 through 509 Processing helix chain 'B' and resid 523 through 533 removed outlier: 4.029A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 549 through 555 removed outlier: 4.237A pdb=" N GLU B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.755A pdb=" N VAL B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 743 removed outlier: 3.627A pdb=" N ALA B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 759 through 768 removed outlier: 4.211A pdb=" N GLU B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 806 through 809 Processing helix chain 'B' and resid 817 through 830 Processing helix chain 'B' and resid 884 through 891 removed outlier: 5.022A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 918 through 920 No H-bonds generated for 'chain 'B' and resid 918 through 920' Processing helix chain 'B' and resid 921 through 930 removed outlier: 4.444A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 942 removed outlier: 4.411A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 970 Processing helix chain 'B' and resid 995 through 1008 Processing helix chain 'B' and resid 1019 through 1022 Processing helix chain 'C' and resid 22 through 48 removed outlier: 4.307A pdb=" N LEU C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 94 through 106 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 150 through 171 removed outlier: 3.850A pdb=" N ALA C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 200 removed outlier: 3.770A pdb=" N ASP C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Proline residue: C 191 - end of helix removed outlier: 3.966A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 removed outlier: 4.481A pdb=" N PHE C 208 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 326 removed outlier: 4.014A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 removed outlier: 3.779A pdb=" N ASP C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 434 through 451 Processing helix chain 'C' and resid 463 through 472 removed outlier: 4.140A pdb=" N ALA C 467 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS C 468 " --> pdb=" O HIS C 464 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 472 " --> pdb=" O HIS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.029A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 547 Processing helix chain 'C' and resid 549 through 555 removed outlier: 4.237A pdb=" N GLU C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 562 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.755A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 704 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.626A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 759 through 768 removed outlier: 4.211A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 806 through 809 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 884 through 891 removed outlier: 5.022A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 918 through 920 No H-bonds generated for 'chain 'C' and resid 918 through 920' Processing helix chain 'C' and resid 921 through 930 removed outlier: 4.443A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 942 removed outlier: 4.410A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 970 Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'C' and resid 1019 through 1022 Processing helix chain 'D' and resid 22 through 48 removed outlier: 4.307A pdb=" N LEU D 26 " --> pdb=" O TRP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 94 through 106 Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 150 through 171 removed outlier: 3.850A pdb=" N ALA D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 200 removed outlier: 3.770A pdb=" N ASP D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Proline residue: D 191 - end of helix removed outlier: 3.966A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 removed outlier: 4.480A pdb=" N PHE D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 229 through 259 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 326 removed outlier: 4.014A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY D 310 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 removed outlier: 3.779A pdb=" N ASP D 362 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 434 through 451 Processing helix chain 'D' and resid 463 through 472 removed outlier: 4.140A pdb=" N ALA D 467 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 468 " --> pdb=" O HIS D 464 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 472 " --> pdb=" O HIS D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.029A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 549 through 555 removed outlier: 4.238A pdb=" N GLU D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'D' and resid 601 through 606 removed outlier: 3.755A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 704 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.626A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 759 through 768 removed outlier: 4.211A pdb=" N GLU D 768 " --> pdb=" O LYS D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 806 through 809 Processing helix chain 'D' and resid 817 through 830 Processing helix chain 'D' and resid 884 through 891 removed outlier: 5.022A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 918 through 920 No H-bonds generated for 'chain 'D' and resid 918 through 920' Processing helix chain 'D' and resid 921 through 930 removed outlier: 4.443A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 942 removed outlier: 4.410A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1019 through 1022 Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 7.290A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 537 through 540 Processing sheet with id=AA4, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.540A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 977 through 981 removed outlier: 7.231A pdb=" N LEU A1048 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE A1014 " --> pdb=" O LEU A1048 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE A1050 " --> pdb=" O PHE A1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AA7, first strand: chain 'B' and resid 398 through 399 removed outlier: 7.290A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 537 through 540 Processing sheet with id=AA9, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.541A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 977 through 981 removed outlier: 7.231A pdb=" N LEU B1048 " --> pdb=" O ILE B1014 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE B1014 " --> pdb=" O LEU B1048 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B1050 " --> pdb=" O PHE B1012 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 139 through 140 Processing sheet with id=AB3, first strand: chain 'C' and resid 398 through 399 removed outlier: 7.290A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 537 through 540 Processing sheet with id=AB5, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.539A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 977 through 981 removed outlier: 7.232A pdb=" N LEU C1048 " --> pdb=" O ILE C1014 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE C1014 " --> pdb=" O LEU C1048 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE C1050 " --> pdb=" O PHE C1012 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 139 through 140 Processing sheet with id=AB8, first strand: chain 'D' and resid 398 through 399 removed outlier: 7.290A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 537 through 540 Processing sheet with id=AC1, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.540A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 977 through 981 removed outlier: 7.232A pdb=" N LEU D1048 " --> pdb=" O ILE D1014 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE D1014 " --> pdb=" O LEU D1048 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE D1050 " --> pdb=" O PHE D1012 " (cutoff:3.500A) 1260 hydrogen bonds defined for protein. 3576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4532 1.31 - 1.44: 8103 1.44 - 1.57: 16665 1.57 - 1.70: 212 1.70 - 1.83: 284 Bond restraints: 29796 Sorted by residual: bond pdb=" C5 CLR C1111 " pdb=" C6 CLR C1111 " ideal model delta sigma weight residual 1.332 1.575 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR A1109 " pdb=" C6 CLR A1109 " ideal model delta sigma weight residual 1.332 1.574 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR D1111 " pdb=" C6 CLR D1111 " ideal model delta sigma weight residual 1.332 1.574 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CLR B1114 " pdb=" C6 CLR B1114 " ideal model delta sigma weight residual 1.332 1.574 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CLR D1112 " pdb=" C6 CLR D1112 " ideal model delta sigma weight residual 1.332 1.573 -0.241 2.00e-02 2.50e+03 1.45e+02 ... (remaining 29791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 39562 4.05 - 8.10: 674 8.10 - 12.14: 83 12.14 - 16.19: 53 16.19 - 20.24: 28 Bond angle restraints: 40400 Sorted by residual: angle pdb=" O13 POV D1107 " pdb=" P POV D1107 " pdb=" O14 POV D1107 " ideal model delta sigma weight residual 121.11 100.87 20.24 3.00e+00 1.11e-01 4.55e+01 angle pdb=" O13 POV A1113 " pdb=" P POV A1113 " pdb=" O14 POV A1113 " ideal model delta sigma weight residual 121.11 100.90 20.21 3.00e+00 1.11e-01 4.54e+01 angle pdb=" O13 POV B1109 " pdb=" P POV B1109 " pdb=" O14 POV B1109 " ideal model delta sigma weight residual 121.11 100.92 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O13 POV A1105 " pdb=" P POV A1105 " pdb=" O14 POV A1105 " ideal model delta sigma weight residual 121.11 100.92 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O13 POV B1102 " pdb=" P POV B1102 " pdb=" O14 POV B1102 " ideal model delta sigma weight residual 121.11 100.92 20.19 3.00e+00 1.11e-01 4.53e+01 ... (remaining 40395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 16780 35.16 - 70.31: 552 70.31 - 105.47: 56 105.47 - 140.63: 4 140.63 - 175.78: 16 Dihedral angle restraints: 17408 sinusoidal: 7184 harmonic: 10224 Sorted by residual: dihedral pdb=" C29 POV C1101 " pdb="C210 POV C1101 " pdb="C211 POV C1101 " pdb="C212 POV C1101 " ideal model delta sinusoidal sigma weight residual 112.25 -71.97 -175.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 POV D1102 " pdb="C210 POV D1102 " pdb="C211 POV D1102 " pdb="C212 POV D1102 " ideal model delta sinusoidal sigma weight residual 112.25 -71.97 -175.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 POV B1103 " pdb="C210 POV B1103 " pdb="C211 POV B1103 " pdb="C212 POV B1103 " ideal model delta sinusoidal sigma weight residual 112.25 -71.97 -175.78 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 17405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3730 0.088 - 0.176: 694 0.176 - 0.264: 116 0.264 - 0.352: 4 0.352 - 0.440: 20 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C13 CLR D1112 " pdb=" C12 CLR D1112 " pdb=" C14 CLR D1112 " pdb=" C17 CLR D1112 " both_signs ideal model delta sigma weight residual False -2.93 -2.49 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" C13 CLR C1112 " pdb=" C12 CLR C1112 " pdb=" C14 CLR C1112 " pdb=" C17 CLR C1112 " both_signs ideal model delta sigma weight residual False -2.93 -2.49 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C13 CLR A1110 " pdb=" C12 CLR A1110 " pdb=" C14 CLR A1110 " pdb=" C17 CLR A1110 " both_signs ideal model delta sigma weight residual False -2.93 -2.49 -0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 4561 not shown) Planarity restraints: 4904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B1103 " 0.367 2.00e-02 2.50e+03 3.38e-01 1.14e+03 pdb=" C29 POV B1103 " -0.465 2.00e-02 2.50e+03 pdb="C210 POV B1103 " -0.176 2.00e-02 2.50e+03 pdb="C211 POV B1103 " 0.273 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1114 " -0.367 2.00e-02 2.50e+03 3.38e-01 1.14e+03 pdb=" C29 POV A1114 " 0.461 2.00e-02 2.50e+03 pdb="C210 POV A1114 " 0.182 2.00e-02 2.50e+03 pdb="C211 POV A1114 " -0.276 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C1101 " 0.367 2.00e-02 2.50e+03 3.38e-01 1.14e+03 pdb=" C29 POV C1101 " -0.463 2.00e-02 2.50e+03 pdb="C210 POV C1101 " -0.178 2.00e-02 2.50e+03 pdb="C211 POV C1101 " 0.274 2.00e-02 2.50e+03 ... (remaining 4901 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7132 2.78 - 3.31: 28131 3.31 - 3.84: 50446 3.84 - 4.37: 57793 4.37 - 4.90: 95766 Nonbonded interactions: 239268 Sorted by model distance: nonbonded pdb=" N ASN C 143 " pdb=" OD1 ASN C 143 " model vdw 2.255 3.120 nonbonded pdb=" N ASN B 143 " pdb=" OD1 ASN B 143 " model vdw 2.255 3.120 nonbonded pdb=" N ASN A 143 " pdb=" OD1 ASN A 143 " model vdw 2.256 3.120 nonbonded pdb=" N ASN D 143 " pdb=" OD1 ASN D 143 " model vdw 2.256 3.120 nonbonded pdb=" O LYS D1002 " pdb=" OG1 THR D1006 " model vdw 2.272 3.040 ... (remaining 239263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 19 through 1056) selection = (chain 'B' and resid 19 through 1056) selection = (chain 'C' and resid 19 through 1056) selection = (chain 'D' and resid 19 through 1056) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.710 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.014 0.243 29796 Z= 0.740 Angle : 1.470 20.241 40400 Z= 0.737 Chirality : 0.073 0.440 4564 Planarity : 0.018 0.338 4904 Dihedral : 18.169 175.783 10784 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.55 % Allowed : 8.73 % Favored : 86.72 % 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: -2.89 (0.12), residues: 3448 helix: -1.56 (0.10), residues: 1764 sheet: -2.10 (0.26), residues: 324 loop : -2.17 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 742 TYR 0.017 0.002 TYR A 463 PHE 0.047 0.003 PHE D1000 TRP 0.014 0.002 TRP D 767 HIS 0.006 0.002 HIS B 753 Details of bonding type rmsd/Z covalent geometry : bond 0.01390 / 0.74 (29796) covalent geometry : angle 1.46975 / 0.74 (40400) hydrogen bonds : bond 0.14788 / 9.56 ( 1260) hydrogen bonds : angle 5.67785 / 4.04 ( 3576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 400 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9201 (mmm) cc_final: 0.8863 (mpp) REVERT: A 304 MET cc_start: 0.9371 (mmm) cc_final: 0.9056 (mmm) REVERT: A 371 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7864 (m) REVERT: A 387 LEU cc_start: 0.9636 (tp) cc_final: 0.9347 (tp) REVERT: A 491 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8692 (mt) REVERT: A 825 LEU cc_start: 0.9445 (mt) cc_final: 0.9244 (mm) REVERT: A 924 MET cc_start: 0.8921 (mmm) cc_final: 0.8717 (mmt) REVERT: B 104 MET cc_start: 0.9111 (mmm) cc_final: 0.8862 (mmm) REVERT: B 152 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8615 (mp) REVERT: B 218 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9055 (p) REVERT: B 304 MET cc_start: 0.9357 (mmm) cc_final: 0.9072 (mmm) REVERT: B 387 LEU cc_start: 0.9667 (tp) cc_final: 0.9376 (tp) REVERT: B 471 ASN cc_start: 0.8364 (m110) cc_final: 0.7801 (m-40) REVERT: B 513 MET cc_start: 0.7801 (mmt) cc_final: 0.7540 (mmm) REVERT: B 597 PHE cc_start: 0.7805 (m-10) cc_final: 0.7561 (m-10) REVERT: B 878 ILE cc_start: 0.9280 (pt) cc_final: 0.8945 (pt) REVERT: B 879 ILE cc_start: 0.9012 (mt) cc_final: 0.8807 (tt) REVERT: B 924 MET cc_start: 0.9031 (mmm) cc_final: 0.8757 (mmt) REVERT: C 30 MET cc_start: 0.8581 (tpp) cc_final: 0.8193 (tpp) REVERT: C 104 MET cc_start: 0.9270 (mmm) cc_final: 0.8947 (mpp) REVERT: C 321 GLU cc_start: 0.8892 (tt0) cc_final: 0.8593 (mt-10) REVERT: C 371 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7740 (m) REVERT: C 372 ASN cc_start: 0.7760 (m-40) cc_final: 0.7429 (p0) REVERT: C 387 LEU cc_start: 0.9641 (tp) cc_final: 0.9287 (tp) REVERT: C 471 ASN cc_start: 0.8365 (m110) cc_final: 0.7796 (m-40) REVERT: C 506 MET cc_start: 0.8832 (tpt) cc_final: 0.8517 (tpp) REVERT: C 565 MET cc_start: 0.6970 (tpt) cc_final: 0.6667 (tpt) REVERT: C 825 LEU cc_start: 0.9546 (mt) cc_final: 0.9341 (mm) REVERT: C 924 MET cc_start: 0.9023 (mmm) cc_final: 0.8641 (mmt) REVERT: D 30 MET cc_start: 0.8604 (tpp) cc_final: 0.8168 (tpp) REVERT: D 104 MET cc_start: 0.9250 (mmm) cc_final: 0.8922 (mpp) REVERT: D 321 GLU cc_start: 0.8795 (tt0) cc_final: 0.8491 (mt-10) REVERT: D 371 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7705 (m) REVERT: D 372 ASN cc_start: 0.7701 (m-40) cc_final: 0.7407 (p0) REVERT: D 387 LEU cc_start: 0.9620 (tp) cc_final: 0.9259 (tp) REVERT: D 506 MET cc_start: 0.8801 (tpt) cc_final: 0.8558 (tpt) REVERT: D 565 MET cc_start: 0.6969 (tpt) cc_final: 0.6658 (tpt) REVERT: D 825 LEU cc_start: 0.9541 (mt) cc_final: 0.9325 (mm) REVERT: D 924 MET cc_start: 0.9004 (mmm) cc_final: 0.8637 (mmt) outliers start: 140 outliers final: 29 residues processed: 502 average time/residue: 0.1597 time to fit residues: 134.8794 Evaluate side-chains 282 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 809 ASN Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 265 ASN A 344 HIS A 372 ASN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN A 462 GLN ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 265 ASN B 372 ASN B 379 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 462 GLN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN B 501 GLN ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 ASN B 971 ASN C 108 GLN C 143 ASN C 200 ASN C 258 ASN C 265 ASN C 344 HIS C 379 HIS ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 GLN C 462 GLN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 971 ASN D 108 GLN D 143 ASN D 200 ASN D 258 ASN D 265 ASN D 344 HIS D 379 HIS D 459 GLN D 462 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 971 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.087485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072654 restraints weight = 105989.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.074736 restraints weight = 57742.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076174 restraints weight = 38110.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077142 restraints weight = 28541.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.077951 restraints weight = 23484.561| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29796 Z= 0.137 Angle : 0.623 13.396 40400 Z= 0.312 Chirality : 0.042 0.195 4564 Planarity : 0.004 0.050 4904 Dihedral : 15.688 179.987 4416 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.85 % Allowed : 12.34 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 3448 helix: -0.31 (0.12), residues: 1772 sheet: -1.45 (0.27), residues: 364 loop : -1.80 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 786 TYR 0.014 0.001 TYR D 928 PHE 0.033 0.002 PHE B1000 TRP 0.013 0.001 TRP C 477 HIS 0.003 0.001 HIS D 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (29796) covalent geometry : angle 0.62349 / 0.31 (40400) hydrogen bonds : bond 0.04186 / 2.73 ( 1260) hydrogen bonds : angle 4.74896 / 3.39 ( 3576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 MET cc_start: 0.9366 (ttp) cc_final: 0.9058 (ttp) REVERT: A 373 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 304 MET cc_start: 0.9282 (mmm) cc_final: 0.9034 (mmm) REVERT: B 314 MET cc_start: 0.9359 (ttp) cc_final: 0.9033 (ttp) REVERT: B 459 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.9209 (pt0) REVERT: B 471 ASN cc_start: 0.8380 (m-40) cc_final: 0.8134 (m110) REVERT: B 764 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8212 (tppt) REVERT: C 30 MET cc_start: 0.8602 (tpp) cc_final: 0.8321 (mmt) REVERT: C 104 MET cc_start: 0.9427 (mmm) cc_final: 0.9108 (mmm) REVERT: C 321 GLU cc_start: 0.8954 (tt0) cc_final: 0.8655 (mt-10) REVERT: C 459 GLN cc_start: 0.9523 (OUTLIER) cc_final: 0.9236 (pt0) REVERT: C 471 ASN cc_start: 0.8396 (m-40) cc_final: 0.8180 (m110) REVERT: C 506 MET cc_start: 0.8851 (tpt) cc_final: 0.8647 (tpp) REVERT: C 924 MET cc_start: 0.8890 (mmm) cc_final: 0.8465 (mmt) REVERT: D 30 MET cc_start: 0.8612 (tpp) cc_final: 0.8167 (mmt) REVERT: D 34 PHE cc_start: 0.8953 (m-80) cc_final: 0.8455 (m-80) REVERT: D 321 GLU cc_start: 0.8903 (tt0) cc_final: 0.8613 (mt-10) REVERT: D 459 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.9244 (pt0) REVERT: D 924 MET cc_start: 0.8871 (mmm) cc_final: 0.8449 (mmt) outliers start: 57 outliers final: 35 residues processed: 325 average time/residue: 0.1481 time to fit residues: 83.6949 Evaluate side-chains 264 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 459 GLN Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 815 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 83 optimal weight: 9.9990 chunk 276 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 228 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 335 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS B 372 ASN B 451 HIS B 459 GLN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 GLN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 459 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.086257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071489 restraints weight = 106661.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.073480 restraints weight = 58506.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074886 restraints weight = 39151.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075700 restraints weight = 29555.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076481 restraints weight = 24879.662| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29796 Z= 0.144 Angle : 0.575 11.791 40400 Z= 0.290 Chirality : 0.042 0.198 4564 Planarity : 0.004 0.048 4904 Dihedral : 14.504 166.487 4368 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.72 % Allowed : 15.00 % Favored : 83.28 % 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: -1.11 (0.14), residues: 3448 helix: 0.10 (0.12), residues: 1800 sheet: -1.09 (0.28), residues: 364 loop : -1.73 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 786 TYR 0.016 0.001 TYR B 928 PHE 0.030 0.001 PHE C1000 TRP 0.008 0.001 TRP D 22 HIS 0.004 0.001 HIS D 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (29796) covalent geometry : angle 0.57502 / 0.29 (40400) hydrogen bonds : bond 0.03844 / 2.51 ( 1260) hydrogen bonds : angle 4.70072 / 3.37 ( 3576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9087 (tpp) cc_final: 0.8839 (mpp) REVERT: A 314 MET cc_start: 0.9383 (ttp) cc_final: 0.9077 (ttp) REVERT: A 373 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 712 MET cc_start: 0.8444 (ptm) cc_final: 0.7960 (ppp) REVERT: B 217 PHE cc_start: 0.8469 (m-10) cc_final: 0.8135 (m-80) REVERT: B 314 MET cc_start: 0.9342 (ttp) cc_final: 0.9027 (ttp) REVERT: B 459 GLN cc_start: 0.9569 (OUTLIER) cc_final: 0.9240 (pt0) REVERT: B 471 ASN cc_start: 0.8185 (m-40) cc_final: 0.7689 (m-40) REVERT: B 712 MET cc_start: 0.8404 (ptp) cc_final: 0.8120 (ptp) REVERT: B 924 MET cc_start: 0.8876 (mmm) cc_final: 0.8402 (mmt) REVERT: C 104 MET cc_start: 0.9439 (mmm) cc_final: 0.9137 (mmm) REVERT: C 321 GLU cc_start: 0.8974 (tt0) cc_final: 0.8663 (mt-10) REVERT: C 459 GLN cc_start: 0.9585 (OUTLIER) cc_final: 0.9322 (pt0) REVERT: C 471 ASN cc_start: 0.8256 (m-40) cc_final: 0.7704 (m-40) REVERT: D 30 MET cc_start: 0.8646 (tpp) cc_final: 0.8415 (tpp) REVERT: D 321 GLU cc_start: 0.8905 (tt0) cc_final: 0.8596 (mt-10) REVERT: D 459 GLN cc_start: 0.9579 (OUTLIER) cc_final: 0.9304 (pt0) REVERT: D 712 MET cc_start: 0.8346 (ptp) cc_final: 0.7709 (ppp) outliers start: 53 outliers final: 34 residues processed: 284 average time/residue: 0.1561 time to fit residues: 76.9126 Evaluate side-chains 256 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 459 GLN Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 815 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 451 HIS ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN B 440 ASN B 459 GLN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 451 HIS C 459 GLN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 ASN C 971 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 ASN D 459 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 ASN D 971 ASN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.085903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071264 restraints weight = 105808.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073287 restraints weight = 57549.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074688 restraints weight = 38130.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075523 restraints weight = 28622.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.076334 restraints weight = 23736.645| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29796 Z= 0.143 Angle : 0.569 11.125 40400 Z= 0.285 Chirality : 0.042 0.254 4564 Planarity : 0.004 0.047 4904 Dihedral : 13.748 151.291 4360 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.05 % Allowed : 15.75 % Favored : 82.21 % 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: -0.84 (0.14), residues: 3448 helix: 0.33 (0.12), residues: 1812 sheet: -0.93 (0.28), residues: 364 loop : -1.67 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.015 0.001 TYR C 130 PHE 0.030 0.001 PHE B1000 TRP 0.031 0.001 TRP B 475 HIS 0.004 0.001 HIS D 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (29796) covalent geometry : angle 0.56872 / 0.29 (40400) hydrogen bonds : bond 0.03719 / 2.42 ( 1260) hydrogen bonds : angle 4.61781 / 3.31 ( 3576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8741 (tpp) cc_final: 0.8492 (tpp) REVERT: A 314 MET cc_start: 0.9366 (ttp) cc_final: 0.9060 (ttp) REVERT: A 372 ASN cc_start: 0.7086 (OUTLIER) cc_final: 0.6809 (t0) REVERT: A 373 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8681 (p) REVERT: A 442 MET cc_start: 0.9065 (tpp) cc_final: 0.8771 (mpp) REVERT: A 712 MET cc_start: 0.8460 (ptm) cc_final: 0.7967 (ppp) REVERT: B 217 PHE cc_start: 0.8504 (m-10) cc_final: 0.8199 (m-80) REVERT: B 314 MET cc_start: 0.9362 (ttp) cc_final: 0.9057 (ttp) REVERT: B 471 ASN cc_start: 0.8204 (m-40) cc_final: 0.7737 (m-40) REVERT: B 712 MET cc_start: 0.8440 (ptp) cc_final: 0.8106 (ptp) REVERT: C 104 MET cc_start: 0.9423 (mmm) cc_final: 0.9093 (mmm) REVERT: C 321 GLU cc_start: 0.8973 (tt0) cc_final: 0.8674 (mt-10) REVERT: C 471 ASN cc_start: 0.8152 (m-40) cc_final: 0.7946 (m-40) REVERT: C 712 MET cc_start: 0.8345 (ptp) cc_final: 0.7702 (ppp) REVERT: D 50 TRP cc_start: 0.6093 (t60) cc_final: 0.5848 (t60) REVERT: D 94 MET cc_start: 0.8701 (mmm) cc_final: 0.8468 (mmt) REVERT: D 321 GLU cc_start: 0.8907 (tt0) cc_final: 0.8606 (mt-10) REVERT: D 442 MET cc_start: 0.8937 (tpp) cc_final: 0.8632 (mpp) REVERT: D 712 MET cc_start: 0.8377 (ptp) cc_final: 0.8007 (ppp) outliers start: 63 outliers final: 49 residues processed: 274 average time/residue: 0.1501 time to fit residues: 71.7728 Evaluate side-chains 267 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 347 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 239 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 HIS ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 464 HIS ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1054 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.084849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.070226 restraints weight = 106507.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072199 restraints weight = 58207.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073605 restraints weight = 38838.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074426 restraints weight = 29136.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075203 restraints weight = 24160.954| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29796 Z= 0.167 Angle : 0.592 11.579 40400 Z= 0.294 Chirality : 0.042 0.207 4564 Planarity : 0.004 0.047 4904 Dihedral : 13.123 132.116 4356 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.18 % Allowed : 17.11 % Favored : 80.71 % 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: -0.68 (0.14), residues: 3448 helix: 0.43 (0.12), residues: 1812 sheet: -0.87 (0.28), residues: 364 loop : -1.54 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 974 TYR 0.019 0.001 TYR C 130 PHE 0.029 0.002 PHE B1000 TRP 0.033 0.001 TRP C 475 HIS 0.004 0.001 HIS D 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (29796) covalent geometry : angle 0.59229 / 0.29 (40400) hydrogen bonds : bond 0.03757 / 2.44 ( 1260) hydrogen bonds : angle 4.63877 / 3.33 ( 3576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 MET cc_start: 0.9360 (ttp) cc_final: 0.9080 (ttp) REVERT: A 373 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 118 LEU cc_start: 0.9399 (mm) cc_final: 0.9170 (mm) REVERT: B 217 PHE cc_start: 0.8503 (m-10) cc_final: 0.8237 (m-80) REVERT: B 314 MET cc_start: 0.9379 (ttp) cc_final: 0.9085 (ttp) REVERT: B 387 LEU cc_start: 0.9661 (tp) cc_final: 0.9411 (mp) REVERT: B 471 ASN cc_start: 0.8255 (m-40) cc_final: 0.7966 (m110) REVERT: B 564 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7915 (tt) REVERT: B 712 MET cc_start: 0.8504 (ptp) cc_final: 0.8149 (ptp) REVERT: B 924 MET cc_start: 0.8867 (mmm) cc_final: 0.8399 (mmt) REVERT: C 104 MET cc_start: 0.9418 (mmm) cc_final: 0.9060 (mmm) REVERT: C 321 GLU cc_start: 0.8935 (tt0) cc_final: 0.8660 (mt-10) REVERT: C 471 ASN cc_start: 0.8250 (m-40) cc_final: 0.7943 (m110) REVERT: C 924 MET cc_start: 0.8931 (mmm) cc_final: 0.8500 (mmt) REVERT: D 50 TRP cc_start: 0.6489 (t60) cc_final: 0.4923 (p-90) REVERT: D 94 MET cc_start: 0.8723 (mmm) cc_final: 0.8492 (mmt) REVERT: D 264 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6573 (mm-30) REVERT: D 321 GLU cc_start: 0.8937 (tt0) cc_final: 0.8660 (mt-10) REVERT: D 712 MET cc_start: 0.8370 (ptp) cc_final: 0.8028 (ppp) REVERT: D 924 MET cc_start: 0.8914 (mmm) cc_final: 0.8475 (mmt) outliers start: 67 outliers final: 54 residues processed: 269 average time/residue: 0.1521 time to fit residues: 71.8323 Evaluate side-chains 268 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 122 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 305 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 240 optimal weight: 0.0070 chunk 253 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 312 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 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 = 0.3502 r_free = 0.3502 target = 0.086321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071697 restraints weight = 104847.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073697 restraints weight = 57274.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.075113 restraints weight = 38131.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075878 restraints weight = 28591.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076613 restraints weight = 24158.633| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29796 Z= 0.110 Angle : 0.544 10.654 40400 Z= 0.270 Chirality : 0.041 0.218 4564 Planarity : 0.003 0.045 4904 Dihedral : 12.399 106.703 4356 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.88 % Allowed : 17.86 % Favored : 80.26 % 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 (0.14), residues: 3448 helix: 0.55 (0.12), residues: 1812 sheet: -0.74 (0.28), residues: 364 loop : -1.43 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.021 0.001 TYR C 130 PHE 0.029 0.001 PHE D1000 TRP 0.019 0.001 TRP D 475 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (29796) covalent geometry : angle 0.54444 / 0.27 (40400) hydrogen bonds : bond 0.03525 / 2.29 ( 1260) hydrogen bonds : angle 4.48501 / 3.22 ( 3576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 253 time to evaluate : 1.104 Fit side-chains REVERT: A 263 TRP cc_start: 0.6644 (OUTLIER) cc_final: 0.6231 (p90) REVERT: A 314 MET cc_start: 0.9357 (ttp) cc_final: 0.9065 (ttp) REVERT: A 321 GLU cc_start: 0.8901 (tt0) cc_final: 0.8658 (mt-10) REVERT: A 722 CYS cc_start: 0.8623 (m) cc_final: 0.8262 (p) REVERT: A 1051 CYS cc_start: 0.6299 (m) cc_final: 0.6046 (p) REVERT: B 277 CYS cc_start: 0.9119 (m) cc_final: 0.8833 (m) REVERT: B 314 MET cc_start: 0.9358 (ttp) cc_final: 0.9058 (ttp) REVERT: B 471 ASN cc_start: 0.8236 (m-40) cc_final: 0.7893 (m110) REVERT: B 712 MET cc_start: 0.8491 (ptp) cc_final: 0.8098 (ptp) REVERT: B 924 MET cc_start: 0.8679 (mmm) cc_final: 0.8452 (tpp) REVERT: C 34 PHE cc_start: 0.8966 (m-80) cc_final: 0.8730 (m-80) REVERT: C 104 MET cc_start: 0.9394 (mmm) cc_final: 0.9027 (mmm) REVERT: C 264 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6757 (mm-30) REVERT: C 321 GLU cc_start: 0.8892 (tt0) cc_final: 0.8625 (mt-10) REVERT: C 471 ASN cc_start: 0.8087 (m-40) cc_final: 0.7740 (m110) REVERT: C 712 MET cc_start: 0.8309 (ptp) cc_final: 0.7941 (ppp) REVERT: C 722 CYS cc_start: 0.8603 (m) cc_final: 0.8307 (p) REVERT: C 1051 CYS cc_start: 0.6800 (m) cc_final: 0.6366 (p) REVERT: D 50 TRP cc_start: 0.6589 (t60) cc_final: 0.5001 (p-90) REVERT: D 94 MET cc_start: 0.8731 (mmm) cc_final: 0.8518 (mmt) REVERT: D 264 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6825 (mm-30) REVERT: D 321 GLU cc_start: 0.8884 (tt0) cc_final: 0.8613 (mt-10) REVERT: D 712 MET cc_start: 0.8308 (ptp) cc_final: 0.7746 (ppp) REVERT: D 722 CYS cc_start: 0.8563 (m) cc_final: 0.8351 (p) REVERT: D 924 MET cc_start: 0.8762 (mmm) cc_final: 0.8514 (tpp) REVERT: D 1051 CYS cc_start: 0.6838 (m) cc_final: 0.6376 (p) outliers start: 58 outliers final: 38 residues processed: 295 average time/residue: 0.1519 time to fit residues: 78.4486 Evaluate side-chains 265 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 120 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 256 optimal weight: 5.9990 chunk 286 optimal weight: 7.9990 chunk 71 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 339 optimal weight: 0.1980 chunk 218 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS A 932 ASN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 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 = 0.3520 r_free = 0.3520 target = 0.087267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.072577 restraints weight = 104528.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074601 restraints weight = 56838.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076024 restraints weight = 37815.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076866 restraints weight = 28392.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077609 restraints weight = 23853.739| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29796 Z= 0.101 Angle : 0.544 10.592 40400 Z= 0.270 Chirality : 0.041 0.225 4564 Planarity : 0.003 0.044 4904 Dihedral : 11.832 101.323 4356 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.62 % Allowed : 18.86 % Favored : 79.51 % 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: -0.41 (0.14), residues: 3448 helix: 0.57 (0.12), residues: 1816 sheet: -0.57 (0.29), residues: 364 loop : -1.34 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 786 TYR 0.027 0.001 TYR D 130 PHE 0.030 0.001 PHE D1000 TRP 0.050 0.001 TRP A 475 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (29796) covalent geometry : angle 0.54442 / 0.27 (40400) hydrogen bonds : bond 0.03419 / 2.22 ( 1260) hydrogen bonds : angle 4.40955 / 3.17 ( 3576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 1.139 Fit side-chains REVERT: A 314 MET cc_start: 0.9349 (ttp) cc_final: 0.9054 (ttp) REVERT: A 321 GLU cc_start: 0.8894 (tt0) cc_final: 0.8624 (mt-10) REVERT: A 722 CYS cc_start: 0.8590 (m) cc_final: 0.8342 (p) REVERT: A 924 MET cc_start: 0.8587 (mmm) cc_final: 0.7261 (mmt) REVERT: A 1009 MET cc_start: 0.6741 (mmt) cc_final: 0.6484 (mmt) REVERT: B 264 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6611 (mm-30) REVERT: B 277 CYS cc_start: 0.9105 (m) cc_final: 0.8830 (m) REVERT: B 314 MET cc_start: 0.9317 (ttp) cc_final: 0.9000 (ttp) REVERT: B 460 MET cc_start: 0.8002 (mpp) cc_final: 0.7741 (mpp) REVERT: B 471 ASN cc_start: 0.8150 (m-40) cc_final: 0.7851 (m110) REVERT: B 712 MET cc_start: 0.8471 (ptp) cc_final: 0.8065 (ptp) REVERT: C 104 MET cc_start: 0.9372 (mmm) cc_final: 0.9006 (mmm) REVERT: C 264 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6746 (mm-30) REVERT: C 277 CYS cc_start: 0.9199 (m) cc_final: 0.8876 (m) REVERT: C 321 GLU cc_start: 0.8888 (tt0) cc_final: 0.8632 (mt-10) REVERT: C 471 ASN cc_start: 0.8186 (m-40) cc_final: 0.7967 (m110) REVERT: C 712 MET cc_start: 0.8296 (ptp) cc_final: 0.7742 (ppp) REVERT: C 799 MET cc_start: 0.8534 (tpp) cc_final: 0.8206 (tpp) REVERT: C 1051 CYS cc_start: 0.6640 (m) cc_final: 0.6260 (p) REVERT: D 50 TRP cc_start: 0.6557 (t60) cc_final: 0.4928 (p-90) REVERT: D 94 MET cc_start: 0.8768 (mmm) cc_final: 0.8565 (mmt) REVERT: D 264 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6867 (mm-30) REVERT: D 321 GLU cc_start: 0.8879 (tt0) cc_final: 0.8606 (mt-10) REVERT: D 1051 CYS cc_start: 0.6667 (m) cc_final: 0.6294 (p) outliers start: 50 outliers final: 38 residues processed: 293 average time/residue: 0.1536 time to fit residues: 78.7194 Evaluate side-chains 265 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 38 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 307 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 274 optimal weight: 0.0980 chunk 212 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 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 = 0.3523 r_free = 0.3523 target = 0.087508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072813 restraints weight = 104692.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074841 restraints weight = 56865.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076280 restraints weight = 37821.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.077135 restraints weight = 28352.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077712 restraints weight = 23756.928| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29796 Z= 0.101 Angle : 0.541 12.275 40400 Z= 0.268 Chirality : 0.041 0.232 4564 Planarity : 0.003 0.044 4904 Dihedral : 11.361 104.637 4352 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.66 % Allowed : 18.54 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3448 helix: 0.67 (0.12), residues: 1788 sheet: -0.47 (0.29), residues: 368 loop : -1.20 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 765 TYR 0.033 0.001 TYR B 130 PHE 0.029 0.001 PHE C1000 TRP 0.032 0.001 TRP A 475 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (29796) covalent geometry : angle 0.54111 / 0.27 (40400) hydrogen bonds : bond 0.03395 / 2.20 ( 1260) hydrogen bonds : angle 4.39557 / 3.15 ( 3576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 314 MET cc_start: 0.9344 (ttp) cc_final: 0.9049 (ttp) REVERT: A 321 GLU cc_start: 0.8872 (tt0) cc_final: 0.8591 (mt-10) REVERT: A 373 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8676 (p) REVERT: A 924 MET cc_start: 0.8531 (mmm) cc_final: 0.7212 (mmt) REVERT: B 264 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6608 (mm-30) REVERT: B 277 CYS cc_start: 0.9072 (m) cc_final: 0.8812 (m) REVERT: B 314 MET cc_start: 0.9305 (ttp) cc_final: 0.8996 (ttp) REVERT: B 471 ASN cc_start: 0.8296 (m-40) cc_final: 0.7978 (m110) REVERT: B 712 MET cc_start: 0.8471 (ptp) cc_final: 0.8129 (ptp) REVERT: B 1051 CYS cc_start: 0.6637 (m) cc_final: 0.6226 (p) REVERT: C 104 MET cc_start: 0.9367 (mmm) cc_final: 0.8994 (mmm) REVERT: C 264 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6819 (mm-30) REVERT: C 277 CYS cc_start: 0.9177 (m) cc_final: 0.8864 (m) REVERT: C 321 GLU cc_start: 0.8892 (tt0) cc_final: 0.8634 (mt-10) REVERT: C 471 ASN cc_start: 0.8215 (m-40) cc_final: 0.7822 (m-40) REVERT: C 1051 CYS cc_start: 0.6541 (m) cc_final: 0.6218 (p) REVERT: D 50 TRP cc_start: 0.6590 (t60) cc_final: 0.4956 (p-90) REVERT: D 264 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6778 (mm-30) REVERT: D 277 CYS cc_start: 0.9182 (m) cc_final: 0.8874 (m) REVERT: D 321 GLU cc_start: 0.8885 (tt0) cc_final: 0.8613 (mt-10) REVERT: D 799 MET cc_start: 0.8571 (tpp) cc_final: 0.8279 (tpp) outliers start: 51 outliers final: 39 residues processed: 288 average time/residue: 0.1537 time to fit residues: 77.4933 Evaluate side-chains 268 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 133 optimal weight: 5.9990 chunk 215 optimal weight: 0.1980 chunk 51 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 328 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 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 = 0.3502 r_free = 0.3502 target = 0.086354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071659 restraints weight = 105524.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073651 restraints weight = 57293.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075070 restraints weight = 38162.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075902 restraints weight = 28721.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076678 restraints weight = 23904.996| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29796 Z= 0.133 Angle : 0.576 11.919 40400 Z= 0.283 Chirality : 0.041 0.228 4564 Planarity : 0.003 0.045 4904 Dihedral : 11.262 104.749 4352 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.49 % Allowed : 18.83 % Favored : 79.68 % 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: -0.26 (0.15), residues: 3448 helix: 0.62 (0.12), residues: 1816 sheet: -0.43 (0.29), residues: 364 loop : -1.17 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 786 TYR 0.034 0.001 TYR A 130 PHE 0.029 0.001 PHE D1000 TRP 0.019 0.001 TRP A 475 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (29796) covalent geometry : angle 0.57583 / 0.28 (40400) hydrogen bonds : bond 0.03484 / 2.27 ( 1260) hydrogen bonds : angle 4.47384 / 3.21 ( 3576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 1.132 Fit side-chains REVERT: A 264 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6610 (mm-30) REVERT: A 277 CYS cc_start: 0.9161 (m) cc_final: 0.8847 (m) REVERT: A 314 MET cc_start: 0.9365 (ttp) cc_final: 0.9082 (ttp) REVERT: A 321 GLU cc_start: 0.8908 (tt0) cc_final: 0.8631 (mt-10) REVERT: A 373 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8828 (p) REVERT: A 924 MET cc_start: 0.8675 (mmm) cc_final: 0.7455 (mmt) REVERT: B 264 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6597 (mm-30) REVERT: B 277 CYS cc_start: 0.9115 (m) cc_final: 0.8824 (m) REVERT: B 314 MET cc_start: 0.9353 (ttp) cc_final: 0.9029 (ttp) REVERT: B 471 ASN cc_start: 0.8288 (m-40) cc_final: 0.7986 (m110) REVERT: B 691 MET cc_start: 0.5488 (tpp) cc_final: 0.5244 (tpp) REVERT: B 712 MET cc_start: 0.8466 (ptp) cc_final: 0.8139 (ptp) REVERT: B 1051 CYS cc_start: 0.6460 (m) cc_final: 0.6141 (p) REVERT: C 104 MET cc_start: 0.9367 (mmm) cc_final: 0.9000 (mmm) REVERT: C 264 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6807 (mm-30) REVERT: C 277 CYS cc_start: 0.9186 (m) cc_final: 0.8860 (m) REVERT: C 321 GLU cc_start: 0.8927 (tt0) cc_final: 0.8681 (mt-10) REVERT: C 471 ASN cc_start: 0.8290 (m-40) cc_final: 0.8001 (m110) REVERT: C 799 MET cc_start: 0.8610 (tpp) cc_final: 0.8338 (tpp) REVERT: C 807 GLN cc_start: 0.7301 (pm20) cc_final: 0.7100 (pm20) REVERT: C 1051 CYS cc_start: 0.6712 (m) cc_final: 0.6347 (p) REVERT: D 50 TRP cc_start: 0.6465 (t60) cc_final: 0.4877 (p-90) REVERT: D 104 MET cc_start: 0.9043 (tpp) cc_final: 0.8731 (tpp) REVERT: D 264 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6783 (mm-30) REVERT: D 277 CYS cc_start: 0.9190 (m) cc_final: 0.8864 (m) REVERT: D 321 GLU cc_start: 0.8927 (tt0) cc_final: 0.8657 (mt-10) REVERT: D 807 GLN cc_start: 0.7356 (pm20) cc_final: 0.7132 (pm20) outliers start: 46 outliers final: 41 residues processed: 272 average time/residue: 0.1636 time to fit residues: 76.8785 Evaluate side-chains 272 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 99 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 325 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 320 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072458 restraints weight = 104829.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.074499 restraints weight = 56952.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075902 restraints weight = 37809.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076875 restraints weight = 28462.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077593 restraints weight = 23398.223| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29796 Z= 0.108 Angle : 0.566 12.814 40400 Z= 0.278 Chirality : 0.041 0.230 4564 Planarity : 0.003 0.044 4904 Dihedral : 10.985 105.278 4352 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.46 % Allowed : 18.86 % Favored : 79.68 % 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: -0.06 (0.15), residues: 3448 helix: 0.78 (0.13), residues: 1760 sheet: -0.41 (0.28), residues: 368 loop : -0.97 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 976 TYR 0.030 0.001 TYR C 130 PHE 0.029 0.001 PHE C1012 TRP 0.020 0.001 TRP A 475 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (29796) covalent geometry : angle 0.56629 / 0.28 (40400) hydrogen bonds : bond 0.03454 / 2.25 ( 1260) hydrogen bonds : angle 4.44189 / 3.18 ( 3576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 1.117 Fit side-chains REVERT: A 104 MET cc_start: 0.8950 (tpp) cc_final: 0.8558 (tpp) REVERT: A 264 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6678 (mm-30) REVERT: A 277 CYS cc_start: 0.9164 (m) cc_final: 0.8856 (m) REVERT: A 314 MET cc_start: 0.9344 (ttp) cc_final: 0.9057 (ttp) REVERT: A 321 GLU cc_start: 0.8896 (tt0) cc_final: 0.8631 (mt-10) REVERT: A 373 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 799 MET cc_start: 0.8566 (tpp) cc_final: 0.8356 (tpp) REVERT: A 924 MET cc_start: 0.8593 (mmm) cc_final: 0.7291 (mmt) REVERT: B 264 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6644 (mm-30) REVERT: B 277 CYS cc_start: 0.9081 (m) cc_final: 0.8819 (m) REVERT: B 314 MET cc_start: 0.9334 (ttp) cc_final: 0.9004 (ttp) REVERT: B 471 ASN cc_start: 0.8288 (m-40) cc_final: 0.7992 (m110) REVERT: B 691 MET cc_start: 0.5546 (tpp) cc_final: 0.5299 (tpp) REVERT: B 712 MET cc_start: 0.8537 (ptp) cc_final: 0.8210 (ptp) REVERT: B 1051 CYS cc_start: 0.6679 (m) cc_final: 0.6213 (p) REVERT: C 104 MET cc_start: 0.9402 (mmm) cc_final: 0.9037 (mmm) REVERT: C 264 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 277 CYS cc_start: 0.9182 (m) cc_final: 0.8861 (m) REVERT: C 321 GLU cc_start: 0.8916 (tt0) cc_final: 0.8683 (mt-10) REVERT: C 471 ASN cc_start: 0.8304 (m-40) cc_final: 0.8010 (m110) REVERT: C 799 MET cc_start: 0.8621 (tpp) cc_final: 0.8351 (tpp) REVERT: C 1051 CYS cc_start: 0.6739 (m) cc_final: 0.6323 (p) REVERT: D 50 TRP cc_start: 0.6461 (t60) cc_final: 0.4887 (p-90) REVERT: D 104 MET cc_start: 0.9003 (tpp) cc_final: 0.8685 (tpp) REVERT: D 277 CYS cc_start: 0.9182 (m) cc_final: 0.8866 (m) REVERT: D 321 GLU cc_start: 0.8912 (tt0) cc_final: 0.8668 (mt-10) REVERT: D 799 MET cc_start: 0.8558 (tpp) cc_final: 0.8336 (tpp) outliers start: 45 outliers final: 39 residues processed: 284 average time/residue: 0.1556 time to fit residues: 77.0384 Evaluate side-chains 276 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 302 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.086217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.071349 restraints weight = 106823.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073340 restraints weight = 58374.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074730 restraints weight = 39072.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075664 restraints weight = 29589.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.076366 restraints weight = 24503.710| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29796 Z= 0.140 Angle : 0.594 13.381 40400 Z= 0.291 Chirality : 0.041 0.228 4564 Planarity : 0.003 0.045 4904 Dihedral : 10.951 105.017 4352 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.46 % Allowed : 19.19 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3448 helix: 0.78 (0.13), residues: 1760 sheet: -0.38 (0.28), residues: 368 loop : -0.93 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 974 TYR 0.032 0.001 TYR D 130 PHE 0.029 0.001 PHE C1000 TRP 0.014 0.001 TRP A 475 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (29796) covalent geometry : angle 0.59375 / 0.29 (40400) hydrogen bonds : bond 0.03516 / 2.28 ( 1260) hydrogen bonds : angle 4.50531 / 3.23 ( 3576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4001.74 seconds wall clock time: 70 minutes 49.84 seconds (4249.84 seconds total)