Starting phenix.real_space_refine on Wed Aug 27 02:43:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fnu_29326/08_2025/8fnu_29326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fnu_29326/08_2025/8fnu_29326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fnu_29326/08_2025/8fnu_29326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fnu_29326/08_2025/8fnu_29326.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fnu_29326/08_2025/8fnu_29326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fnu_29326/08_2025/8fnu_29326.map" } resolution = 2.5 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= -0.001 sd= 0.264 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 154 5.16 5 C 29939 2.51 5 N 7574 2.21 5 O 8547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 273 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46214 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6602 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 16, 'TRANS': 779} Chain breaks: 7 Chain: "B" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6602 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 16, 'TRANS': 779} Chain breaks: 7 Chain: "E" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6602 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 16, 'TRANS': 779} Chain breaks: 7 Chain: "F" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6602 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 16, 'TRANS': 779} Chain breaks: 7 Chain: "G" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6602 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 16, 'TRANS': 779} Chain breaks: 7 Chain: "D" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6602 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 16, 'TRANS': 779} Chain breaks: 7 Chain: "C" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6602 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 16, 'TRANS': 779} Chain breaks: 7 Time building chain proxies: 8.61, per 1000 atoms: 0.19 Number of scatterers: 46214 At special positions: 0 Unit cell: (163.9, 165, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 154 16.00 O 8547 8.00 N 7574 7.00 C 29939 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: 3.03 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10752 Finding SS restraints... Secondary structure from input PDB file: 308 helices and 28 sheets defined 65.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 31 through 48 removed outlier: 3.765A pdb=" N THR A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 48 " --> pdb=" O HIS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 80 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 98 through 114 removed outlier: 4.062A pdb=" N PHE A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 141 removed outlier: 4.307A pdb=" N ARG A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 155 through 165 removed outlier: 4.027A pdb=" N ASP A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 201 through 206 removed outlier: 4.095A pdb=" N LEU A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 205 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU A 206 " --> pdb=" O ASP A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 206' Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.877A pdb=" N TYR A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.523A pdb=" N HIS A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 258 through 274 removed outlier: 3.759A pdb=" N ILE A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 324 through 335 removed outlier: 4.391A pdb=" N GLU A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.593A pdb=" N GLU A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 350 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA A 351 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER A 352 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 383 through 403 removed outlier: 4.527A pdb=" N GLY A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 424 through 440 removed outlier: 4.548A pdb=" N TYR A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.771A pdb=" N ILE A 471 " --> pdb=" O PRO A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 491 through 518 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 522 through 535 removed outlier: 4.287A pdb=" N ALA A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 670 through 673 Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 700 through 709 Processing helix chain 'A' and resid 719 through 729 Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 761 through 774 removed outlier: 3.578A pdb=" N ASP A 765 " --> pdb=" O HIS A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 807 Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 814 through 817 removed outlier: 3.591A pdb=" N HIS A 817 " --> pdb=" O SER A 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 814 through 817' Processing helix chain 'A' and resid 824 through 827 removed outlier: 3.736A pdb=" N SER A 827 " --> pdb=" O GLU A 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 824 through 827' Processing helix chain 'A' and resid 828 through 847 removed outlier: 3.578A pdb=" N TYR A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 867 Processing helix chain 'A' and resid 869 through 879 removed outlier: 3.747A pdb=" N GLN A 873 " --> pdb=" O TYR A 869 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 899 Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.764A pdb=" N THR B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 48 " --> pdb=" O HIS B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 98 through 114 removed outlier: 4.061A pdb=" N PHE B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 141 removed outlier: 4.306A pdb=" N ARG B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 155 through 165 removed outlier: 4.027A pdb=" N ASP B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 201 through 206 removed outlier: 4.095A pdb=" N LEU B 204 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 205 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU B 206 " --> pdb=" O ASP B 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 206' Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.877A pdb=" N TYR B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 248 removed outlier: 3.523A pdb=" N HIS B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 258 through 274 removed outlier: 3.759A pdb=" N ILE B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.391A pdb=" N GLU B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.593A pdb=" N GLU B 349 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 350 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA B 351 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER B 352 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 383 through 403 removed outlier: 4.526A pdb=" N GLY B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 424 through 440 removed outlier: 4.548A pdb=" N TYR B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.771A pdb=" N ILE B 471 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 Processing helix chain 'B' and resid 491 through 518 Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 535 removed outlier: 4.287A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 569 Processing helix chain 'B' and resid 570 through 580 Processing helix chain 'B' and resid 608 through 612 Processing helix chain 'B' and resid 617 through 622 Processing helix chain 'B' and resid 670 through 673 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 700 through 709 Processing helix chain 'B' and resid 719 through 729 Processing helix chain 'B' and resid 745 through 750 Processing helix chain 'B' and resid 761 through 774 removed outlier: 3.579A pdb=" N ASP B 765 " --> pdb=" O HIS B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 807 Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 814 through 817 removed outlier: 3.591A pdb=" N HIS B 817 " --> pdb=" O SER B 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 814 through 817' Processing helix chain 'B' and resid 824 through 827 removed outlier: 3.736A pdb=" N SER B 827 " --> pdb=" O GLU B 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 824 through 827' Processing helix chain 'B' and resid 828 through 847 removed outlier: 3.578A pdb=" N TYR B 845 " --> pdb=" O LYS B 841 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 846 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 867 Processing helix chain 'B' and resid 869 through 879 removed outlier: 3.746A pdb=" N GLN B 873 " --> pdb=" O TYR B 869 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 874 " --> pdb=" O PRO B 870 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 875 " --> pdb=" O SER B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 899 Processing helix chain 'E' and resid 31 through 48 removed outlier: 3.765A pdb=" N THR E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL E 48 " --> pdb=" O HIS E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 98 through 114 removed outlier: 4.062A pdb=" N PHE E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 141 removed outlier: 4.308A pdb=" N ARG E 125 " --> pdb=" O HIS E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 155 through 165 removed outlier: 4.027A pdb=" N ASP E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 184 Processing helix chain 'E' and resid 201 through 206 removed outlier: 4.095A pdb=" N LEU E 204 " --> pdb=" O ASP E 201 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL E 205 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU E 206 " --> pdb=" O ASP E 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 201 through 206' Processing helix chain 'E' and resid 207 through 220 removed outlier: 3.876A pdb=" N TYR E 211 " --> pdb=" O ASN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 248 removed outlier: 3.523A pdb=" N HIS E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS E 246 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 254 Processing helix chain 'E' and resid 258 through 274 removed outlier: 3.759A pdb=" N ILE E 262 " --> pdb=" O ASP E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 291 Processing helix chain 'E' and resid 292 through 301 Processing helix chain 'E' and resid 324 through 335 removed outlier: 4.391A pdb=" N GLU E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 354 removed outlier: 3.593A pdb=" N GLU E 349 " --> pdb=" O ASP E 346 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 350 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA E 351 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER E 352 " --> pdb=" O GLU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'E' and resid 383 through 403 removed outlier: 4.526A pdb=" N GLY E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS E 390 " --> pdb=" O GLU E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 420 Processing helix chain 'E' and resid 424 through 440 removed outlier: 4.548A pdb=" N TYR E 428 " --> pdb=" O HIS E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 471 removed outlier: 3.771A pdb=" N ILE E 471 " --> pdb=" O PRO E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 485 Processing helix chain 'E' and resid 491 through 518 Processing helix chain 'E' and resid 519 through 521 No H-bonds generated for 'chain 'E' and resid 519 through 521' Processing helix chain 'E' and resid 522 through 535 removed outlier: 4.287A pdb=" N ALA E 535 " --> pdb=" O THR E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 569 Processing helix chain 'E' and resid 570 through 580 Processing helix chain 'E' and resid 608 through 612 Processing helix chain 'E' and resid 617 through 622 Processing helix chain 'E' and resid 670 through 673 Processing helix chain 'E' and resid 674 through 688 Processing helix chain 'E' and resid 700 through 709 Processing helix chain 'E' and resid 719 through 729 Processing helix chain 'E' and resid 745 through 750 Processing helix chain 'E' and resid 761 through 774 removed outlier: 3.579A pdb=" N ASP E 765 " --> pdb=" O HIS E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 807 Processing helix chain 'E' and resid 808 through 813 Processing helix chain 'E' and resid 814 through 817 removed outlier: 3.591A pdb=" N HIS E 817 " --> pdb=" O SER E 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 814 through 817' Processing helix chain 'E' and resid 824 through 827 removed outlier: 3.736A pdb=" N SER E 827 " --> pdb=" O GLU E 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 824 through 827' Processing helix chain 'E' and resid 828 through 847 removed outlier: 3.578A pdb=" N TYR E 845 " --> pdb=" O LYS E 841 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 846 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 854 through 867 Processing helix chain 'E' and resid 869 through 879 removed outlier: 3.747A pdb=" N GLN E 873 " --> pdb=" O TYR E 869 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 874 " --> pdb=" O PRO E 870 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU E 875 " --> pdb=" O SER E 871 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 899 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.764A pdb=" N THR F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 89 through 94 Processing helix chain 'F' and resid 98 through 114 removed outlier: 4.062A pdb=" N PHE F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 141 removed outlier: 4.307A pdb=" N ARG F 125 " --> pdb=" O HIS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 155 through 165 removed outlier: 4.027A pdb=" N ASP F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG F 163 " --> pdb=" O ASP F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 184 Processing helix chain 'F' and resid 201 through 206 removed outlier: 4.095A pdb=" N LEU F 204 " --> pdb=" O ASP F 201 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL F 205 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU F 206 " --> pdb=" O ASP F 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 206' Processing helix chain 'F' and resid 207 through 220 removed outlier: 3.877A pdb=" N TYR F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 248 removed outlier: 3.523A pdb=" N HIS F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS F 246 " --> pdb=" O GLU F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 254 Processing helix chain 'F' and resid 258 through 274 removed outlier: 3.759A pdb=" N ILE F 262 " --> pdb=" O ASP F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 291 Processing helix chain 'F' and resid 292 through 301 Processing helix chain 'F' and resid 324 through 335 removed outlier: 4.391A pdb=" N GLU F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR F 331 " --> pdb=" O ARG F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 354 removed outlier: 3.594A pdb=" N GLU F 349 " --> pdb=" O ASP F 346 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU F 350 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA F 351 " --> pdb=" O ARG F 348 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER F 352 " --> pdb=" O GLU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'F' and resid 383 through 403 removed outlier: 4.526A pdb=" N GLY F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS F 390 " --> pdb=" O GLU F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 420 Processing helix chain 'F' and resid 424 through 440 removed outlier: 4.548A pdb=" N TYR F 428 " --> pdb=" O HIS F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 471 removed outlier: 3.771A pdb=" N ILE F 471 " --> pdb=" O PRO F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 485 Processing helix chain 'F' and resid 491 through 518 Processing helix chain 'F' and resid 519 through 521 No H-bonds generated for 'chain 'F' and resid 519 through 521' Processing helix chain 'F' and resid 522 through 535 removed outlier: 4.287A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 569 Processing helix chain 'F' and resid 570 through 580 Processing helix chain 'F' and resid 608 through 612 Processing helix chain 'F' and resid 617 through 622 Processing helix chain 'F' and resid 670 through 673 Processing helix chain 'F' and resid 674 through 688 Processing helix chain 'F' and resid 700 through 709 Processing helix chain 'F' and resid 719 through 729 Processing helix chain 'F' and resid 745 through 750 Processing helix chain 'F' and resid 761 through 774 removed outlier: 3.578A pdb=" N ASP F 765 " --> pdb=" O HIS F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 807 Processing helix chain 'F' and resid 808 through 813 Processing helix chain 'F' and resid 814 through 817 removed outlier: 3.592A pdb=" N HIS F 817 " --> pdb=" O SER F 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 814 through 817' Processing helix chain 'F' and resid 824 through 827 removed outlier: 3.736A pdb=" N SER F 827 " --> pdb=" O GLU F 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 824 through 827' Processing helix chain 'F' and resid 828 through 847 removed outlier: 3.579A pdb=" N TYR F 845 " --> pdb=" O LYS F 841 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 846 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 854 through 867 Processing helix chain 'F' and resid 869 through 879 removed outlier: 3.747A pdb=" N GLN F 873 " --> pdb=" O TYR F 869 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL F 874 " --> pdb=" O PRO F 870 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU F 875 " --> pdb=" O SER F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 886 through 899 Processing helix chain 'G' and resid 31 through 48 removed outlier: 3.765A pdb=" N THR G 47 " --> pdb=" O GLU G 43 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL G 48 " --> pdb=" O HIS G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 89 through 94 Processing helix chain 'G' and resid 98 through 114 removed outlier: 4.062A pdb=" N PHE G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 141 removed outlier: 4.307A pdb=" N ARG G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 148 Processing helix chain 'G' and resid 155 through 165 removed outlier: 4.028A pdb=" N ASP G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG G 163 " --> pdb=" O ASP G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 184 Processing helix chain 'G' and resid 201 through 206 removed outlier: 4.095A pdb=" N LEU G 204 " --> pdb=" O ASP G 201 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL G 205 " --> pdb=" O LEU G 202 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU G 206 " --> pdb=" O ASP G 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 201 through 206' Processing helix chain 'G' and resid 207 through 220 removed outlier: 3.876A pdb=" N TYR G 211 " --> pdb=" O ASN G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 248 removed outlier: 3.524A pdb=" N HIS G 243 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 254 Processing helix chain 'G' and resid 258 through 274 removed outlier: 3.759A pdb=" N ILE G 262 " --> pdb=" O ASP G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 291 Processing helix chain 'G' and resid 292 through 301 Processing helix chain 'G' and resid 324 through 335 removed outlier: 4.391A pdb=" N GLU G 328 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 354 removed outlier: 3.593A pdb=" N GLU G 349 " --> pdb=" O ASP G 346 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU G 350 " --> pdb=" O ILE G 347 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA G 351 " --> pdb=" O ARG G 348 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER G 352 " --> pdb=" O GLU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'G' and resid 383 through 403 removed outlier: 4.526A pdb=" N GLY G 387 " --> pdb=" O ALA G 383 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS G 390 " --> pdb=" O GLU G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 420 Processing helix chain 'G' and resid 424 through 440 removed outlier: 4.547A pdb=" N TYR G 428 " --> pdb=" O HIS G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 471 removed outlier: 3.771A pdb=" N ILE G 471 " --> pdb=" O PRO G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 485 Processing helix chain 'G' and resid 491 through 518 Processing helix chain 'G' and resid 519 through 521 No H-bonds generated for 'chain 'G' and resid 519 through 521' Processing helix chain 'G' and resid 522 through 535 removed outlier: 4.287A pdb=" N ALA G 535 " --> pdb=" O THR G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 569 Processing helix chain 'G' and resid 570 through 580 Processing helix chain 'G' and resid 608 through 612 Processing helix chain 'G' and resid 617 through 622 Processing helix chain 'G' and resid 670 through 673 Processing helix chain 'G' and resid 674 through 688 Processing helix chain 'G' and resid 700 through 709 Processing helix chain 'G' and resid 719 through 729 Processing helix chain 'G' and resid 745 through 750 Processing helix chain 'G' and resid 761 through 774 removed outlier: 3.578A pdb=" N ASP G 765 " --> pdb=" O HIS G 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 787 through 807 Processing helix chain 'G' and resid 808 through 813 Processing helix chain 'G' and resid 814 through 817 removed outlier: 3.592A pdb=" N HIS G 817 " --> pdb=" O SER G 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 814 through 817' Processing helix chain 'G' and resid 824 through 827 removed outlier: 3.736A pdb=" N SER G 827 " --> pdb=" O GLU G 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 824 through 827' Processing helix chain 'G' and resid 828 through 847 removed outlier: 3.578A pdb=" N TYR G 845 " --> pdb=" O LYS G 841 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 846 " --> pdb=" O LEU G 842 " (cutoff:3.500A) Processing helix chain 'G' and resid 854 through 867 Processing helix chain 'G' and resid 869 through 879 removed outlier: 3.747A pdb=" N GLN G 873 " --> pdb=" O TYR G 869 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL G 874 " --> pdb=" O PRO G 870 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU G 875 " --> pdb=" O SER G 871 " (cutoff:3.500A) Processing helix chain 'G' and resid 886 through 899 Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.764A pdb=" N THR D 47 " --> pdb=" O GLU D 43 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 98 through 114 removed outlier: 4.062A pdb=" N PHE D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 141 removed outlier: 4.307A pdb=" N ARG D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 155 through 165 removed outlier: 4.027A pdb=" N ASP D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 184 Processing helix chain 'D' and resid 201 through 206 removed outlier: 4.095A pdb=" N LEU D 204 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 205 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU D 206 " --> pdb=" O ASP D 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 201 through 206' Processing helix chain 'D' and resid 207 through 220 removed outlier: 3.876A pdb=" N TYR D 211 " --> pdb=" O ASN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 248 removed outlier: 3.524A pdb=" N HIS D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 254 Processing helix chain 'D' and resid 258 through 274 removed outlier: 3.759A pdb=" N ILE D 262 " --> pdb=" O ASP D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 291 Processing helix chain 'D' and resid 292 through 301 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.391A pdb=" N GLU D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR D 331 " --> pdb=" O ARG D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.593A pdb=" N GLU D 349 " --> pdb=" O ASP D 346 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 350 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA D 351 " --> pdb=" O ARG D 348 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER D 352 " --> pdb=" O GLU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'D' and resid 383 through 403 removed outlier: 4.527A pdb=" N GLY D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 420 Processing helix chain 'D' and resid 424 through 440 removed outlier: 4.548A pdb=" N TYR D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 removed outlier: 3.771A pdb=" N ILE D 471 " --> pdb=" O PRO D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 491 through 518 Processing helix chain 'D' and resid 519 through 521 No H-bonds generated for 'chain 'D' and resid 519 through 521' Processing helix chain 'D' and resid 522 through 535 removed outlier: 4.287A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 Processing helix chain 'D' and resid 570 through 580 Processing helix chain 'D' and resid 608 through 612 Processing helix chain 'D' and resid 617 through 622 Processing helix chain 'D' and resid 670 through 673 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 700 through 709 Processing helix chain 'D' and resid 719 through 729 Processing helix chain 'D' and resid 745 through 750 Processing helix chain 'D' and resid 761 through 774 removed outlier: 3.578A pdb=" N ASP D 765 " --> pdb=" O HIS D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 807 Processing helix chain 'D' and resid 808 through 813 Processing helix chain 'D' and resid 814 through 817 removed outlier: 3.592A pdb=" N HIS D 817 " --> pdb=" O SER D 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 814 through 817' Processing helix chain 'D' and resid 824 through 827 removed outlier: 3.736A pdb=" N SER D 827 " --> pdb=" O GLU D 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 824 through 827' Processing helix chain 'D' and resid 828 through 847 removed outlier: 3.578A pdb=" N TYR D 845 " --> pdb=" O LYS D 841 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 846 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 867 Processing helix chain 'D' and resid 869 through 879 removed outlier: 3.748A pdb=" N GLN D 873 " --> pdb=" O TYR D 869 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 874 " --> pdb=" O PRO D 870 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 875 " --> pdb=" O SER D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 899 Processing helix chain 'C' and resid 31 through 48 removed outlier: 3.764A pdb=" N THR C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 48 " --> pdb=" O HIS C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 80 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 98 through 114 removed outlier: 4.062A pdb=" N PHE C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 141 removed outlier: 4.307A pdb=" N ARG C 125 " --> pdb=" O HIS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 155 through 165 removed outlier: 4.028A pdb=" N ASP C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 184 Processing helix chain 'C' and resid 201 through 206 removed outlier: 4.095A pdb=" N LEU C 204 " --> pdb=" O ASP C 201 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 205 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU C 206 " --> pdb=" O ASP C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 206' Processing helix chain 'C' and resid 207 through 220 removed outlier: 3.876A pdb=" N TYR C 211 " --> pdb=" O ASN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 248 removed outlier: 3.523A pdb=" N HIS C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 258 through 274 removed outlier: 3.759A pdb=" N ILE C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 291 Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 324 through 335 removed outlier: 4.391A pdb=" N GLU C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR C 331 " --> pdb=" O ARG C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.593A pdb=" N GLU C 349 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 350 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA C 351 " --> pdb=" O ARG C 348 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER C 352 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'C' and resid 383 through 403 removed outlier: 4.526A pdb=" N GLY C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 424 through 440 removed outlier: 4.547A pdb=" N TYR C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.771A pdb=" N ILE C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 485 Processing helix chain 'C' and resid 491 through 518 Processing helix chain 'C' and resid 519 through 521 No H-bonds generated for 'chain 'C' and resid 519 through 521' Processing helix chain 'C' and resid 522 through 535 removed outlier: 4.287A pdb=" N ALA C 535 " --> pdb=" O THR C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 569 Processing helix chain 'C' and resid 570 through 580 Processing helix chain 'C' and resid 608 through 612 Processing helix chain 'C' and resid 617 through 622 Processing helix chain 'C' and resid 670 through 673 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 700 through 709 Processing helix chain 'C' and resid 719 through 729 Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 761 through 774 removed outlier: 3.578A pdb=" N ASP C 765 " --> pdb=" O HIS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 807 Processing helix chain 'C' and resid 808 through 813 Processing helix chain 'C' and resid 814 through 817 removed outlier: 3.592A pdb=" N HIS C 817 " --> pdb=" O SER C 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 814 through 817' Processing helix chain 'C' and resid 824 through 827 removed outlier: 3.736A pdb=" N SER C 827 " --> pdb=" O GLU C 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 824 through 827' Processing helix chain 'C' and resid 828 through 847 removed outlier: 3.578A pdb=" N TYR C 845 " --> pdb=" O LYS C 841 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 846 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 867 Processing helix chain 'C' and resid 869 through 879 removed outlier: 3.747A pdb=" N GLN C 873 " --> pdb=" O TYR C 869 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 874 " --> pdb=" O PRO C 870 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU C 875 " --> pdb=" O SER C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 899 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.579A pdb=" N TYR A 83 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE A 198 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 195 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE A 228 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 197 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA3, first strand: chain 'A' and resid 603 through 604 Processing sheet with id=AA4, first strand: chain 'A' and resid 692 through 694 removed outlier: 6.300A pdb=" N ILE A 693 " --> pdb=" O GLU A 758 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.580A pdb=" N TYR B 83 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE B 198 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 195 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE B 228 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 197 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 305 through 306 Processing sheet with id=AA7, first strand: chain 'B' and resid 603 through 604 Processing sheet with id=AA8, first strand: chain 'B' and resid 692 through 694 removed outlier: 6.300A pdb=" N ILE B 693 " --> pdb=" O GLU B 758 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.580A pdb=" N TYR E 83 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE E 198 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU E 195 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE E 228 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU E 197 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 305 through 306 Processing sheet with id=AB2, first strand: chain 'E' and resid 603 through 604 Processing sheet with id=AB3, first strand: chain 'E' and resid 692 through 694 removed outlier: 6.299A pdb=" N ILE E 693 " --> pdb=" O GLU E 758 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 83 through 84 removed outlier: 6.580A pdb=" N TYR F 83 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE F 198 " --> pdb=" O TYR F 83 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU F 195 " --> pdb=" O ILE F 226 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE F 228 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU F 197 " --> pdb=" O ILE F 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 305 through 306 Processing sheet with id=AB6, first strand: chain 'F' and resid 603 through 604 Processing sheet with id=AB7, first strand: chain 'F' and resid 692 through 694 removed outlier: 6.300A pdb=" N ILE F 693 " --> pdb=" O GLU F 758 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.580A pdb=" N TYR G 83 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE G 198 " --> pdb=" O TYR G 83 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU G 195 " --> pdb=" O ILE G 226 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE G 228 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 197 " --> pdb=" O ILE G 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 305 through 306 Processing sheet with id=AC1, first strand: chain 'G' and resid 603 through 604 Processing sheet with id=AC2, first strand: chain 'G' and resid 692 through 694 removed outlier: 6.300A pdb=" N ILE G 693 " --> pdb=" O GLU G 758 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 83 through 84 removed outlier: 6.580A pdb=" N TYR D 83 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE D 198 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU D 195 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE D 228 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 197 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 305 through 306 Processing sheet with id=AC5, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AC6, first strand: chain 'D' and resid 692 through 694 removed outlier: 6.300A pdb=" N ILE D 693 " --> pdb=" O GLU D 758 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.580A pdb=" N TYR C 83 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE C 198 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU C 195 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE C 228 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 197 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 305 through 306 Processing sheet with id=AC9, first strand: chain 'C' and resid 603 through 604 Processing sheet with id=AD1, first strand: chain 'C' and resid 692 through 694 removed outlier: 6.299A pdb=" N ILE C 693 " --> pdb=" O GLU C 758 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 2338 hydrogen bonds defined for protein. 6741 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: 9.44 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14650 1.34 - 1.46: 11425 1.46 - 1.59: 20804 1.59 - 1.71: 7 1.71 - 1.84: 287 Bond restraints: 47173 Sorted by residual: bond pdb=" CD1 TYR D 401 " pdb=" CE1 TYR D 401 " ideal model delta sigma weight residual 1.382 1.293 0.089 3.00e-02 1.11e+03 8.84e+00 bond pdb=" CD1 TYR G 401 " pdb=" CE1 TYR G 401 " ideal model delta sigma weight residual 1.382 1.293 0.089 3.00e-02 1.11e+03 8.81e+00 bond pdb=" CG TYR A 401 " pdb=" CD1 TYR A 401 " ideal model delta sigma weight residual 1.389 1.327 0.062 2.10e-02 2.27e+03 8.80e+00 bond pdb=" CD1 TYR C 401 " pdb=" CE1 TYR C 401 " ideal model delta sigma weight residual 1.382 1.293 0.089 3.00e-02 1.11e+03 8.80e+00 bond pdb=" CD1 TYR F 401 " pdb=" CE1 TYR F 401 " ideal model delta sigma weight residual 1.382 1.293 0.089 3.00e-02 1.11e+03 8.78e+00 ... (remaining 47168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.64: 63378 7.64 - 15.28: 168 15.28 - 22.92: 35 22.92 - 30.55: 14 30.55 - 38.19: 14 Bond angle restraints: 63609 Sorted by residual: angle pdb=" CB MET E 45 " pdb=" CG MET E 45 " pdb=" SD MET E 45 " ideal model delta sigma weight residual 112.70 150.89 -38.19 3.00e+00 1.11e-01 1.62e+02 angle pdb=" CB MET G 45 " pdb=" CG MET G 45 " pdb=" SD MET G 45 " ideal model delta sigma weight residual 112.70 150.89 -38.19 3.00e+00 1.11e-01 1.62e+02 angle pdb=" CB MET F 45 " pdb=" CG MET F 45 " pdb=" SD MET F 45 " ideal model delta sigma weight residual 112.70 150.89 -38.19 3.00e+00 1.11e-01 1.62e+02 angle pdb=" CB MET B 45 " pdb=" CG MET B 45 " pdb=" SD MET B 45 " ideal model delta sigma weight residual 112.70 150.89 -38.19 3.00e+00 1.11e-01 1.62e+02 angle pdb=" CB MET A 45 " pdb=" CG MET A 45 " pdb=" SD MET A 45 " ideal model delta sigma weight residual 112.70 150.88 -38.18 3.00e+00 1.11e-01 1.62e+02 ... (remaining 63604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 24529 17.70 - 35.41: 2772 35.41 - 53.11: 643 53.11 - 70.81: 273 70.81 - 88.52: 105 Dihedral angle restraints: 28322 sinusoidal: 11718 harmonic: 16604 Sorted by residual: dihedral pdb=" CA MET C 355 " pdb=" C MET C 355 " pdb=" N PRO C 356 " pdb=" CA PRO C 356 " ideal model delta harmonic sigma weight residual 180.00 142.93 37.07 0 5.00e+00 4.00e-02 5.50e+01 dihedral pdb=" CA MET A 355 " pdb=" C MET A 355 " pdb=" N PRO A 356 " pdb=" CA PRO A 356 " ideal model delta harmonic sigma weight residual 180.00 142.97 37.03 0 5.00e+00 4.00e-02 5.49e+01 dihedral pdb=" CA MET E 355 " pdb=" C MET E 355 " pdb=" N PRO E 356 " pdb=" CA PRO E 356 " ideal model delta harmonic sigma weight residual 180.00 142.97 37.03 0 5.00e+00 4.00e-02 5.48e+01 ... (remaining 28319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 6880 0.116 - 0.233: 120 0.233 - 0.349: 21 0.349 - 0.465: 14 0.465 - 0.582: 21 Chirality restraints: 7056 Sorted by residual: chirality pdb=" CG LEU F 276 " pdb=" CB LEU F 276 " pdb=" CD1 LEU F 276 " pdb=" CD2 LEU F 276 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" CG LEU G 276 " pdb=" CB LEU G 276 " pdb=" CD1 LEU G 276 " pdb=" CD2 LEU G 276 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.44e+00 chirality pdb=" CG LEU B 276 " pdb=" CB LEU B 276 " pdb=" CD1 LEU B 276 " pdb=" CD2 LEU B 276 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.41e+00 ... (remaining 7053 not shown) Planarity restraints: 8015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 648 " 0.924 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG D 648 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG D 648 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG D 648 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 648 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 648 " -0.924 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG F 648 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG F 648 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG F 648 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 648 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 648 " -0.924 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG C 648 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG C 648 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 648 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 648 " -0.026 2.00e-02 2.50e+03 ... (remaining 8012 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 245 2.47 - 3.08: 33453 3.08 - 3.69: 70893 3.69 - 4.29: 110489 4.29 - 4.90: 176446 Nonbonded interactions: 391526 Sorted by model distance: nonbonded pdb=" NH2 ARG A 464 " pdb=" OE2 GLU B 487 " model vdw 1.867 3.120 nonbonded pdb=" NH2 ARG B 464 " pdb=" OE2 GLU D 487 " model vdw 2.015 3.120 nonbonded pdb=" O GLY B 63 " pdb=" OG1 THR B 64 " model vdw 2.046 3.040 nonbonded pdb=" O GLY E 63 " pdb=" OG1 THR E 64 " model vdw 2.046 3.040 nonbonded pdb=" O GLY G 63 " pdb=" OG1 THR G 64 " model vdw 2.046 3.040 ... (remaining 391521 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'D' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 35.320 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 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 : 0.006 0.089 47173 Z= 0.242 Angle : 1.293 38.193 63609 Z= 0.608 Chirality : 0.058 0.582 7056 Planarity : 0.019 0.414 8015 Dihedral : 17.418 88.515 17570 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.10 % Favored : 90.00 % Rotamer: Outliers : 4.47 % Allowed : 9.42 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: -0.70 (0.12), residues: 5460 helix: 0.93 (0.10), residues: 3157 sheet: -1.61 (0.38), residues: 168 loop : -2.61 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.073 0.004 ARG B 125 TYR 0.106 0.004 TYR F 220 PHE 0.113 0.002 PHE C 407 TRP 0.007 0.001 TRP B 418 HIS 0.039 0.003 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00563 (47173) covalent geometry : angle 1.29304 (63609) hydrogen bonds : bond 0.16358 ( 2338) hydrogen bonds : angle 6.10384 ( 6741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 713 time to evaluate : 1.420 Fit side-chains REVERT: A 254 HIS cc_start: 0.6832 (m90) cc_final: 0.6574 (m90) REVERT: A 290 ASN cc_start: 0.7373 (m-40) cc_final: 0.7172 (m-40) REVERT: A 291 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6448 (ptpp) REVERT: A 467 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: A 534 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.6055 (tmm) REVERT: A 888 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5306 (pm20) REVERT: B 171 LYS cc_start: 0.8299 (ttpp) cc_final: 0.8094 (tttt) REVERT: B 201 ASP cc_start: 0.6567 (m-30) cc_final: 0.6319 (m-30) REVERT: B 240 MET cc_start: 0.7704 (mtp) cc_final: 0.7491 (mtp) REVERT: B 467 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6328 (mm-30) REVERT: B 534 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6312 (mmm) REVERT: B 700 MET cc_start: 0.6839 (mtp) cc_final: 0.6588 (mtp) REVERT: B 863 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6939 (mttm) REVERT: B 888 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5604 (pm20) REVERT: E 368 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6010 (mm-30) REVERT: E 379 MET cc_start: 0.2148 (ppp) cc_final: 0.1445 (ppp) REVERT: E 435 MET cc_start: 0.8836 (mmm) cc_final: 0.8536 (mmm) REVERT: E 466 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6770 (tpp) REVERT: E 888 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6450 (pm20) REVERT: F 134 MET cc_start: 0.8196 (mtp) cc_final: 0.7991 (mtp) REVERT: F 475 ASP cc_start: 0.7594 (m-30) cc_final: 0.7345 (m-30) REVERT: F 863 LYS cc_start: 0.7338 (mtmt) cc_final: 0.7073 (mttm) REVERT: F 888 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6435 (pm20) REVERT: G 368 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6125 (mm-30) REVERT: G 379 MET cc_start: 0.2443 (ppp) cc_final: 0.2229 (ppp) REVERT: G 475 ASP cc_start: 0.8019 (m-30) cc_final: 0.7779 (m-30) REVERT: G 789 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7048 (mtm110) REVERT: G 810 SER cc_start: 0.7909 (t) cc_final: 0.7685 (p) REVERT: G 851 ASN cc_start: 0.8658 (m110) cc_final: 0.8451 (m110) REVERT: G 888 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6125 (pm20) REVERT: D 79 LYS cc_start: 0.7880 (pttm) cc_final: 0.7546 (pttm) REVERT: D 201 ASP cc_start: 0.6720 (m-30) cc_final: 0.6477 (m-30) REVERT: D 268 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6795 (ptt90) REVERT: D 291 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7408 (ptpt) REVERT: D 435 MET cc_start: 0.9192 (mmm) cc_final: 0.8289 (mmm) REVERT: D 564 MET cc_start: 0.8183 (mtm) cc_final: 0.7921 (mtp) REVERT: D 888 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6278 (pm20) REVERT: C 32 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8102 (m) REVERT: C 379 MET cc_start: 0.2464 (ppp) cc_final: 0.2151 (ppp) REVERT: C 475 ASP cc_start: 0.8199 (m-30) cc_final: 0.7785 (m-30) REVERT: C 789 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7072 (mtm110) REVERT: C 843 GLU cc_start: 0.7587 (pt0) cc_final: 0.7243 (pt0) REVERT: C 888 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6479 (pm20) outliers start: 228 outliers final: 18 residues processed: 802 average time/residue: 0.7373 time to fit residues: 718.5672 Evaluate side-chains 584 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 546 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 789 ARG Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 888 GLU Chi-restraints excluded: chain F residue 856 SER Chi-restraints excluded: chain F residue 888 GLU Chi-restraints excluded: chain G residue 368 GLU Chi-restraints excluded: chain G residue 466 MET Chi-restraints excluded: chain G residue 657 GLN Chi-restraints excluded: chain G residue 789 ARG Chi-restraints excluded: chain G residue 856 SER Chi-restraints excluded: chain G residue 888 GLU Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 888 GLU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 789 ARG Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 888 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 265 optimal weight: 0.0040 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 80 GLN A 129 HIS A 253 ASN A 439 GLN A 524 HIS ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 439 GLN B 524 HIS B 712 ASN B 769 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 ASN E 439 GLN E 657 GLN F 129 HIS F 183 ASN F 253 ASN F 439 GLN F 524 HIS ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 ASN G 439 GLN G 524 HIS ** G 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 HIS ** D 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN C 253 ASN C 439 GLN ** C 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.175017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.146133 restraints weight = 44266.244| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.53 r_work: 0.3420 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 47173 Z= 0.183 Angle : 0.726 12.239 63609 Z= 0.380 Chirality : 0.046 0.252 7056 Planarity : 0.005 0.112 8015 Dihedral : 7.738 117.791 6189 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.78 % Favored : 91.08 % Rotamer: Outliers : 3.57 % Allowed : 12.54 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: 0.01 (0.12), residues: 5460 helix: 1.43 (0.10), residues: 3192 sheet: -1.32 (0.39), residues: 168 loop : -2.24 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 789 TYR 0.027 0.002 TYR A 651 PHE 0.020 0.002 PHE F 433 TRP 0.015 0.002 TRP C 745 HIS 0.010 0.001 HIS F 424 Details of bonding type rmsd covalent geometry : bond 0.00417 (47173) covalent geometry : angle 0.72636 (63609) hydrogen bonds : bond 0.05134 ( 2338) hydrogen bonds : angle 4.18768 ( 6741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 692 time to evaluate : 1.634 Fit side-chains REVERT: A 30 ILE cc_start: 0.7976 (tt) cc_final: 0.7737 (pt) REVERT: A 40 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7919 (mt) REVERT: A 282 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7152 (pp) REVERT: A 284 LYS cc_start: 0.8526 (pttt) cc_final: 0.8194 (pttm) REVERT: A 290 ASN cc_start: 0.8158 (m-40) cc_final: 0.7800 (m-40) REVERT: A 350 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8021 (mm-30) REVERT: A 368 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: A 372 MET cc_start: 0.6347 (OUTLIER) cc_final: 0.6112 (mtp) REVERT: A 534 MET cc_start: 0.7971 (mmm) cc_final: 0.7689 (mmm) REVERT: A 611 ASP cc_start: 0.6926 (t0) cc_final: 0.6589 (t0) REVERT: A 648 ARG cc_start: 0.6832 (mtt180) cc_final: 0.6547 (mtp180) REVERT: A 794 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7905 (tttm) REVERT: A 843 GLU cc_start: 0.8164 (pt0) cc_final: 0.7931 (pt0) REVERT: A 863 LYS cc_start: 0.7218 (mtmt) cc_final: 0.6917 (mttt) REVERT: B 40 LEU cc_start: 0.8301 (mm) cc_final: 0.8039 (mt) REVERT: B 43 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: B 134 MET cc_start: 0.9029 (mtp) cc_final: 0.8770 (mtp) REVERT: B 140 GLU cc_start: 0.8352 (tt0) cc_final: 0.8027 (tt0) REVERT: B 248 ASN cc_start: 0.8443 (m-40) cc_final: 0.8227 (m110) REVERT: B 276 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7381 (mp) REVERT: B 284 LYS cc_start: 0.8377 (pttt) cc_final: 0.7067 (mmtm) REVERT: B 299 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.8014 (t) REVERT: B 527 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6579 (tm-30) REVERT: B 561 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: B 611 ASP cc_start: 0.7247 (t0) cc_final: 0.7011 (t0) REVERT: B 648 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7220 (mtp180) REVERT: B 700 MET cc_start: 0.8069 (mtp) cc_final: 0.7748 (mtm) REVERT: B 794 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7961 (mtpp) REVERT: B 863 LYS cc_start: 0.7474 (mtmt) cc_final: 0.7200 (mtpt) REVERT: E 153 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: E 172 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8103 (mm-30) REVERT: E 267 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7627 (tm-30) REVERT: E 282 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7386 (pp) REVERT: E 379 MET cc_start: 0.1680 (OUTLIER) cc_final: 0.1403 (ppp) REVERT: E 397 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8540 (ttm110) REVERT: E 525 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7799 (t) REVERT: E 528 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7423 (mt-10) REVERT: E 561 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: E 611 ASP cc_start: 0.6895 (t0) cc_final: 0.6589 (t0) REVERT: E 614 GLU cc_start: 0.7987 (tp30) cc_final: 0.7742 (tp30) REVERT: E 648 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7002 (ttp-170) REVERT: E 679 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8879 (mtp) REVERT: E 755 THR cc_start: 0.8456 (m) cc_final: 0.8110 (p) REVERT: E 809 MET cc_start: 0.8783 (tpp) cc_final: 0.8475 (tpt) REVERT: E 822 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8595 (tp) REVERT: E 888 GLU cc_start: 0.7630 (mp0) cc_final: 0.6670 (pm20) REVERT: F 40 LEU cc_start: 0.8413 (tp) cc_final: 0.8211 (tt) REVERT: F 43 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7431 (tt0) REVERT: F 75 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8582 (mt) REVERT: F 276 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8247 (pt) REVERT: F 284 LYS cc_start: 0.7933 (pttt) cc_final: 0.7732 (ptmt) REVERT: F 323 ASN cc_start: 0.7600 (p0) cc_final: 0.7338 (p0) REVERT: F 480 MET cc_start: 0.9291 (mtm) cc_final: 0.8986 (mtm) REVERT: F 533 TYR cc_start: 0.6210 (p90) cc_final: 0.5909 (p90) REVERT: F 557 LYS cc_start: 0.8148 (tmmt) cc_final: 0.7260 (tptp) REVERT: F 561 GLU cc_start: 0.8132 (pt0) cc_final: 0.7804 (mm-30) REVERT: F 569 LYS cc_start: 0.8114 (ptpp) cc_final: 0.7877 (mtmm) REVERT: F 611 ASP cc_start: 0.7050 (t0) cc_final: 0.6814 (t0) REVERT: F 648 ARG cc_start: 0.7573 (mtt180) cc_final: 0.6835 (ttp-170) REVERT: F 700 MET cc_start: 0.8062 (mtp) cc_final: 0.7675 (mtp) REVERT: F 864 LYS cc_start: 0.7979 (tttt) cc_final: 0.7680 (ttmm) REVERT: F 886 TYR cc_start: 0.8599 (m-80) cc_final: 0.8222 (m-80) REVERT: G 168 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: G 282 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7580 (pp) REVERT: G 323 ASN cc_start: 0.7497 (p0) cc_final: 0.7081 (m110) REVERT: G 475 ASP cc_start: 0.8596 (m-30) cc_final: 0.8330 (m-30) REVERT: G 480 MET cc_start: 0.9272 (mtm) cc_final: 0.8836 (mtt) REVERT: G 557 LYS cc_start: 0.8159 (tmmt) cc_final: 0.7519 (tptp) REVERT: G 611 ASP cc_start: 0.7061 (t0) cc_final: 0.6804 (t0) REVERT: G 648 ARG cc_start: 0.7515 (mtt180) cc_final: 0.6921 (mtm180) REVERT: G 755 THR cc_start: 0.8371 (m) cc_final: 0.8031 (p) REVERT: G 768 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7523 (mm-30) REVERT: G 795 LYS cc_start: 0.8182 (mttp) cc_final: 0.7402 (mtmt) REVERT: G 864 LYS cc_start: 0.7816 (tttt) cc_final: 0.7616 (tttm) REVERT: D 153 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: D 249 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7712 (tm-30) REVERT: D 291 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8217 (ptmt) REVERT: D 379 MET cc_start: 0.1574 (OUTLIER) cc_final: 0.0741 (ppp) REVERT: D 439 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: D 611 ASP cc_start: 0.7043 (t0) cc_final: 0.6758 (t0) REVERT: D 795 LYS cc_start: 0.8170 (mttp) cc_final: 0.7716 (mtmt) REVERT: C 153 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7959 (mp0) REVERT: C 291 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7762 (ptmt) REVERT: C 350 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: C 362 MET cc_start: 0.9224 (tpt) cc_final: 0.8990 (mmm) REVERT: C 416 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8140 (tm130) REVERT: C 528 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7872 (mt-10) REVERT: C 611 ASP cc_start: 0.6950 (t0) cc_final: 0.6740 (t0) REVERT: C 648 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7133 (mtm180) REVERT: C 755 THR cc_start: 0.8319 (m) cc_final: 0.8029 (p) REVERT: C 756 LYS cc_start: 0.8370 (ptpt) cc_final: 0.8035 (ptpt) REVERT: C 795 LYS cc_start: 0.8146 (mttp) cc_final: 0.7873 (mtpt) REVERT: C 798 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: C 843 GLU cc_start: 0.7658 (pt0) cc_final: 0.7232 (pt0) outliers start: 182 outliers final: 47 residues processed: 792 average time/residue: 0.7772 time to fit residues: 748.4164 Evaluate side-chains 652 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 577 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 379 MET Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 679 MET Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 175 CYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 692 THR Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 798 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 266 optimal weight: 0.4980 chunk 539 optimal weight: 4.9990 chunk 362 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 438 optimal weight: 0.6980 chunk 414 optimal weight: 4.9990 chunk 440 optimal weight: 0.9990 chunk 276 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 371 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN B 208 ASN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 769 GLN F 183 ASN F 253 ASN ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 ASN D 39 ASN D 208 ASN D 439 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 GLN C 80 GLN C 253 ASN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.176943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148257 restraints weight = 44425.387| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.50 r_work: 0.3432 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 47173 Z= 0.130 Angle : 0.603 11.301 63609 Z= 0.318 Chirality : 0.042 0.248 7056 Planarity : 0.004 0.107 8015 Dihedral : 5.331 58.780 6094 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 1.14 % Allowed : 6.90 % Favored : 91.96 % Rotamer: Outliers : 3.91 % Allowed : 13.89 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: 0.18 (0.12), residues: 5460 helix: 1.60 (0.09), residues: 3227 sheet: -1.27 (0.38), residues: 175 loop : -2.30 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 560 TYR 0.027 0.002 TYR A 651 PHE 0.017 0.002 PHE F 433 TRP 0.012 0.001 TRP C 418 HIS 0.009 0.001 HIS F 424 Details of bonding type rmsd covalent geometry : bond 0.00284 (47173) covalent geometry : angle 0.60269 (63609) hydrogen bonds : bond 0.04246 ( 2338) hydrogen bonds : angle 3.89986 ( 6741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 632 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8208 (mm) cc_final: 0.7977 (mt) REVERT: A 284 LYS cc_start: 0.8507 (pttt) cc_final: 0.8209 (pttm) REVERT: A 290 ASN cc_start: 0.8042 (m-40) cc_final: 0.7670 (m-40) REVERT: A 291 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8033 (ptpp) REVERT: A 350 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7928 (mm-30) REVERT: A 368 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: A 379 MET cc_start: 0.2897 (ppp) cc_final: 0.2113 (ppp) REVERT: A 420 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7570 (tt) REVERT: A 439 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7170 (mt0) REVERT: A 611 ASP cc_start: 0.6783 (t0) cc_final: 0.6435 (t0) REVERT: A 648 ARG cc_start: 0.7043 (mtt180) cc_final: 0.6761 (mtp180) REVERT: A 697 MET cc_start: 0.9075 (tpp) cc_final: 0.8818 (tpt) REVERT: A 794 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7681 (tttm) REVERT: A 843 GLU cc_start: 0.7998 (pt0) cc_final: 0.7795 (pt0) REVERT: A 863 LYS cc_start: 0.7279 (mtmt) cc_final: 0.6952 (mttt) REVERT: B 40 LEU cc_start: 0.8419 (mm) cc_final: 0.8209 (mt) REVERT: B 43 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: B 134 MET cc_start: 0.8956 (mtp) cc_final: 0.8752 (mtp) REVERT: B 140 GLU cc_start: 0.8417 (tt0) cc_final: 0.8210 (tt0) REVERT: B 153 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7470 (mm-30) REVERT: B 156 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7853 (ptp) REVERT: B 201 ASP cc_start: 0.7269 (m-30) cc_final: 0.6920 (m-30) REVERT: B 209 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8179 (mm) REVERT: B 248 ASN cc_start: 0.8662 (m-40) cc_final: 0.8376 (m110) REVERT: B 276 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7480 (mp) REVERT: B 284 LYS cc_start: 0.8326 (pttt) cc_final: 0.6998 (mmtm) REVERT: B 350 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8072 (mt-10) REVERT: B 413 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: B 527 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: B 611 ASP cc_start: 0.7235 (t0) cc_final: 0.6935 (t0) REVERT: B 648 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7134 (mtp180) REVERT: B 794 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7975 (mtpp) REVERT: B 830 GLU cc_start: 0.8271 (mp0) cc_final: 0.8036 (mp0) REVERT: B 863 LYS cc_start: 0.7388 (mtmt) cc_final: 0.7119 (mtpt) REVERT: E 153 GLU cc_start: 0.7870 (mp0) cc_final: 0.7268 (mp0) REVERT: E 172 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8162 (mm-30) REVERT: E 201 ASP cc_start: 0.7026 (m-30) cc_final: 0.6742 (m-30) REVERT: E 249 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7872 (tp30) REVERT: E 284 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.6936 (mmtm) REVERT: E 308 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7633 (pp20) REVERT: E 362 MET cc_start: 0.9164 (tpt) cc_final: 0.8894 (tmm) REVERT: E 525 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7728 (t) REVERT: E 528 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7633 (mt-10) REVERT: E 561 GLU cc_start: 0.7815 (pt0) cc_final: 0.7457 (tp30) REVERT: E 611 ASP cc_start: 0.6936 (t0) cc_final: 0.6537 (t0) REVERT: E 614 GLU cc_start: 0.8015 (tp30) cc_final: 0.7764 (tp30) REVERT: E 648 ARG cc_start: 0.7587 (mtt180) cc_final: 0.6822 (ttp-170) REVERT: E 679 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8934 (mtp) REVERT: E 755 THR cc_start: 0.8444 (m) cc_final: 0.8130 (p) REVERT: E 809 MET cc_start: 0.8737 (tpp) cc_final: 0.8400 (tpt) REVERT: E 822 ILE cc_start: 0.8925 (tt) cc_final: 0.8701 (tp) REVERT: E 888 GLU cc_start: 0.7669 (mp0) cc_final: 0.6770 (pm20) REVERT: E 895 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: F 40 LEU cc_start: 0.8464 (tp) cc_final: 0.8238 (tt) REVERT: F 43 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7500 (tt0) REVERT: F 75 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8635 (mt) REVERT: F 192 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7768 (mt) REVERT: F 323 ASN cc_start: 0.7757 (p0) cc_final: 0.7270 (m110) REVERT: F 437 TYR cc_start: 0.8849 (m-80) cc_final: 0.8640 (m-80) REVERT: F 480 MET cc_start: 0.9271 (mtm) cc_final: 0.8938 (mtm) REVERT: F 557 LYS cc_start: 0.8075 (tmmt) cc_final: 0.7284 (tptp) REVERT: F 561 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: F 611 ASP cc_start: 0.7003 (t0) cc_final: 0.6706 (t0) REVERT: F 648 ARG cc_start: 0.7522 (mtt180) cc_final: 0.6631 (ttp-170) REVERT: F 795 LYS cc_start: 0.8033 (mttp) cc_final: 0.7496 (mtmt) REVERT: F 864 LYS cc_start: 0.8019 (tttt) cc_final: 0.7697 (ttmm) REVERT: F 886 TYR cc_start: 0.8593 (m-80) cc_final: 0.8259 (m-80) REVERT: F 888 GLU cc_start: 0.7216 (mp0) cc_final: 0.6285 (pm20) REVERT: F 895 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6216 (mm-30) REVERT: F 900 LEU cc_start: 0.8303 (tp) cc_final: 0.7977 (tp) REVERT: G 282 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7448 (pp) REVERT: G 323 ASN cc_start: 0.7471 (p0) cc_final: 0.7046 (m110) REVERT: G 397 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8636 (ttm110) REVERT: G 413 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: G 439 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: G 475 ASP cc_start: 0.8316 (m-30) cc_final: 0.8024 (m-30) REVERT: G 480 MET cc_start: 0.9319 (mtm) cc_final: 0.8854 (mtt) REVERT: G 558 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: G 611 ASP cc_start: 0.6930 (t0) cc_final: 0.6687 (t0) REVERT: G 755 THR cc_start: 0.8383 (m) cc_final: 0.8061 (p) REVERT: G 795 LYS cc_start: 0.8127 (mttp) cc_final: 0.7644 (mmpt) REVERT: D 153 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: D 249 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7869 (tm-30) REVERT: D 291 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8248 (ptmt) REVERT: D 379 MET cc_start: 0.1441 (OUTLIER) cc_final: 0.0648 (ppp) REVERT: D 413 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: D 420 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6725 (tt) REVERT: D 464 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7797 (mtp-110) REVERT: D 558 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: D 611 ASP cc_start: 0.6905 (t0) cc_final: 0.6625 (t0) REVERT: D 648 ARG cc_start: 0.7557 (mmt90) cc_final: 0.6952 (mtp180) REVERT: D 659 THR cc_start: 0.8063 (p) cc_final: 0.7678 (t) REVERT: D 795 LYS cc_start: 0.8078 (mttp) cc_final: 0.7490 (mmpt) REVERT: C 248 ASN cc_start: 0.8639 (m-40) cc_final: 0.8319 (m110) REVERT: C 276 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7661 (mp) REVERT: C 362 MET cc_start: 0.9206 (tpt) cc_final: 0.8984 (mmm) REVERT: C 416 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8246 (tm130) REVERT: C 558 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: C 755 THR cc_start: 0.8420 (m) cc_final: 0.8103 (p) REVERT: C 798 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8098 (mt-10) outliers start: 199 outliers final: 53 residues processed: 757 average time/residue: 0.6923 time to fit residues: 635.5457 Evaluate side-chains 641 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 555 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 610 ASP Chi-restraints excluded: chain E residue 657 GLN Chi-restraints excluded: chain E residue 679 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 299 SER Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 413 GLU Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 558 GLU Chi-restraints excluded: chain G residue 609 ASP Chi-restraints excluded: chain G residue 610 ASP Chi-restraints excluded: chain G residue 836 SER Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 798 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 101 optimal weight: 7.9990 chunk 253 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 356 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 469 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN B 403 ASN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 183 ASN E 439 GLN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 403 ASN ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 769 GLN ** F 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 ASN G 403 ASN G 439 GLN ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 769 GLN ** G 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 ASN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN C 712 ASN ** C 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137510 restraints weight = 44094.276| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.54 r_work: 0.3316 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 47173 Z= 0.230 Angle : 0.762 14.013 63609 Z= 0.400 Chirality : 0.049 0.260 7056 Planarity : 0.006 0.128 8015 Dihedral : 5.963 51.655 6094 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.24 % Favored : 90.62 % Rotamer: Outliers : 4.98 % Allowed : 13.68 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: 0.02 (0.12), residues: 5460 helix: 1.35 (0.09), residues: 3262 sheet: -0.95 (0.42), residues: 182 loop : -2.23 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 507 TYR 0.030 0.003 TYR E 651 PHE 0.022 0.002 PHE F 414 TRP 0.017 0.002 TRP G 745 HIS 0.024 0.002 HIS F 424 Details of bonding type rmsd covalent geometry : bond 0.00547 (47173) covalent geometry : angle 0.76191 (63609) hydrogen bonds : bond 0.05640 ( 2338) hydrogen bonds : angle 4.06376 ( 6741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 632 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.7872 (t0) cc_final: 0.7629 (t0) REVERT: A 249 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7555 (tp30) REVERT: A 282 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7546 (pp) REVERT: A 284 LYS cc_start: 0.8588 (pttt) cc_final: 0.8273 (pttm) REVERT: A 323 ASN cc_start: 0.7630 (p0) cc_final: 0.7187 (m-40) REVERT: A 350 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8041 (mm-30) REVERT: A 368 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: A 379 MET cc_start: 0.3261 (ppp) cc_final: 0.2330 (ppp) REVERT: A 534 MET cc_start: 0.8245 (mmm) cc_final: 0.8031 (mmm) REVERT: A 611 ASP cc_start: 0.7005 (t0) cc_final: 0.6608 (t0) REVERT: A 697 MET cc_start: 0.9312 (tpp) cc_final: 0.8951 (tpt) REVERT: A 794 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7745 (tttm) REVERT: A 843 GLU cc_start: 0.7899 (pt0) cc_final: 0.7681 (pt0) REVERT: A 863 LYS cc_start: 0.7520 (mtmt) cc_final: 0.7087 (mtpt) REVERT: B 40 LEU cc_start: 0.8556 (mm) cc_final: 0.8311 (OUTLIER) REVERT: B 43 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: B 122 ASP cc_start: 0.7850 (m-30) cc_final: 0.7547 (m-30) REVERT: B 153 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7844 (mm-30) REVERT: B 209 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 284 LYS cc_start: 0.8382 (pttt) cc_final: 0.7219 (mmtm) REVERT: B 299 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8361 (t) REVERT: B 323 ASN cc_start: 0.7329 (p0) cc_final: 0.6965 (m110) REVERT: B 412 MET cc_start: 0.8887 (mmm) cc_final: 0.8635 (mmm) REVERT: B 424 HIS cc_start: 0.7586 (OUTLIER) cc_final: 0.6090 (t-90) REVERT: B 527 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: B 533 TYR cc_start: 0.6259 (p90) cc_final: 0.5759 (p90) REVERT: B 557 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7270 (mppt) REVERT: B 611 ASP cc_start: 0.7298 (t0) cc_final: 0.7006 (t0) REVERT: B 620 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7163 (ttmt) REVERT: B 794 LYS cc_start: 0.8524 (mtpt) cc_final: 0.8265 (mtpp) REVERT: B 863 LYS cc_start: 0.7416 (mtmt) cc_final: 0.7198 (mtpt) REVERT: B 888 GLU cc_start: 0.7429 (mp0) cc_final: 0.6723 (pm20) REVERT: E 276 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8138 (pt) REVERT: E 282 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7470 (pp) REVERT: E 308 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7644 (pp20) REVERT: E 362 MET cc_start: 0.9200 (tpt) cc_final: 0.8960 (tpt) REVERT: E 416 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: E 528 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8157 (mt-10) REVERT: E 558 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: E 611 ASP cc_start: 0.7050 (t0) cc_final: 0.6624 (t0) REVERT: E 614 GLU cc_start: 0.8030 (tp30) cc_final: 0.7726 (tp30) REVERT: E 648 ARG cc_start: 0.7710 (mtt180) cc_final: 0.6985 (ttp-170) REVERT: E 649 ASN cc_start: 0.6478 (OUTLIER) cc_final: 0.6126 (t0) REVERT: E 679 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8974 (mtp) REVERT: E 697 MET cc_start: 0.8962 (tpt) cc_final: 0.8477 (tpt) REVERT: E 755 THR cc_start: 0.8589 (m) cc_final: 0.8343 (p) REVERT: E 809 MET cc_start: 0.8826 (tpp) cc_final: 0.8521 (tpt) REVERT: E 822 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8771 (tp) REVERT: E 888 GLU cc_start: 0.7614 (mp0) cc_final: 0.6853 (pm20) REVERT: F 43 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7599 (tt0) REVERT: F 75 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8537 (mt) REVERT: F 249 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7881 (tp30) REVERT: F 284 LYS cc_start: 0.8266 (ptmt) cc_final: 0.7343 (mmtm) REVERT: F 437 TYR cc_start: 0.8950 (m-80) cc_final: 0.8749 (m-80) REVERT: F 525 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8216 (t) REVERT: F 557 LYS cc_start: 0.8213 (tmmt) cc_final: 0.7462 (tptp) REVERT: F 611 ASP cc_start: 0.7087 (t0) cc_final: 0.6794 (t0) REVERT: F 648 ARG cc_start: 0.7669 (mtt180) cc_final: 0.6904 (ttp-170) REVERT: F 864 LYS cc_start: 0.7990 (tttt) cc_final: 0.7678 (ttmm) REVERT: F 886 TYR cc_start: 0.8567 (m-80) cc_final: 0.8282 (m-80) REVERT: F 900 LEU cc_start: 0.8614 (tp) cc_final: 0.8313 (tp) REVERT: G 282 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7691 (pp) REVERT: G 290 ASN cc_start: 0.8465 (m-40) cc_final: 0.8229 (m-40) REVERT: G 323 ASN cc_start: 0.7675 (p0) cc_final: 0.7297 (m110) REVERT: G 413 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: G 533 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6788 (p90) REVERT: G 558 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: G 561 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7897 (tm-30) REVERT: G 564 MET cc_start: 0.8965 (mtm) cc_final: 0.8762 (mtm) REVERT: G 611 ASP cc_start: 0.6981 (t0) cc_final: 0.6688 (t0) REVERT: G 648 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7010 (ptt180) REVERT: G 755 THR cc_start: 0.8605 (m) cc_final: 0.8368 (p) REVERT: G 756 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8596 (pttp) REVERT: G 795 LYS cc_start: 0.8199 (mttp) cc_final: 0.7677 (mmpt) REVERT: D 149 GLN cc_start: 0.7995 (tt0) cc_final: 0.7427 (tt0) REVERT: D 153 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: D 249 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7699 (tm-30) REVERT: D 284 LYS cc_start: 0.8409 (pttt) cc_final: 0.7351 (mmtm) REVERT: D 291 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8207 (ptmt) REVERT: D 379 MET cc_start: 0.1641 (OUTLIER) cc_final: 0.0930 (ppp) REVERT: D 558 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: D 611 ASP cc_start: 0.7010 (t0) cc_final: 0.6688 (t0) REVERT: D 648 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7527 (mmm-85) REVERT: D 659 THR cc_start: 0.8222 (p) cc_final: 0.7851 (t) REVERT: D 700 MET cc_start: 0.8294 (mtp) cc_final: 0.7894 (mtt) REVERT: D 755 THR cc_start: 0.8634 (m) cc_final: 0.8278 (p) REVERT: D 888 GLU cc_start: 0.7604 (mp0) cc_final: 0.6857 (pp20) REVERT: C 40 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8071 (tt) REVERT: C 276 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7763 (mp) REVERT: C 350 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6734 (mm-30) REVERT: C 748 SER cc_start: 0.9077 (p) cc_final: 0.8756 (m) REVERT: C 798 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8096 (mt-10) outliers start: 254 outliers final: 106 residues processed: 803 average time/residue: 0.7874 time to fit residues: 773.6100 Evaluate side-chains 730 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 591 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 424 HIS Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 620 LYS Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 416 GLN Chi-restraints excluded: chain E residue 558 GLU Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 610 ASP Chi-restraints excluded: chain E residue 649 ASN Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 657 GLN Chi-restraints excluded: chain E residue 679 MET Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 756 LYS Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 864 LYS Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 299 SER Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 175 CYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 413 GLU Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 558 GLU Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 609 ASP Chi-restraints excluded: chain G residue 610 ASP Chi-restraints excluded: chain G residue 659 THR Chi-restraints excluded: chain G residue 692 THR Chi-restraints excluded: chain G residue 756 LYS Chi-restraints excluded: chain G residue 836 SER Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 863 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 296 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 379 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 367 optimal weight: 1.9990 chunk 449 optimal weight: 0.4980 chunk 266 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 253 ASN A 439 GLN A 657 GLN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN E 248 ASN E 253 ASN E 712 ASN ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 712 ASN ** F 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 880 HIS G 248 ASN ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 880 HIS D 253 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 HIS ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.171990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143798 restraints weight = 44399.676| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.47 r_work: 0.3385 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47173 Z= 0.128 Angle : 0.602 11.063 63609 Z= 0.318 Chirality : 0.042 0.304 7056 Planarity : 0.004 0.131 8015 Dihedral : 5.470 58.284 6094 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 1.10 % Allowed : 6.76 % Favored : 92.14 % Rotamer: Outliers : 4.22 % Allowed : 15.07 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: 0.22 (0.12), residues: 5460 helix: 1.65 (0.09), residues: 3199 sheet: -1.11 (0.39), residues: 175 loop : -2.27 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 464 TYR 0.025 0.002 TYR G 651 PHE 0.015 0.001 PHE B 433 TRP 0.013 0.001 TRP C 418 HIS 0.007 0.001 HIS G 880 Details of bonding type rmsd covalent geometry : bond 0.00282 (47173) covalent geometry : angle 0.60240 (63609) hydrogen bonds : bond 0.04130 ( 2338) hydrogen bonds : angle 3.78173 ( 6741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 622 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: A 282 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7048 (pp) REVERT: A 284 LYS cc_start: 0.8474 (pttt) cc_final: 0.8140 (pttm) REVERT: A 323 ASN cc_start: 0.7504 (p0) cc_final: 0.7113 (m-40) REVERT: A 350 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7728 (mm-30) REVERT: A 379 MET cc_start: 0.2681 (ppp) cc_final: 0.2111 (ppp) REVERT: A 424 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.5010 (t70) REVERT: A 439 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: A 561 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7776 (tm-30) REVERT: A 611 ASP cc_start: 0.6805 (t0) cc_final: 0.6491 (t0) REVERT: A 648 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7144 (mtp180) REVERT: A 794 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7646 (tttm) REVERT: A 863 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6854 (mtpt) REVERT: B 43 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: B 122 ASP cc_start: 0.7911 (m-30) cc_final: 0.7591 (m-30) REVERT: B 134 MET cc_start: 0.8972 (mtp) cc_final: 0.8719 (mtp) REVERT: B 248 ASN cc_start: 0.8721 (m-40) cc_final: 0.8506 (m110) REVERT: B 284 LYS cc_start: 0.8191 (pttt) cc_final: 0.7255 (mmtm) REVERT: B 299 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8313 (t) REVERT: B 350 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8166 (mt-10) REVERT: B 424 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.6557 (t-170) REVERT: B 557 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7365 (mppt) REVERT: B 611 ASP cc_start: 0.7061 (t0) cc_final: 0.6737 (t0) REVERT: B 648 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7059 (mtm180) REVERT: B 791 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: B 830 GLU cc_start: 0.8062 (mp0) cc_final: 0.7816 (mp0) REVERT: B 888 GLU cc_start: 0.7380 (mp0) cc_final: 0.6681 (pm20) REVERT: E 40 LEU cc_start: 0.8387 (tp) cc_final: 0.8159 (mm) REVERT: E 201 ASP cc_start: 0.7486 (m-30) cc_final: 0.7094 (m-30) REVERT: E 249 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7885 (tp30) REVERT: E 276 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.7894 (mp) REVERT: E 282 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7266 (pp) REVERT: E 308 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7618 (pp20) REVERT: E 362 MET cc_start: 0.9157 (tpt) cc_final: 0.8881 (tmm) REVERT: E 614 GLU cc_start: 0.8034 (tp30) cc_final: 0.7735 (tp30) REVERT: E 755 THR cc_start: 0.8466 (m) cc_final: 0.8232 (p) REVERT: E 809 MET cc_start: 0.8722 (tpp) cc_final: 0.8404 (tpt) REVERT: E 822 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8826 (tp) REVERT: E 888 GLU cc_start: 0.7706 (mp0) cc_final: 0.7040 (pm20) REVERT: E 895 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.5910 (mp0) REVERT: F 43 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7620 (tt0) REVERT: F 75 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8656 (mt) REVERT: F 276 LEU cc_start: 0.8755 (pp) cc_final: 0.8125 (mp) REVERT: F 424 HIS cc_start: 0.7283 (OUTLIER) cc_final: 0.6762 (t70) REVERT: F 437 TYR cc_start: 0.8842 (m-80) cc_final: 0.8595 (m-80) REVERT: F 480 MET cc_start: 0.9228 (mtm) cc_final: 0.8943 (mtm) REVERT: F 525 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8139 (t) REVERT: F 557 LYS cc_start: 0.8110 (tmmt) cc_final: 0.7555 (tptp) REVERT: F 611 ASP cc_start: 0.6913 (t0) cc_final: 0.6660 (t0) REVERT: F 688 GLU cc_start: 0.7357 (mp0) cc_final: 0.7114 (mp0) REVERT: F 795 LYS cc_start: 0.8225 (mttp) cc_final: 0.7583 (mmpt) REVERT: F 864 LYS cc_start: 0.8052 (tttt) cc_final: 0.7751 (ttmm) REVERT: F 886 TYR cc_start: 0.8584 (m-80) cc_final: 0.8298 (m-80) REVERT: F 888 GLU cc_start: 0.7318 (mp0) cc_final: 0.6424 (pm20) REVERT: G 123 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.5988 (mtp85) REVERT: G 282 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7460 (pp) REVERT: G 290 ASN cc_start: 0.8445 (m-40) cc_final: 0.8189 (m-40) REVERT: G 323 ASN cc_start: 0.7534 (p0) cc_final: 0.7164 (m110) REVERT: G 424 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.5192 (t70) REVERT: G 439 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7669 (mt0) REVERT: G 480 MET cc_start: 0.9086 (mtp) cc_final: 0.8873 (mtt) REVERT: G 533 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6659 (p90) REVERT: G 561 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7779 (tm-30) REVERT: G 564 MET cc_start: 0.8960 (mtm) cc_final: 0.8758 (mtm) REVERT: G 611 ASP cc_start: 0.6874 (t0) cc_final: 0.6628 (t0) REVERT: G 755 THR cc_start: 0.8525 (m) cc_final: 0.8308 (p) REVERT: G 795 LYS cc_start: 0.8104 (mttp) cc_final: 0.7585 (mmpt) REVERT: G 863 LYS cc_start: 0.7541 (mttt) cc_final: 0.7174 (mtpt) REVERT: D 123 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7270 (ttt-90) REVERT: D 249 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7849 (tm-30) REVERT: D 284 LYS cc_start: 0.8050 (pttt) cc_final: 0.7083 (mmtm) REVERT: D 291 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8210 (ptmt) REVERT: D 379 MET cc_start: 0.1645 (OUTLIER) cc_final: 0.1016 (ppp) REVERT: D 406 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.5081 (p90) REVERT: D 464 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7672 (mtp-110) REVERT: D 611 ASP cc_start: 0.6997 (t0) cc_final: 0.6660 (t0) REVERT: D 648 ARG cc_start: 0.7598 (mmt90) cc_final: 0.7019 (mtp180) REVERT: D 659 THR cc_start: 0.8109 (p) cc_final: 0.7769 (t) REVERT: D 755 THR cc_start: 0.8560 (m) cc_final: 0.8230 (p) REVERT: D 888 GLU cc_start: 0.7652 (mp0) cc_final: 0.6960 (pp20) REVERT: C 40 LEU cc_start: 0.8445 (tp) cc_final: 0.8027 (tt) REVERT: C 248 ASN cc_start: 0.8631 (m-40) cc_final: 0.8345 (m110) REVERT: C 276 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.7896 (mp) REVERT: C 350 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6756 (mm-30) REVERT: C 362 MET cc_start: 0.9193 (tpt) cc_final: 0.8987 (mmm) REVERT: C 416 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8201 (tm-30) REVERT: C 424 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.5810 (t70) REVERT: C 659 THR cc_start: 0.8303 (p) cc_final: 0.7940 (t) REVERT: C 798 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8089 (mt-10) outliers start: 215 outliers final: 85 residues processed: 770 average time/residue: 0.5343 time to fit residues: 504.9406 Evaluate side-chains 691 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 576 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 424 HIS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 406 TYR Chi-restraints excluded: chain E residue 424 HIS Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 610 ASP Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 864 LYS Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 424 HIS Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 610 ASP Chi-restraints excluded: chain G residue 756 LYS Chi-restraints excluded: chain G residue 836 SER Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 175 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 863 LYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 424 HIS Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 864 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 521 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 359 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 210 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 263 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 HIS ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 248 ASN E 439 GLN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 880 HIS ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 880 HIS D 253 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 ASN ** D 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.168666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140620 restraints weight = 44218.698| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.51 r_work: 0.3354 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47173 Z= 0.149 Angle : 0.631 12.570 63609 Z= 0.333 Chirality : 0.043 0.251 7056 Planarity : 0.005 0.127 8015 Dihedral : 5.550 57.770 6094 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.49 % Favored : 91.47 % Rotamer: Outliers : 4.24 % Allowed : 15.80 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: 0.27 (0.12), residues: 5460 helix: 1.66 (0.09), residues: 3206 sheet: -0.90 (0.41), residues: 189 loop : -2.23 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 648 TYR 0.026 0.002 TYR G 651 PHE 0.014 0.002 PHE F 414 TRP 0.013 0.002 TRP C 418 HIS 0.008 0.001 HIS G 880 Details of bonding type rmsd covalent geometry : bond 0.00341 (47173) covalent geometry : angle 0.63078 (63609) hydrogen bonds : bond 0.04539 ( 2338) hydrogen bonds : angle 3.79726 ( 6741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 611 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.7437 (m-80) cc_final: 0.7173 (t80) REVERT: A 284 LYS cc_start: 0.8435 (pttt) cc_final: 0.8138 (pttm) REVERT: A 323 ASN cc_start: 0.7636 (p0) cc_final: 0.7241 (m-40) REVERT: A 350 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7812 (mm-30) REVERT: A 379 MET cc_start: 0.2792 (ppp) cc_final: 0.1990 (ppp) REVERT: A 406 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.3838 (p90) REVERT: A 424 HIS cc_start: 0.7428 (OUTLIER) cc_final: 0.5777 (t70) REVERT: A 561 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7794 (tm-30) REVERT: A 648 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7314 (mtp180) REVERT: A 794 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7757 (tttm) REVERT: A 822 ILE cc_start: 0.8883 (tp) cc_final: 0.8563 (pp) REVERT: A 863 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6863 (mtpt) REVERT: B 43 GLU cc_start: 0.7864 (tp30) cc_final: 0.7592 (mt-10) REVERT: B 122 ASP cc_start: 0.7930 (m-30) cc_final: 0.7596 (m-30) REVERT: B 248 ASN cc_start: 0.8791 (m-40) cc_final: 0.8563 (m110) REVERT: B 284 LYS cc_start: 0.8220 (pttt) cc_final: 0.7233 (mmtm) REVERT: B 299 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8319 (t) REVERT: B 424 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.6622 (t70) REVERT: B 611 ASP cc_start: 0.7121 (t0) cc_final: 0.6836 (t0) REVERT: B 791 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: B 830 GLU cc_start: 0.8029 (mp0) cc_final: 0.7805 (mp0) REVERT: B 888 GLU cc_start: 0.7410 (mp0) cc_final: 0.6698 (pm20) REVERT: E 201 ASP cc_start: 0.7684 (m-30) cc_final: 0.7322 (m-30) REVERT: E 276 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7889 (mp) REVERT: E 282 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7305 (pp) REVERT: E 308 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: E 362 MET cc_start: 0.9151 (tpt) cc_final: 0.8915 (tmm) REVERT: E 614 GLU cc_start: 0.7972 (tp30) cc_final: 0.7670 (tp30) REVERT: E 755 THR cc_start: 0.8497 (m) cc_final: 0.8266 (p) REVERT: E 794 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8089 (tttm) REVERT: E 809 MET cc_start: 0.8737 (tpp) cc_final: 0.8459 (tpt) REVERT: E 822 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8828 (tp) REVERT: E 888 GLU cc_start: 0.7651 (mp0) cc_final: 0.6967 (pm20) REVERT: F 43 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7600 (tt0) REVERT: F 75 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8632 (mt) REVERT: F 276 LEU cc_start: 0.8713 (pp) cc_final: 0.8182 (mp) REVERT: F 424 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.6867 (t70) REVERT: F 437 TYR cc_start: 0.8869 (m-80) cc_final: 0.8631 (m-80) REVERT: F 557 LYS cc_start: 0.8128 (tmmt) cc_final: 0.7567 (tptp) REVERT: F 611 ASP cc_start: 0.6802 (t0) cc_final: 0.6589 (t0) REVERT: F 688 GLU cc_start: 0.7237 (mp0) cc_final: 0.6981 (mp0) REVERT: F 864 LYS cc_start: 0.8031 (tttt) cc_final: 0.7724 (ttmm) REVERT: F 886 TYR cc_start: 0.8514 (m-80) cc_final: 0.8289 (m-80) REVERT: F 888 GLU cc_start: 0.7299 (mp0) cc_final: 0.6460 (pm20) REVERT: G 123 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6066 (mtp85) REVERT: G 249 GLU cc_start: 0.8035 (tp30) cc_final: 0.7825 (tp30) REVERT: G 282 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7555 (pp) REVERT: G 290 ASN cc_start: 0.8467 (m-40) cc_final: 0.8147 (m-40) REVERT: G 323 ASN cc_start: 0.7560 (p0) cc_final: 0.7185 (m110) REVERT: G 424 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.5483 (t70) REVERT: G 439 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: G 480 MET cc_start: 0.9101 (mtp) cc_final: 0.8834 (mtt) REVERT: G 533 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6730 (p90) REVERT: G 561 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7791 (tm-30) REVERT: G 755 THR cc_start: 0.8621 (m) cc_final: 0.8419 (p) REVERT: G 795 LYS cc_start: 0.8138 (mttp) cc_final: 0.7605 (mmpt) REVERT: D 68 SER cc_start: 0.8074 (m) cc_final: 0.7605 (t) REVERT: D 123 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7291 (ttt-90) REVERT: D 152 PRO cc_start: 0.8171 (Cg_exo) cc_final: 0.7948 (Cg_endo) REVERT: D 249 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7758 (tm-30) REVERT: D 284 LYS cc_start: 0.8054 (pttt) cc_final: 0.7085 (mmtm) REVERT: D 350 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: D 379 MET cc_start: 0.1948 (OUTLIER) cc_final: 0.1440 (ppp) REVERT: D 406 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.4723 (p90) REVERT: D 534 MET cc_start: 0.8137 (mmm) cc_final: 0.7878 (tpp) REVERT: D 648 ARG cc_start: 0.7597 (mmt90) cc_final: 0.7110 (mtp180) REVERT: D 659 THR cc_start: 0.8175 (p) cc_final: 0.7823 (t) REVERT: D 755 THR cc_start: 0.8589 (m) cc_final: 0.8283 (p) REVERT: D 888 GLU cc_start: 0.7675 (mp0) cc_final: 0.7036 (pp20) REVERT: C 40 LEU cc_start: 0.8420 (tp) cc_final: 0.8024 (tt) REVERT: C 248 ASN cc_start: 0.8643 (m-40) cc_final: 0.8341 (m110) REVERT: C 249 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: C 276 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7851 (mp) REVERT: C 350 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: C 368 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7066 (mm-30) REVERT: C 424 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.6319 (t-170) REVERT: C 798 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8065 (mt-10) outliers start: 216 outliers final: 100 residues processed: 758 average time/residue: 0.5210 time to fit residues: 485.8538 Evaluate side-chains 719 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 592 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 424 HIS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 406 TYR Chi-restraints excluded: chain E residue 424 HIS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 610 ASP Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 756 LYS Chi-restraints excluded: chain E residue 794 LYS Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 864 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 299 SER Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 424 HIS Chi-restraints excluded: chain F residue 534 MET Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 610 ASP Chi-restraints excluded: chain G residue 756 LYS Chi-restraints excluded: chain G residue 836 SER Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 175 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 863 LYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 424 HIS Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 864 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 448 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 131 optimal weight: 0.0570 chunk 112 optimal weight: 0.9980 chunk 279 optimal weight: 0.4980 chunk 547 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 444 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 532 optimal weight: 0.6980 chunk 394 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 439 GLN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 HIS B 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN E 439 GLN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 ASN ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 712 ASN G 880 HIS D 253 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.172444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144671 restraints weight = 44231.075| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.47 r_work: 0.3402 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 47173 Z= 0.119 Angle : 0.580 11.194 63609 Z= 0.306 Chirality : 0.041 0.352 7056 Planarity : 0.004 0.117 8015 Dihedral : 5.269 38.708 6090 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.95 % Allowed : 7.07 % Favored : 91.98 % Rotamer: Outliers : 3.41 % Allowed : 16.84 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: 0.34 (0.12), residues: 5460 helix: 1.80 (0.09), residues: 3199 sheet: -1.06 (0.39), residues: 175 loop : -2.31 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 648 TYR 0.023 0.001 TYR E 651 PHE 0.014 0.001 PHE D 330 TRP 0.013 0.001 TRP C 418 HIS 0.007 0.001 HIS G 880 Details of bonding type rmsd covalent geometry : bond 0.00259 (47173) covalent geometry : angle 0.58016 (63609) hydrogen bonds : bond 0.03913 ( 2338) hydrogen bonds : angle 3.69683 ( 6741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 613 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: A 284 LYS cc_start: 0.8403 (pttt) cc_final: 0.8052 (pttm) REVERT: A 323 ASN cc_start: 0.7567 (p0) cc_final: 0.7215 (m-40) REVERT: A 350 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7709 (mm-30) REVERT: A 379 MET cc_start: 0.2568 (ppp) cc_final: 0.2030 (ppp) REVERT: A 406 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.3916 (p90) REVERT: A 424 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.5644 (t70) REVERT: A 561 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7744 (tm-30) REVERT: A 648 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7185 (mtp180) REVERT: A 822 ILE cc_start: 0.8836 (tp) cc_final: 0.8598 (pt) REVERT: A 863 LYS cc_start: 0.7214 (mtmt) cc_final: 0.6812 (mtpt) REVERT: A 888 GLU cc_start: 0.7555 (mp0) cc_final: 0.6806 (pm20) REVERT: B 122 ASP cc_start: 0.7920 (m-30) cc_final: 0.7593 (m-30) REVERT: B 134 MET cc_start: 0.8951 (mtp) cc_final: 0.8715 (mtp) REVERT: B 140 GLU cc_start: 0.8474 (tt0) cc_final: 0.8235 (tt0) REVERT: B 248 ASN cc_start: 0.8712 (m-40) cc_final: 0.8511 (m110) REVERT: B 299 SER cc_start: 0.8482 (OUTLIER) cc_final: 0.8275 (t) REVERT: B 424 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6139 (t70) REVERT: B 574 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: B 611 ASP cc_start: 0.7043 (t0) cc_final: 0.6698 (t0) REVERT: B 648 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7093 (mtm180) REVERT: B 791 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6862 (mm-30) REVERT: B 830 GLU cc_start: 0.8077 (mp0) cc_final: 0.7840 (mp0) REVERT: E 40 LEU cc_start: 0.8538 (mt) cc_final: 0.8209 (mm) REVERT: E 201 ASP cc_start: 0.7553 (m-30) cc_final: 0.7203 (m-30) REVERT: E 276 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7914 (mp) REVERT: E 308 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7532 (pp20) REVERT: E 362 MET cc_start: 0.9133 (tpt) cc_final: 0.8828 (tmm) REVERT: E 534 MET cc_start: 0.7810 (mmm) cc_final: 0.7575 (tpt) REVERT: E 557 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7314 (tptp) REVERT: E 755 THR cc_start: 0.8470 (m) cc_final: 0.8228 (p) REVERT: E 794 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8163 (tttp) REVERT: E 809 MET cc_start: 0.8715 (tpp) cc_final: 0.8451 (tpt) REVERT: E 822 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8813 (tp) REVERT: E 888 GLU cc_start: 0.7683 (mp0) cc_final: 0.6923 (pm20) REVERT: E 895 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: F 43 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7627 (tt0) REVERT: F 276 LEU cc_start: 0.8673 (pp) cc_final: 0.8163 (mp) REVERT: F 284 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7271 (mmtm) REVERT: F 406 TYR cc_start: 0.5812 (OUTLIER) cc_final: 0.4061 (p90) REVERT: F 424 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.6848 (t70) REVERT: F 437 TYR cc_start: 0.8825 (m-80) cc_final: 0.8530 (m-80) REVERT: F 557 LYS cc_start: 0.7973 (tmmt) cc_final: 0.7480 (tptp) REVERT: F 558 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8111 (mt-10) REVERT: F 679 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: F 688 GLU cc_start: 0.7231 (mp0) cc_final: 0.6943 (mp0) REVERT: F 864 LYS cc_start: 0.8066 (tttt) cc_final: 0.7769 (ttmm) REVERT: F 886 TYR cc_start: 0.8553 (m-80) cc_final: 0.8327 (m-80) REVERT: F 888 GLU cc_start: 0.7377 (mp0) cc_final: 0.6547 (pm20) REVERT: G 249 GLU cc_start: 0.7935 (tp30) cc_final: 0.7708 (tp30) REVERT: G 282 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7438 (pp) REVERT: G 290 ASN cc_start: 0.8327 (m-40) cc_final: 0.8024 (m-40) REVERT: G 323 ASN cc_start: 0.7531 (p0) cc_final: 0.7163 (m110) REVERT: G 406 TYR cc_start: 0.5815 (OUTLIER) cc_final: 0.4737 (p90) REVERT: G 424 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.5537 (t70) REVERT: G 439 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: G 475 ASP cc_start: 0.8357 (m-30) cc_final: 0.8115 (m-30) REVERT: G 480 MET cc_start: 0.9149 (mtp) cc_final: 0.8800 (mtt) REVERT: G 533 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6910 (p90) REVERT: G 561 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7754 (tm-30) REVERT: G 756 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8647 (pttm) REVERT: G 795 LYS cc_start: 0.8176 (mttp) cc_final: 0.7633 (mmpt) REVERT: D 68 SER cc_start: 0.7845 (m) cc_final: 0.7463 (t) REVERT: D 123 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7288 (ttt-90) REVERT: D 152 PRO cc_start: 0.8051 (Cg_exo) cc_final: 0.7840 (Cg_endo) REVERT: D 248 ASN cc_start: 0.8721 (m-40) cc_final: 0.8520 (m110) REVERT: D 284 LYS cc_start: 0.7985 (pttt) cc_final: 0.7009 (mmtm) REVERT: D 350 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7961 (mt-10) REVERT: D 379 MET cc_start: 0.1819 (OUTLIER) cc_final: 0.1308 (ppp) REVERT: D 406 TYR cc_start: 0.6414 (OUTLIER) cc_final: 0.4797 (p90) REVERT: D 557 LYS cc_start: 0.7799 (ttpp) cc_final: 0.7203 (tptp) REVERT: D 648 ARG cc_start: 0.7540 (mmt90) cc_final: 0.7036 (mtp180) REVERT: D 659 THR cc_start: 0.7972 (p) cc_final: 0.7646 (t) REVERT: D 700 MET cc_start: 0.7965 (mtp) cc_final: 0.7730 (mtt) REVERT: D 755 THR cc_start: 0.8513 (m) cc_final: 0.8219 (p) REVERT: D 888 GLU cc_start: 0.7658 (mp0) cc_final: 0.7036 (pp20) REVERT: C 248 ASN cc_start: 0.8586 (m-40) cc_final: 0.8329 (m110) REVERT: C 249 GLU cc_start: 0.8347 (tt0) cc_final: 0.8128 (tp30) REVERT: C 276 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7903 (mp) REVERT: C 350 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6729 (mm-30) REVERT: C 362 MET cc_start: 0.9163 (tpt) cc_final: 0.8948 (mmm) REVERT: C 368 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6922 (mm-30) REVERT: C 413 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: C 416 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8225 (tm130) REVERT: C 424 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.5971 (t-170) REVERT: C 659 THR cc_start: 0.8249 (p) cc_final: 0.7875 (t) REVERT: C 798 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: C 888 GLU cc_start: 0.7251 (mp0) cc_final: 0.6348 (pm20) outliers start: 174 outliers final: 97 residues processed: 733 average time/residue: 0.5162 time to fit residues: 465.7450 Evaluate side-chains 707 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 580 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 HIS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 574 GLN Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 863 LYS Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 406 TYR Chi-restraints excluded: chain E residue 424 HIS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 610 ASP Chi-restraints excluded: chain E residue 794 LYS Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 864 LYS Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain E residue 900 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 406 TYR Chi-restraints excluded: chain F residue 424 HIS Chi-restraints excluded: chain F residue 534 MET Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 679 MET Chi-restraints excluded: chain F residue 756 LYS Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 406 TYR Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 618 LEU Chi-restraints excluded: chain G residue 756 LYS Chi-restraints excluded: chain G residue 836 SER Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 175 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 863 LYS Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 424 HIS Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 836 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 32 optimal weight: 0.0000 chunk 545 optimal weight: 0.4980 chunk 14 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 469 optimal weight: 0.0770 chunk 462 optimal weight: 4.9990 chunk 360 optimal weight: 4.9990 chunk 537 optimal weight: 1.9990 overall best weight: 0.9146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS B 149 GLN B 424 HIS B 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN E 439 GLN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 HIS ** F 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 806 HIS G 880 HIS D 253 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.169609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.141884 restraints weight = 44417.537| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.49 r_work: 0.3374 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 47173 Z= 0.139 Angle : 0.611 12.210 63609 Z= 0.323 Chirality : 0.042 0.250 7056 Planarity : 0.005 0.118 8015 Dihedral : 5.372 39.445 6090 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 1.01 % Allowed : 7.56 % Favored : 91.43 % Rotamer: Outliers : 3.81 % Allowed : 16.80 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: 0.34 (0.12), residues: 5460 helix: 1.77 (0.09), residues: 3199 sheet: -1.00 (0.39), residues: 175 loop : -2.27 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 648 TYR 0.024 0.002 TYR G 651 PHE 0.016 0.002 PHE B 433 TRP 0.013 0.001 TRP C 418 HIS 0.008 0.001 HIS G 880 Details of bonding type rmsd covalent geometry : bond 0.00314 (47173) covalent geometry : angle 0.61148 (63609) hydrogen bonds : bond 0.04298 ( 2338) hydrogen bonds : angle 3.71892 ( 6741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 605 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: A 282 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7244 (pp) REVERT: A 283 PHE cc_start: 0.7412 (m-80) cc_final: 0.7121 (t80) REVERT: A 284 LYS cc_start: 0.8433 (pttt) cc_final: 0.8072 (pttm) REVERT: A 323 ASN cc_start: 0.7589 (p0) cc_final: 0.7233 (m-40) REVERT: A 350 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7809 (mm-30) REVERT: A 368 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: A 379 MET cc_start: 0.2547 (ppp) cc_final: 0.1665 (ppp) REVERT: A 406 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.3963 (p90) REVERT: A 424 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.5780 (t70) REVERT: A 561 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7753 (tm-30) REVERT: A 648 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7161 (mtm180) REVERT: A 758 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7200 (pt0) REVERT: A 822 ILE cc_start: 0.8873 (tp) cc_final: 0.8609 (pt) REVERT: A 863 LYS cc_start: 0.7181 (mtmt) cc_final: 0.6791 (mtpt) REVERT: A 888 GLU cc_start: 0.7483 (mp0) cc_final: 0.6720 (pm20) REVERT: B 134 MET cc_start: 0.9008 (mtp) cc_final: 0.8736 (mtp) REVERT: B 140 GLU cc_start: 0.8456 (tt0) cc_final: 0.8200 (tt0) REVERT: B 248 ASN cc_start: 0.8726 (m-40) cc_final: 0.8507 (m110) REVERT: B 276 LEU cc_start: 0.8376 (pp) cc_final: 0.7864 (mt) REVERT: B 299 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8284 (t) REVERT: B 424 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.5908 (t70) REVERT: B 534 MET cc_start: 0.8118 (mmm) cc_final: 0.7799 (tpt) REVERT: B 574 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: B 611 ASP cc_start: 0.6840 (t0) cc_final: 0.6473 (t0) REVERT: B 791 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: B 830 GLU cc_start: 0.8009 (mp0) cc_final: 0.7792 (mp0) REVERT: E 112 ASP cc_start: 0.6420 (OUTLIER) cc_final: 0.5817 (m-30) REVERT: E 152 PRO cc_start: 0.8106 (Cg_exo) cc_final: 0.7788 (Cg_endo) REVERT: E 201 ASP cc_start: 0.7629 (m-30) cc_final: 0.7253 (m-30) REVERT: E 276 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7853 (mp) REVERT: E 282 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7261 (pp) REVERT: E 308 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: E 362 MET cc_start: 0.9143 (tpt) cc_final: 0.8891 (tmm) REVERT: E 557 LYS cc_start: 0.7847 (ttpp) cc_final: 0.7306 (tptp) REVERT: E 755 THR cc_start: 0.8611 (m) cc_final: 0.8314 (p) REVERT: E 794 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8096 (tttm) REVERT: E 809 MET cc_start: 0.8710 (tpp) cc_final: 0.8454 (tpt) REVERT: E 822 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8804 (tp) REVERT: E 888 GLU cc_start: 0.7631 (mp0) cc_final: 0.6944 (pm20) REVERT: E 895 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: F 43 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7591 (tt0) REVERT: F 80 GLN cc_start: 0.8182 (mt0) cc_final: 0.7942 (tt0) REVERT: F 276 LEU cc_start: 0.8742 (pp) cc_final: 0.8201 (mp) REVERT: F 284 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7341 (mmtm) REVERT: F 406 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.4356 (p90) REVERT: F 424 HIS cc_start: 0.7542 (OUTLIER) cc_final: 0.6977 (t70) REVERT: F 437 TYR cc_start: 0.8848 (m-80) cc_final: 0.8568 (m-80) REVERT: F 557 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7526 (tptp) REVERT: F 679 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8532 (mtp) REVERT: F 688 GLU cc_start: 0.7343 (mp0) cc_final: 0.7077 (mp0) REVERT: F 864 LYS cc_start: 0.7985 (tttt) cc_final: 0.7678 (ttmm) REVERT: F 888 GLU cc_start: 0.7326 (mp0) cc_final: 0.6495 (pm20) REVERT: G 249 GLU cc_start: 0.7920 (tp30) cc_final: 0.7693 (tp30) REVERT: G 282 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7519 (pp) REVERT: G 290 ASN cc_start: 0.8341 (m-40) cc_final: 0.8023 (m-40) REVERT: G 323 ASN cc_start: 0.7581 (p0) cc_final: 0.7181 (m110) REVERT: G 406 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.4811 (p90) REVERT: G 424 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6496 (t70) REVERT: G 439 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: G 480 MET cc_start: 0.9100 (mtp) cc_final: 0.8813 (mtt) REVERT: G 533 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6843 (p90) REVERT: G 569 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8182 (mtpt) REVERT: G 795 LYS cc_start: 0.8131 (mttp) cc_final: 0.7563 (mmpt) REVERT: D 68 SER cc_start: 0.7912 (m) cc_final: 0.7547 (t) REVERT: D 123 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7264 (ttt-90) REVERT: D 152 PRO cc_start: 0.8107 (Cg_exo) cc_final: 0.7881 (Cg_endo) REVERT: D 284 LYS cc_start: 0.8042 (pttt) cc_final: 0.7054 (mmtm) REVERT: D 350 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: D 379 MET cc_start: 0.2013 (OUTLIER) cc_final: 0.1439 (ppp) REVERT: D 406 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.4685 (p90) REVERT: D 534 MET cc_start: 0.7980 (mmm) cc_final: 0.7760 (tpp) REVERT: D 557 LYS cc_start: 0.7815 (ttpp) cc_final: 0.7214 (tptp) REVERT: D 659 THR cc_start: 0.8056 (p) cc_final: 0.7739 (t) REVERT: D 755 THR cc_start: 0.8560 (m) cc_final: 0.8260 (p) REVERT: D 888 GLU cc_start: 0.7637 (mp0) cc_final: 0.7015 (pp20) REVERT: C 30 ILE cc_start: 0.8023 (tt) cc_final: 0.7786 (tp) REVERT: C 248 ASN cc_start: 0.8613 (m-40) cc_final: 0.8328 (m110) REVERT: C 276 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7840 (mp) REVERT: C 350 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6782 (mm-30) REVERT: C 368 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6906 (mm-30) REVERT: C 413 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8291 (tm-30) REVERT: C 416 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8230 (tm130) REVERT: C 424 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.6461 (t-170) REVERT: C 564 MET cc_start: 0.8633 (mtp) cc_final: 0.8322 (mtm) REVERT: C 798 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: C 888 GLU cc_start: 0.7197 (mp0) cc_final: 0.6318 (pm20) outliers start: 194 outliers final: 107 residues processed: 742 average time/residue: 0.5152 time to fit residues: 469.2433 Evaluate side-chains 732 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 590 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 HIS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 574 GLN Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 863 LYS Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 406 TYR Chi-restraints excluded: chain E residue 424 HIS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 610 ASP Chi-restraints excluded: chain E residue 756 LYS Chi-restraints excluded: chain E residue 794 LYS Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 864 LYS Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 299 SER Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 406 TYR Chi-restraints excluded: chain F residue 424 HIS Chi-restraints excluded: chain F residue 534 MET Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 679 MET Chi-restraints excluded: chain F residue 756 LYS Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 406 TYR Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 569 LYS Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 618 LEU Chi-restraints excluded: chain G residue 756 LYS Chi-restraints excluded: chain G residue 836 SER Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 175 CYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 863 LYS Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 424 HIS Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 836 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 88 optimal weight: 2.9990 chunk 472 optimal weight: 0.0980 chunk 497 optimal weight: 0.9990 chunk 412 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 chunk 457 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 374 optimal weight: 3.9990 chunk 296 optimal weight: 0.0670 chunk 525 optimal weight: 0.6980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 320 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 HIS B 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN E 439 GLN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 HIS F 143 GLN F 260 ASN ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 149 GLN ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 880 HIS D 253 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.174411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146962 restraints weight = 44448.587| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.48 r_work: 0.3429 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 47173 Z= 0.111 Angle : 0.566 11.283 63609 Z= 0.297 Chirality : 0.041 0.239 7056 Planarity : 0.004 0.113 8015 Dihedral : 5.148 38.740 6090 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.95 % Allowed : 7.00 % Favored : 92.05 % Rotamer: Outliers : 2.83 % Allowed : 18.13 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % 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 aren not related in a simple way. whole: 0.42 (0.12), residues: 5460 helix: 1.89 (0.09), residues: 3199 sheet: -0.94 (0.39), residues: 175 loop : -2.33 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 648 TYR 0.022 0.001 TYR B 651 PHE 0.016 0.001 PHE B 433 TRP 0.013 0.001 TRP F 418 HIS 0.008 0.001 HIS G 880 Details of bonding type rmsd covalent geometry : bond 0.00239 (47173) covalent geometry : angle 0.56575 (63609) hydrogen bonds : bond 0.03669 ( 2338) hydrogen bonds : angle 3.63446 ( 6741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 614 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: A 282 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7088 (pp) REVERT: A 284 LYS cc_start: 0.8362 (pttt) cc_final: 0.8146 (pttm) REVERT: A 323 ASN cc_start: 0.7539 (p0) cc_final: 0.7198 (m-40) REVERT: A 406 TYR cc_start: 0.5843 (OUTLIER) cc_final: 0.3941 (p90) REVERT: A 424 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.5652 (t70) REVERT: A 561 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7726 (tm-30) REVERT: A 648 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7126 (mtp180) REVERT: A 758 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7319 (pt0) REVERT: A 822 ILE cc_start: 0.8809 (tp) cc_final: 0.8587 (pt) REVERT: A 863 LYS cc_start: 0.7125 (mtmt) cc_final: 0.6731 (mtpt) REVERT: A 888 GLU cc_start: 0.7534 (mp0) cc_final: 0.6780 (pm20) REVERT: B 134 MET cc_start: 0.9011 (mtp) cc_final: 0.8746 (mtp) REVERT: B 140 GLU cc_start: 0.8481 (tt0) cc_final: 0.8208 (tt0) REVERT: B 276 LEU cc_start: 0.8307 (pp) cc_final: 0.7770 (mt) REVERT: B 284 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7276 (mmtm) REVERT: B 299 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8226 (t) REVERT: B 424 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.5669 (t70) REVERT: B 534 MET cc_start: 0.7975 (mmm) cc_final: 0.7647 (tpt) REVERT: B 611 ASP cc_start: 0.6790 (t0) cc_final: 0.6436 (t0) REVERT: B 791 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6896 (mm-30) REVERT: B 830 GLU cc_start: 0.8051 (mp0) cc_final: 0.7841 (mp0) REVERT: B 888 GLU cc_start: 0.7322 (mp0) cc_final: 0.6535 (pm20) REVERT: E 40 LEU cc_start: 0.8574 (mt) cc_final: 0.8248 (mm) REVERT: E 153 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: E 276 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7945 (mp) REVERT: E 282 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7060 (pp) REVERT: E 308 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7511 (pp20) REVERT: E 557 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7299 (mppt) REVERT: E 755 THR cc_start: 0.8518 (m) cc_final: 0.8204 (p) REVERT: E 794 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8179 (tttm) REVERT: E 809 MET cc_start: 0.8686 (tpp) cc_final: 0.8442 (tpt) REVERT: E 822 ILE cc_start: 0.9003 (tt) cc_final: 0.8794 (tp) REVERT: E 888 GLU cc_start: 0.7662 (mp0) cc_final: 0.6880 (pm20) REVERT: E 895 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: F 43 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7461 (tt0) REVERT: F 80 GLN cc_start: 0.8151 (mt0) cc_final: 0.7880 (tt0) REVERT: F 112 ASP cc_start: 0.6408 (m-30) cc_final: 0.6124 (m-30) REVERT: F 201 ASP cc_start: 0.6995 (m-30) cc_final: 0.6597 (m-30) REVERT: F 276 LEU cc_start: 0.8549 (pp) cc_final: 0.8054 (mp) REVERT: F 284 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7265 (mmtm) REVERT: F 325 THR cc_start: 0.7672 (p) cc_final: 0.7400 (t) REVERT: F 406 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.4210 (p90) REVERT: F 424 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6836 (t70) REVERT: F 437 TYR cc_start: 0.8813 (m-80) cc_final: 0.8532 (m-80) REVERT: F 557 LYS cc_start: 0.7972 (tmmt) cc_final: 0.7422 (tptp) REVERT: F 679 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8425 (mtp) REVERT: F 688 GLU cc_start: 0.7250 (mp0) cc_final: 0.6912 (mp0) REVERT: F 700 MET cc_start: 0.7852 (mtp) cc_final: 0.7346 (mtp) REVERT: F 864 LYS cc_start: 0.8038 (tttt) cc_final: 0.7734 (ttmm) REVERT: G 249 GLU cc_start: 0.7933 (tp30) cc_final: 0.7689 (tp30) REVERT: G 282 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7404 (pp) REVERT: G 290 ASN cc_start: 0.8273 (m-40) cc_final: 0.7952 (m-40) REVERT: G 323 ASN cc_start: 0.7532 (p0) cc_final: 0.7168 (m110) REVERT: G 406 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.4720 (p90) REVERT: G 424 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.5555 (t70) REVERT: G 439 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7477 (mt0) REVERT: G 475 ASP cc_start: 0.8309 (m-30) cc_final: 0.8092 (m-30) REVERT: G 480 MET cc_start: 0.9134 (mtp) cc_final: 0.8857 (mtt) REVERT: G 533 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6625 (p90) REVERT: G 564 MET cc_start: 0.8764 (mtm) cc_final: 0.8472 (mtp) REVERT: G 648 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.6872 (mtp180) REVERT: G 795 LYS cc_start: 0.8143 (mttp) cc_final: 0.7598 (mmpt) REVERT: D 123 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7248 (ttt-90) REVERT: D 248 ASN cc_start: 0.8685 (m-40) cc_final: 0.8485 (m110) REVERT: D 284 LYS cc_start: 0.8064 (pttt) cc_final: 0.7713 (ptpt) REVERT: D 379 MET cc_start: 0.1762 (OUTLIER) cc_final: 0.1233 (ppp) REVERT: D 406 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.4710 (p90) REVERT: D 557 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7093 (tptp) REVERT: D 648 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.6940 (mtp180) REVERT: D 659 THR cc_start: 0.7915 (p) cc_final: 0.7599 (t) REVERT: D 825 ILE cc_start: 0.8485 (tp) cc_final: 0.8222 (mt) REVERT: D 888 GLU cc_start: 0.7631 (mp0) cc_final: 0.7008 (pp20) REVERT: C 248 ASN cc_start: 0.8498 (m-40) cc_final: 0.8286 (m110) REVERT: C 276 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.7900 (mp) REVERT: C 325 THR cc_start: 0.7679 (p) cc_final: 0.7418 (m) REVERT: C 350 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6697 (mm-30) REVERT: C 368 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6693 (mm-30) REVERT: C 413 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8344 (tm-30) REVERT: C 416 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8203 (tm130) REVERT: C 557 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7327 (mppt) REVERT: C 564 MET cc_start: 0.8562 (mtp) cc_final: 0.8330 (mtm) REVERT: C 648 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7129 (mtp180) REVERT: C 700 MET cc_start: 0.7936 (mtt) cc_final: 0.7667 (mtm) REVERT: C 798 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: C 888 GLU cc_start: 0.7240 (mp0) cc_final: 0.6325 (pm20) outliers start: 144 outliers final: 76 residues processed: 717 average time/residue: 0.5239 time to fit residues: 460.4447 Evaluate side-chains 687 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 581 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 HIS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 863 LYS Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 406 TYR Chi-restraints excluded: chain E residue 424 HIS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 794 LYS Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 406 TYR Chi-restraints excluded: chain F residue 424 HIS Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 679 MET Chi-restraints excluded: chain F residue 756 LYS Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 406 TYR Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 618 LEU Chi-restraints excluded: chain G residue 756 LYS Chi-restraints excluded: chain G residue 836 SER Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 175 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 424 HIS Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 798 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 159 optimal weight: 1.9990 chunk 363 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 492 optimal weight: 0.5980 chunk 250 optimal weight: 0.5980 chunk 343 optimal weight: 0.9980 chunk 245 optimal weight: 0.3980 chunk 249 optimal weight: 0.7980 chunk 418 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 248 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 320 ASN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN E 439 GLN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 248 ASN ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 880 HIS D 253 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 HIS C 149 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.172491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144803 restraints weight = 44562.625| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.47 r_work: 0.3395 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 47173 Z= 0.121 Angle : 0.584 11.837 63609 Z= 0.306 Chirality : 0.041 0.242 7056 Planarity : 0.004 0.114 8015 Dihedral : 5.190 39.458 6090 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.53 % Favored : 91.63 % Rotamer: Outliers : 2.67 % Allowed : 18.50 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.46 % 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 aren not related in a simple way. whole: 0.44 (0.12), residues: 5460 helix: 1.88 (0.09), residues: 3199 sheet: -0.85 (0.39), residues: 175 loop : -2.29 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 648 TYR 0.023 0.001 TYR F 651 PHE 0.015 0.001 PHE B 433 TRP 0.012 0.001 TRP C 418 HIS 0.009 0.001 HIS G 880 Details of bonding type rmsd covalent geometry : bond 0.00269 (47173) covalent geometry : angle 0.58389 (63609) hydrogen bonds : bond 0.03905 ( 2338) hydrogen bonds : angle 3.63159 ( 6741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 591 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7220 (pp) REVERT: A 284 LYS cc_start: 0.8397 (pttt) cc_final: 0.8179 (pttm) REVERT: A 323 ASN cc_start: 0.7475 (p0) cc_final: 0.7132 (m-40) REVERT: A 350 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7527 (mm-30) REVERT: A 406 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.4031 (p90) REVERT: A 424 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.5730 (t70) REVERT: A 561 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7740 (tm-30) REVERT: A 648 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7101 (mtm180) REVERT: A 822 ILE cc_start: 0.8839 (tp) cc_final: 0.8627 (pt) REVERT: A 843 GLU cc_start: 0.7544 (tt0) cc_final: 0.7326 (tt0) REVERT: A 863 LYS cc_start: 0.7233 (mtmt) cc_final: 0.6824 (mtpt) REVERT: A 888 GLU cc_start: 0.7532 (mp0) cc_final: 0.6711 (pm20) REVERT: B 134 MET cc_start: 0.9014 (mtp) cc_final: 0.8726 (mtp) REVERT: B 276 LEU cc_start: 0.8348 (pp) cc_final: 0.7829 (mt) REVERT: B 284 LYS cc_start: 0.8221 (ptpt) cc_final: 0.7330 (mmtm) REVERT: B 299 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (t) REVERT: B 424 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6260 (t-90) REVERT: B 611 ASP cc_start: 0.6733 (t0) cc_final: 0.6393 (t0) REVERT: B 791 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6881 (mm-30) REVERT: B 830 GLU cc_start: 0.8024 (mp0) cc_final: 0.7817 (mp0) REVERT: B 888 GLU cc_start: 0.7311 (mp0) cc_final: 0.6561 (pm20) REVERT: E 40 LEU cc_start: 0.8605 (mt) cc_final: 0.8286 (mm) REVERT: E 152 PRO cc_start: 0.7986 (Cg_exo) cc_final: 0.7651 (Cg_endo) REVERT: E 153 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: E 156 MET cc_start: 0.8698 (mtm) cc_final: 0.8482 (mtt) REVERT: E 201 ASP cc_start: 0.7430 (m-30) cc_final: 0.7167 (m-30) REVERT: E 276 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7905 (mp) REVERT: E 282 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7184 (pp) REVERT: E 308 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7539 (pp20) REVERT: E 755 THR cc_start: 0.8549 (m) cc_final: 0.8214 (p) REVERT: E 794 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8169 (tttm) REVERT: E 809 MET cc_start: 0.8705 (tpp) cc_final: 0.8450 (tpt) REVERT: E 822 ILE cc_start: 0.9036 (tt) cc_final: 0.8828 (tp) REVERT: E 888 GLU cc_start: 0.7678 (mp0) cc_final: 0.6990 (pm20) REVERT: E 895 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.5797 (mp0) REVERT: F 43 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7469 (tt0) REVERT: F 80 GLN cc_start: 0.8181 (mt0) cc_final: 0.7917 (tt0) REVERT: F 201 ASP cc_start: 0.7076 (m-30) cc_final: 0.6666 (m-30) REVERT: F 276 LEU cc_start: 0.8576 (pp) cc_final: 0.8048 (mp) REVERT: F 284 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7326 (mmtm) REVERT: F 325 THR cc_start: 0.7701 (p) cc_final: 0.7464 (t) REVERT: F 406 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.4476 (p90) REVERT: F 424 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6887 (t70) REVERT: F 437 TYR cc_start: 0.8848 (m-80) cc_final: 0.8565 (m-80) REVERT: F 679 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8519 (mtp) REVERT: F 758 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7439 (pt0) REVERT: F 843 GLU cc_start: 0.7592 (tt0) cc_final: 0.7208 (tt0) REVERT: F 864 LYS cc_start: 0.8040 (tttt) cc_final: 0.7735 (ttmm) REVERT: G 249 GLU cc_start: 0.7954 (tp30) cc_final: 0.7713 (tp30) REVERT: G 282 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7425 (pp) REVERT: G 290 ASN cc_start: 0.8281 (m-40) cc_final: 0.7963 (m-40) REVERT: G 323 ASN cc_start: 0.7594 (p0) cc_final: 0.7229 (m110) REVERT: G 406 TYR cc_start: 0.6228 (OUTLIER) cc_final: 0.4711 (p90) REVERT: G 424 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.6149 (t70) REVERT: G 439 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7438 (mt0) REVERT: G 475 ASP cc_start: 0.8369 (m-30) cc_final: 0.8148 (m-30) REVERT: G 480 MET cc_start: 0.9152 (mtp) cc_final: 0.8773 (mtt) REVERT: G 533 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6608 (p90) REVERT: G 564 MET cc_start: 0.8761 (mtm) cc_final: 0.8513 (mtp) REVERT: G 648 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.6913 (mtp180) REVERT: G 795 LYS cc_start: 0.8137 (mttp) cc_final: 0.7619 (mmpt) REVERT: D 123 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7305 (ttt-90) REVERT: D 248 ASN cc_start: 0.8690 (m-40) cc_final: 0.8479 (m110) REVERT: D 276 LEU cc_start: 0.8443 (pp) cc_final: 0.7876 (mp) REVERT: D 284 LYS cc_start: 0.8054 (pttt) cc_final: 0.7077 (mmtm) REVERT: D 350 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 379 MET cc_start: 0.1704 (OUTLIER) cc_final: 0.0994 (ppp) REVERT: D 406 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.4629 (p90) REVERT: D 557 LYS cc_start: 0.7705 (ttpp) cc_final: 0.7109 (tptp) REVERT: D 659 THR cc_start: 0.7993 (p) cc_final: 0.7673 (t) REVERT: D 825 ILE cc_start: 0.8489 (tp) cc_final: 0.8265 (mt) REVERT: D 888 GLU cc_start: 0.7657 (mp0) cc_final: 0.6854 (pm20) REVERT: C 209 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7960 (mm) REVERT: C 248 ASN cc_start: 0.8538 (m-40) cc_final: 0.8296 (m110) REVERT: C 276 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.7945 (mp) REVERT: C 284 LYS cc_start: 0.8568 (ptpt) cc_final: 0.7611 (mmtm) REVERT: C 325 THR cc_start: 0.7669 (p) cc_final: 0.7443 (m) REVERT: C 350 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6748 (mm-30) REVERT: C 368 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6725 (mm-30) REVERT: C 413 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: C 416 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8190 (tm130) REVERT: C 557 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7353 (mppt) REVERT: C 564 MET cc_start: 0.8593 (mtp) cc_final: 0.8275 (mtm) REVERT: C 648 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7064 (mtp180) REVERT: C 758 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7544 (pt0) REVERT: C 798 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: C 888 GLU cc_start: 0.7258 (mp0) cc_final: 0.6391 (pm20) outliers start: 136 outliers final: 82 residues processed: 687 average time/residue: 0.5155 time to fit residues: 433.6066 Evaluate side-chains 698 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 586 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 HIS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 863 LYS Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 406 TYR Chi-restraints excluded: chain E residue 424 HIS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 610 ASP Chi-restraints excluded: chain E residue 794 LYS Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 299 SER Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 406 TYR Chi-restraints excluded: chain F residue 424 HIS Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 679 MET Chi-restraints excluded: chain F residue 756 LYS Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 406 TYR Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 618 LEU Chi-restraints excluded: chain G residue 756 LYS Chi-restraints excluded: chain G residue 836 SER Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 175 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 424 HIS Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 798 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 305 optimal weight: 2.9990 chunk 545 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 319 optimal weight: 0.0040 chunk 322 optimal weight: 2.9990 chunk 435 optimal weight: 0.8980 chunk 393 optimal weight: 0.2980 chunk 258 optimal weight: 5.9990 chunk 408 optimal weight: 5.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 GLN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 248 ASN ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 880 HIS D 253 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.169112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.141291 restraints weight = 44249.467| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.50 r_work: 0.3365 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47173 Z= 0.146 Angle : 0.628 12.506 63609 Z= 0.329 Chirality : 0.043 0.252 7056 Planarity : 0.005 0.117 8015 Dihedral : 5.413 40.570 6090 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.92 % Allowed : 7.73 % Favored : 91.36 % Rotamer: Outliers : 2.73 % Allowed : 18.64 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % 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 aren not related in a simple way. whole: 0.40 (0.12), residues: 5460 helix: 1.78 (0.09), residues: 3206 sheet: -0.71 (0.41), residues: 189 loop : -2.22 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 648 TYR 0.025 0.002 TYR G 651 PHE 0.017 0.002 PHE C 296 TRP 0.010 0.001 TRP C 418 HIS 0.009 0.001 HIS G 880 Details of bonding type rmsd covalent geometry : bond 0.00335 (47173) covalent geometry : angle 0.62808 (63609) hydrogen bonds : bond 0.04380 ( 2338) hydrogen bonds : angle 3.70564 ( 6741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14498.83 seconds wall clock time: 246 minutes 47.28 seconds (14807.28 seconds total)