Starting phenix.real_space_refine on Thu Dec 26 15:42:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fnu_29326/12_2024/8fnu_29326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fnu_29326/12_2024/8fnu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fnu_29326/12_2024/8fnu_29326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fnu_29326/12_2024/8fnu_29326.map" model { file = "/net/cci-nas-00/data/ceres_data/8fnu_29326/12_2024/8fnu_29326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fnu_29326/12_2024/8fnu_29326.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 22.97, per 1000 atoms: 0.50 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: 11.04 Conformation dependent library (CDL) restraints added in 5.4 seconds 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: 5.28 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: 19.21 Time building geometry restraints manager: 12.71 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 5.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.530 Check model and map are aligned: 0.340 Set scattering table: 0.400 Process input model: 93.120 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.290 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: 0.020 Load rotamer database and sin/cos tables:15.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.520 ------------------------------------------------------------------------------- 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= 0.363 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (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 TRP 0.007 0.001 TRP B 418 HIS 0.039 0.003 HIS B 44 PHE 0.113 0.002 PHE C 407 TYR 0.106 0.004 TYR F 220 ARG 0.073 0.004 ARG B 125 *********************** 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 : 5.358 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: 0.6011 (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: 0.7346 (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: 1.8090 time to fit residues: 1768.9690 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 : 5.427 ------------------------------------------------------------------------------- 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 466 optimal weight: 0.0870 chunk 419 optimal weight: 0.8980 chunk 232 optimal weight: 0.3980 chunk 143 optimal weight: 1.9990 chunk 282 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 433 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 322 optimal weight: 0.5980 chunk 502 optimal weight: 0.1980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 129 HIS A 143 GLN A 439 GLN A 524 HIS A 769 GLN B 44 HIS B 135 ASN B 439 GLN B 524 HIS B 769 GLN E 253 ASN E 439 GLN E 657 GLN F 129 HIS F 183 ASN F 253 ASN F 439 GLN ** F 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 ASN G 439 GLN G 524 HIS D 129 HIS D 524 HIS C 253 ASN C 439 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 47173 Z= 0.176 Angle : 0.616 10.493 63609 Z= 0.323 Chirality : 0.042 0.230 7056 Planarity : 0.005 0.104 8015 Dihedral : 7.313 116.516 6189 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.33 % Favored : 91.79 % Rotamer: Outliers : 2.75 % Allowed : 12.95 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.12), residues: 5460 helix: 1.69 (0.10), residues: 3143 sheet: -1.42 (0.38), residues: 168 loop : -2.31 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 418 HIS 0.006 0.001 HIS B 44 PHE 0.022 0.001 PHE F 433 TYR 0.021 0.001 TYR A 651 ARG 0.012 0.001 ARG D 789 *********************** 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 855 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 715 time to evaluate : 5.476 Fit side-chains REVERT: A 282 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6557 (pp) REVERT: A 290 ASN cc_start: 0.7393 (m-40) cc_final: 0.7191 (m-40) REVERT: A 368 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: A 439 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.5957 (mp-120) REVERT: A 466 MET cc_start: 0.8164 (tpp) cc_final: 0.7755 (mmm) REVERT: A 534 MET cc_start: 0.5855 (mmm) cc_final: 0.5521 (mmm) REVERT: A 794 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7637 (tttm) REVERT: A 843 GLU cc_start: 0.7743 (pt0) cc_final: 0.7408 (pt0) REVERT: A 863 LYS cc_start: 0.7272 (mtmt) cc_final: 0.7024 (mttt) REVERT: B 43 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6134 (mp0) REVERT: B 123 ARG cc_start: 0.7600 (ttt90) cc_final: 0.7372 (ttt180) REVERT: B 155 GLU cc_start: 0.7187 (mp0) cc_final: 0.6814 (tm-30) REVERT: B 171 LYS cc_start: 0.8417 (ttpp) cc_final: 0.8208 (tttt) REVERT: B 201 ASP cc_start: 0.6636 (m-30) cc_final: 0.6385 (m-30) REVERT: B 276 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6482 (mp) REVERT: B 413 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: B 480 MET cc_start: 0.8915 (mtm) cc_final: 0.8473 (mtt) REVERT: B 700 MET cc_start: 0.7257 (mtp) cc_final: 0.6628 (mtp) REVERT: E 172 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7525 (mm-30) REVERT: E 397 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.8176 (ttm110) REVERT: E 435 MET cc_start: 0.9077 (mmm) cc_final: 0.8668 (mmm) REVERT: E 462 THR cc_start: 0.8338 (p) cc_final: 0.7996 (p) REVERT: E 525 VAL cc_start: 0.7191 (OUTLIER) cc_final: 0.6732 (t) REVERT: E 611 ASP cc_start: 0.6786 (t0) cc_final: 0.6436 (t0) REVERT: E 614 GLU cc_start: 0.7297 (tp30) cc_final: 0.7057 (tp30) REVERT: E 888 GLU cc_start: 0.7155 (mp0) cc_final: 0.6585 (pm20) REVERT: F 134 MET cc_start: 0.8222 (mtp) cc_final: 0.7979 (mtp) REVERT: F 276 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7508 (pt) REVERT: F 697 MET cc_start: 0.8408 (tpt) cc_final: 0.8123 (tpp) REVERT: F 700 MET cc_start: 0.7416 (mtp) cc_final: 0.6807 (mtp) REVERT: F 886 TYR cc_start: 0.8314 (m-80) cc_final: 0.8067 (m-80) REVERT: G 282 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7322 (pp) REVERT: G 379 MET cc_start: 0.2105 (OUTLIER) cc_final: 0.1796 (ppp) REVERT: G 518 HIS cc_start: 0.7778 (m170) cc_final: 0.7563 (m-70) REVERT: G 557 LYS cc_start: 0.7970 (tmmt) cc_final: 0.7576 (tptp) REVERT: G 755 THR cc_start: 0.7951 (m) cc_final: 0.7698 (p) REVERT: G 810 SER cc_start: 0.8147 (t) cc_final: 0.7937 (p) REVERT: G 851 ASN cc_start: 0.8671 (m110) cc_final: 0.8465 (m110) REVERT: G 900 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7985 (tp) REVERT: D 153 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: D 201 ASP cc_start: 0.6714 (m-30) cc_final: 0.6509 (m-30) REVERT: D 291 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8051 (ptmt) REVERT: D 558 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: D 697 MET cc_start: 0.8399 (tpt) cc_final: 0.8139 (tpp) REVERT: C 350 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5759 (mm-30) REVERT: C 368 GLU cc_start: 0.6323 (mm-30) cc_final: 0.6098 (mm-30) REVERT: C 416 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7638 (tm130) REVERT: C 480 MET cc_start: 0.9058 (mtm) cc_final: 0.8751 (mtm) REVERT: C 700 MET cc_start: 0.7435 (mtp) cc_final: 0.7205 (mtm) REVERT: C 755 THR cc_start: 0.7928 (m) cc_final: 0.7633 (p) outliers start: 140 outliers final: 24 residues processed: 779 average time/residue: 1.8448 time to fit residues: 1747.6736 Evaluate side-chains 598 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 558 time to evaluate : 5.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 439 GLN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 210 VAL 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 836 SER Chi-restraints excluded: chain E residue 887 VAL 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 525 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 379 MET Chi-restraints excluded: chain G residue 592 ASP Chi-restraints excluded: chain G residue 900 LEU 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 291 LYS Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain C residue 59 THR 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 277 SER Chi-restraints excluded: chain C residue 350 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 279 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 417 optimal weight: 0.6980 chunk 341 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 503 optimal weight: 2.9990 chunk 543 optimal weight: 2.9990 chunk 448 optimal weight: 9.9990 chunk 498 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 403 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 135 ASN A 149 GLN A 253 ASN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 254 HIS ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN E 253 ASN E 769 GLN ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN F 253 ASN F 403 ASN F 769 GLN G 39 ASN G 253 ASN G 439 GLN ** G 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 ASN D 769 GLN C 39 ASN C 248 ASN C 253 ASN C 769 GLN ** C 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 47173 Z= 0.254 Angle : 0.692 11.333 63609 Z= 0.366 Chirality : 0.045 0.256 7056 Planarity : 0.005 0.110 8015 Dihedral : 5.580 56.805 6096 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.84 % Favored : 91.03 % Rotamer: Outliers : 3.67 % Allowed : 13.87 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.12), residues: 5460 helix: 1.47 (0.09), residues: 3248 sheet: -1.08 (0.41), residues: 182 loop : -2.25 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 745 HIS 0.014 0.001 HIS F 424 PHE 0.018 0.002 PHE E 701 TYR 0.029 0.002 TYR A 651 ARG 0.006 0.001 ARG D 507 *********************** 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 825 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 638 time to evaluate : 5.484 Fit side-chains revert: symmetry clash REVERT: A 282 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7000 (pp) REVERT: A 284 LYS cc_start: 0.8119 (pttt) cc_final: 0.7857 (pttm) REVERT: A 290 ASN cc_start: 0.7933 (m-40) cc_final: 0.7584 (m-40) REVERT: A 368 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: A 420 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7039 (tt) REVERT: A 439 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6883 (mt0) REVERT: A 466 MET cc_start: 0.8305 (tpp) cc_final: 0.8060 (tpt) REVERT: A 794 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7696 (tttm) REVERT: A 863 LYS cc_start: 0.7547 (mtmt) cc_final: 0.7297 (mttt) REVERT: B 43 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: B 209 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8201 (mm) REVERT: B 284 LYS cc_start: 0.8119 (pttt) cc_final: 0.7334 (mmtm) REVERT: B 299 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8139 (t) REVERT: B 437 TYR cc_start: 0.8691 (m-80) cc_final: 0.8491 (m-80) REVERT: B 557 LYS cc_start: 0.7864 (tttt) cc_final: 0.7376 (mppt) REVERT: E 153 GLU cc_start: 0.7521 (mp0) cc_final: 0.7093 (mp0) REVERT: E 201 ASP cc_start: 0.6843 (m-30) cc_final: 0.6528 (m-30) REVERT: E 276 LEU cc_start: 0.8348 (pp) cc_final: 0.7800 (mp) REVERT: E 282 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7378 (pp) REVERT: E 362 MET cc_start: 0.8927 (tpt) cc_final: 0.8483 (tmm) REVERT: E 558 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6752 (mt-10) REVERT: E 611 ASP cc_start: 0.6779 (t0) cc_final: 0.6547 (t0) REVERT: E 614 GLU cc_start: 0.7362 (tp30) cc_final: 0.7064 (tp30) REVERT: E 648 ARG cc_start: 0.7185 (mtm180) cc_final: 0.6764 (ttp-170) REVERT: E 755 THR cc_start: 0.8383 (m) cc_final: 0.8141 (p) REVERT: E 809 MET cc_start: 0.8609 (tpp) cc_final: 0.8341 (tpt) REVERT: E 822 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8432 (tp) REVERT: E 888 GLU cc_start: 0.7309 (mp0) cc_final: 0.6731 (pm20) REVERT: F 75 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8706 (mt) REVERT: F 323 ASN cc_start: 0.7556 (p0) cc_final: 0.7186 (m-40) REVERT: F 659 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7636 (t) REVERT: F 794 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7967 (mtpp) REVERT: F 836 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8164 (m) REVERT: F 864 LYS cc_start: 0.7952 (tttt) cc_final: 0.7693 (ttmm) REVERT: F 886 TYR cc_start: 0.8308 (m-80) cc_final: 0.7916 (m-80) REVERT: F 900 LEU cc_start: 0.8504 (tp) cc_final: 0.8197 (tp) REVERT: G 282 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7553 (pp) REVERT: G 299 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8411 (t) REVERT: G 350 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: G 413 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: G 480 MET cc_start: 0.9005 (mtp) cc_final: 0.8737 (mtt) REVERT: G 557 LYS cc_start: 0.7993 (tmmt) cc_final: 0.7599 (tptp) REVERT: G 558 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: G 648 ARG cc_start: 0.7075 (mtm180) cc_final: 0.6404 (mmm-85) REVERT: G 755 THR cc_start: 0.8390 (m) cc_final: 0.8135 (p) REVERT: G 795 LYS cc_start: 0.7909 (mttp) cc_final: 0.7222 (mttt) REVERT: G 880 HIS cc_start: 0.6185 (t-90) cc_final: 0.5963 (t-170) REVERT: D 284 LYS cc_start: 0.8018 (pttt) cc_final: 0.7496 (mmtm) REVERT: D 291 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8016 (ptmt) REVERT: D 413 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: D 558 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: D 659 THR cc_start: 0.8060 (p) cc_final: 0.7747 (t) REVERT: C 40 LEU cc_start: 0.8484 (tp) cc_final: 0.8082 (tt) REVERT: C 268 ARG cc_start: 0.7564 (ptp90) cc_final: 0.7289 (mtt90) REVERT: C 276 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7482 (mp) REVERT: C 362 MET cc_start: 0.8995 (tpt) cc_final: 0.8705 (mmm) REVERT: C 368 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6787 (tp30) REVERT: C 413 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: C 416 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7780 (tm130) REVERT: C 558 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: C 769 GLN cc_start: 0.7606 (mt0) cc_final: 0.7179 (mt0) outliers start: 187 outliers final: 56 residues processed: 763 average time/residue: 1.7403 time to fit residues: 1622.6992 Evaluate side-chains 662 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 581 time to evaluate : 5.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 210 VAL 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 374 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 VAL 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 E residue 123 ARG 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 350 GLU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 558 GLU Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 657 GLN 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 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 209 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 648 ARG Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 794 LYS Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 413 GLU Chi-restraints excluded: chain G residue 558 GLU Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 609 ASP Chi-restraints excluded: chain G residue 659 THR Chi-restraints excluded: chain G residue 692 THR 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 369 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 825 ILE 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 369 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 692 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 497 optimal weight: 1.9990 chunk 378 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 240 optimal weight: 0.9990 chunk 337 optimal weight: 5.9990 chunk 504 optimal weight: 2.9990 chunk 534 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 478 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 253 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 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 253 ASN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 253 ASN G 248 ASN G 253 ASN G 769 GLN ** G 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 47173 Z= 0.241 Angle : 0.661 14.798 63609 Z= 0.347 Chirality : 0.044 0.242 7056 Planarity : 0.005 0.107 8015 Dihedral : 5.555 58.789 6094 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 1.15 % Allowed : 7.11 % Favored : 91.74 % Rotamer: Outliers : 4.08 % Allowed : 14.19 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.12), residues: 5460 helix: 1.54 (0.09), residues: 3234 sheet: -1.16 (0.39), residues: 175 loop : -2.28 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 745 HIS 0.017 0.001 HIS F 424 PHE 0.017 0.002 PHE F 414 TYR 0.027 0.002 TYR E 651 ARG 0.004 0.001 ARG F 507 *********************** 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 836 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 628 time to evaluate : 5.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7266 (pp) REVERT: A 290 ASN cc_start: 0.8099 (m-40) cc_final: 0.7739 (m-40) REVERT: A 291 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7897 (ptpp) REVERT: A 323 ASN cc_start: 0.7021 (p0) cc_final: 0.6800 (m-40) REVERT: A 350 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7452 (mm-30) REVERT: A 368 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: A 379 MET cc_start: 0.3778 (ppp) cc_final: 0.2650 (ppp) REVERT: A 420 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6777 (tt) REVERT: A 466 MET cc_start: 0.8299 (tpp) cc_final: 0.8095 (tpt) REVERT: A 863 LYS cc_start: 0.7578 (mtmt) cc_final: 0.7235 (mtpt) REVERT: B 122 ASP cc_start: 0.7447 (m-30) cc_final: 0.7185 (m-30) REVERT: B 284 LYS cc_start: 0.7872 (pttt) cc_final: 0.7385 (mmtm) REVERT: B 299 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8297 (t) REVERT: B 323 ASN cc_start: 0.7092 (p0) cc_final: 0.6866 (m110) REVERT: B 413 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: B 437 TYR cc_start: 0.8645 (m-80) cc_final: 0.8339 (m-80) REVERT: B 557 LYS cc_start: 0.7907 (tttt) cc_final: 0.7582 (mppt) REVERT: B 884 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8354 (ptpt) REVERT: B 888 GLU cc_start: 0.7130 (mp0) cc_final: 0.6563 (pm20) REVERT: E 153 GLU cc_start: 0.7578 (mp0) cc_final: 0.7169 (mp0) REVERT: E 201 ASP cc_start: 0.7134 (m-30) cc_final: 0.6843 (m-30) REVERT: E 276 LEU cc_start: 0.8490 (pp) cc_final: 0.7942 (mp) REVERT: E 282 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7246 (pp) REVERT: E 323 ASN cc_start: 0.7228 (p0) cc_final: 0.7020 (m-40) REVERT: E 362 MET cc_start: 0.8912 (tpt) cc_final: 0.8450 (tmm) REVERT: E 528 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7477 (mt-10) REVERT: E 558 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6805 (mt-10) REVERT: E 614 GLU cc_start: 0.7348 (tp30) cc_final: 0.7031 (tp30) REVERT: E 648 ARG cc_start: 0.7123 (mtm180) cc_final: 0.6297 (mmm-85) REVERT: E 649 ASN cc_start: 0.5781 (OUTLIER) cc_final: 0.5397 (t0) REVERT: E 755 THR cc_start: 0.8474 (m) cc_final: 0.8261 (p) REVERT: E 809 MET cc_start: 0.8541 (tpp) cc_final: 0.8339 (tpt) REVERT: E 822 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8556 (tp) REVERT: E 888 GLU cc_start: 0.7313 (mp0) cc_final: 0.6827 (pm20) REVERT: E 895 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5709 (mp0) REVERT: F 75 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8669 (mt) REVERT: F 249 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: F 323 ASN cc_start: 0.7260 (p0) cc_final: 0.6964 (m110) REVERT: F 437 TYR cc_start: 0.8706 (m-80) cc_final: 0.8504 (m-80) REVERT: F 480 MET cc_start: 0.9123 (mtm) cc_final: 0.8886 (mtm) REVERT: F 557 LYS cc_start: 0.7821 (tmtm) cc_final: 0.7479 (tptp) REVERT: F 794 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7987 (mtpp) REVERT: F 795 LYS cc_start: 0.8017 (mttp) cc_final: 0.7521 (mmpt) REVERT: F 836 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8210 (m) REVERT: F 864 LYS cc_start: 0.7950 (tttt) cc_final: 0.7717 (ttmm) REVERT: F 886 TYR cc_start: 0.8230 (m-80) cc_final: 0.7838 (m-80) REVERT: F 900 LEU cc_start: 0.8695 (tp) cc_final: 0.8442 (tp) REVERT: G 68 SER cc_start: 0.7752 (m) cc_final: 0.7494 (t) REVERT: G 282 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7405 (pp) REVERT: G 299 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8448 (t) REVERT: G 350 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6891 (mt-10) REVERT: G 413 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: G 533 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6352 (p90) REVERT: G 558 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: G 648 ARG cc_start: 0.7043 (mtm180) cc_final: 0.6351 (mmm-85) REVERT: G 795 LYS cc_start: 0.7862 (mttp) cc_final: 0.7617 (mmpt) REVERT: G 880 HIS cc_start: 0.6334 (t-90) cc_final: 0.6092 (t-170) REVERT: D 284 LYS cc_start: 0.8027 (pttt) cc_final: 0.7426 (mmtm) REVERT: D 379 MET cc_start: 0.2120 (ppp) cc_final: 0.1025 (ppp) REVERT: D 413 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: D 659 THR cc_start: 0.8005 (p) cc_final: 0.7720 (t) REVERT: D 755 THR cc_start: 0.8532 (m) cc_final: 0.8232 (p) REVERT: D 888 GLU cc_start: 0.7327 (mp0) cc_final: 0.7012 (pp20) REVERT: C 40 LEU cc_start: 0.8505 (tp) cc_final: 0.8071 (tt) REVERT: C 276 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7634 (mp) REVERT: C 350 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6294 (mm-30) REVERT: C 362 MET cc_start: 0.8978 (tpt) cc_final: 0.8690 (mmm) REVERT: C 368 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6653 (mm-30) REVERT: C 416 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7766 (tm130) REVERT: C 558 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: C 648 ARG cc_start: 0.7139 (mtm180) cc_final: 0.6647 (mmm-85) outliers start: 208 outliers final: 79 residues processed: 762 average time/residue: 1.6774 time to fit residues: 1566.6856 Evaluate side-chains 679 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 574 time to evaluate : 5.652 ------------------------------------------------------------------------------- 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 282 LEU Chi-restraints excluded: chain A residue 291 LYS 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 420 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 210 VAL 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 374 VAL Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 884 LYS Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 299 SER 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 525 VAL Chi-restraints excluded: chain E residue 558 GLU Chi-restraints excluded: chain E residue 579 LEU 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 657 GLN 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 E residue 864 LYS Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain F residue 40 LEU 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 153 GLU Chi-restraints excluded: chain F residue 209 LEU 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 355 MET 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 579 LEU Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 794 LYS Chi-restraints excluded: chain F residue 836 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 413 GLU 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 610 ASP Chi-restraints excluded: chain G residue 756 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 79 LYS 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 282 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 756 LYS Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain C residue 59 THR 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 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 558 GLU Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 692 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 445 optimal weight: 3.9990 chunk 303 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 397 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 456 optimal weight: 7.9990 chunk 369 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 chunk 479 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 248 ASN B 253 ASN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN E 253 ASN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 424 HIS ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 HIS ** F 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 403 ASN ** G 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 424 HIS D 880 HIS C 149 GLN C 248 ASN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN ** C 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 47173 Z= 0.285 Angle : 0.697 13.599 63609 Z= 0.367 Chirality : 0.046 0.247 7056 Planarity : 0.005 0.116 8015 Dihedral : 5.713 39.404 6090 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.93 % Favored : 90.93 % Rotamer: Outliers : 4.75 % Allowed : 14.64 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.12), residues: 5460 helix: 1.49 (0.09), residues: 3248 sheet: -0.84 (0.43), residues: 182 loop : -2.28 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 418 HIS 0.017 0.001 HIS C 424 PHE 0.019 0.002 PHE F 414 TYR 0.028 0.002 TYR E 651 ARG 0.004 0.001 ARG B 597 *********************** 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 844 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 602 time to evaluate : 4.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: A 282 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7288 (pp) REVERT: A 323 ASN cc_start: 0.7262 (p0) cc_final: 0.7002 (m-40) REVERT: A 350 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7424 (mm-30) REVERT: A 368 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: A 379 MET cc_start: 0.3448 (ppp) cc_final: 0.2624 (ppp) REVERT: A 420 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6911 (tt) REVERT: A 863 LYS cc_start: 0.7370 (mtmt) cc_final: 0.7097 (mtpt) REVERT: B 122 ASP cc_start: 0.7602 (m-30) cc_final: 0.7289 (m-30) REVERT: B 284 LYS cc_start: 0.7935 (pttt) cc_final: 0.7533 (mmtm) REVERT: B 299 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8386 (t) REVERT: B 412 MET cc_start: 0.8108 (mmm) cc_final: 0.7776 (mmm) REVERT: B 557 LYS cc_start: 0.7909 (tttt) cc_final: 0.7678 (mppt) REVERT: B 884 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8419 (ptpt) REVERT: B 888 GLU cc_start: 0.7102 (mp0) cc_final: 0.6576 (pm20) REVERT: E 153 GLU cc_start: 0.7657 (mp0) cc_final: 0.7281 (mp0) REVERT: E 282 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7266 (pp) REVERT: E 308 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: E 362 MET cc_start: 0.8924 (tpt) cc_final: 0.8491 (tmm) REVERT: E 614 GLU cc_start: 0.7349 (tp30) cc_final: 0.7013 (tp30) REVERT: E 648 ARG cc_start: 0.7059 (mtm180) cc_final: 0.6517 (mmm-85) REVERT: E 649 ASN cc_start: 0.5841 (OUTLIER) cc_final: 0.5476 (t0) REVERT: E 755 THR cc_start: 0.8417 (m) cc_final: 0.8207 (p) REVERT: E 794 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7994 (tttm) REVERT: E 809 MET cc_start: 0.8576 (tpp) cc_final: 0.8365 (tpt) REVERT: E 822 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8540 (tp) REVERT: E 888 GLU cc_start: 0.7325 (mp0) cc_final: 0.6883 (pm20) REVERT: F 75 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8603 (mt) REVERT: F 80 GLN cc_start: 0.8175 (mt0) cc_final: 0.7935 (mt0) REVERT: F 200 ASP cc_start: 0.7486 (t0) cc_final: 0.7151 (t70) REVERT: F 249 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: F 276 LEU cc_start: 0.8535 (pp) cc_final: 0.7945 (mp) REVERT: F 284 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7527 (mmtm) REVERT: F 424 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6324 (t70) REVERT: F 557 LYS cc_start: 0.7781 (tmtm) cc_final: 0.7467 (tptp) REVERT: F 611 ASP cc_start: 0.7213 (t0) cc_final: 0.7007 (t0) REVERT: F 836 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8224 (m) REVERT: F 864 LYS cc_start: 0.8006 (tttt) cc_final: 0.7769 (ttmm) REVERT: F 886 TYR cc_start: 0.8311 (m-80) cc_final: 0.8056 (m-80) REVERT: G 68 SER cc_start: 0.7857 (m) cc_final: 0.7641 (t) REVERT: G 282 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7485 (pp) REVERT: G 299 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8435 (t) REVERT: G 350 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: G 413 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: G 424 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6019 (t70) REVERT: G 475 ASP cc_start: 0.7898 (m-30) cc_final: 0.7679 (m-30) REVERT: G 512 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8846 (tm) REVERT: G 533 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6417 (p90) REVERT: G 648 ARG cc_start: 0.7117 (mtm180) cc_final: 0.6407 (mmm-85) REVERT: G 795 LYS cc_start: 0.7863 (mttp) cc_final: 0.7624 (mmpt) REVERT: G 863 LYS cc_start: 0.7765 (mttt) cc_final: 0.7463 (mtpt) REVERT: G 880 HIS cc_start: 0.6602 (t-90) cc_final: 0.6300 (t-170) REVERT: D 123 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7425 (ttt-90) REVERT: D 268 ARG cc_start: 0.7548 (ptp90) cc_final: 0.7256 (mtt90) REVERT: D 284 LYS cc_start: 0.8095 (pttt) cc_final: 0.7472 (mmtm) REVERT: D 350 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: D 379 MET cc_start: 0.2113 (ppp) cc_final: 0.1132 (ppp) REVERT: D 413 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: D 424 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.5405 (t70) REVERT: D 648 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6820 (mtp180) REVERT: D 659 THR cc_start: 0.8072 (p) cc_final: 0.7799 (t) REVERT: D 755 THR cc_start: 0.8564 (m) cc_final: 0.8245 (p) REVERT: D 888 GLU cc_start: 0.7350 (mp0) cc_final: 0.6710 (pm20) REVERT: C 276 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7659 (mp) REVERT: C 350 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6230 (mm-30) REVERT: C 368 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6730 (mm-30) REVERT: C 534 MET cc_start: 0.7937 (mmm) cc_final: 0.7692 (mmm) REVERT: C 558 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: C 648 ARG cc_start: 0.7179 (mtm180) cc_final: 0.6673 (mmm-85) REVERT: C 769 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7429 (mt0) outliers start: 242 outliers final: 116 residues processed: 774 average time/residue: 1.5565 time to fit residues: 1481.4943 Evaluate side-chains 721 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 573 time to evaluate : 5.038 ------------------------------------------------------------------------------- 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 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 249 GLU Chi-restraints excluded: chain A residue 282 LEU 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 420 LEU Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 609 ASP 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 61 ASP 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 317 SER Chi-restraints excluded: chain B residue 355 MET 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 472 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 884 LYS Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 123 ARG 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 249 GLU 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 406 TYR Chi-restraints excluded: chain E residue 424 HIS Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 579 LEU 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 657 GLN 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 153 GLU Chi-restraints excluded: chain F residue 192 ILE 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 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 579 LEU Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 650 LEU 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 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 350 GLU 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 424 HIS Chi-restraints excluded: chain G residue 512 LEU 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 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 406 TYR Chi-restraints excluded: chain D residue 413 GLU 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 648 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 756 LYS 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 210 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 SER 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 409 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 769 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 179 optimal weight: 8.9990 chunk 481 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 535 optimal weight: 0.9980 chunk 444 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 403 ASN A 657 GLN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN B 248 ASN B 253 ASN B 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN ** E 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 424 HIS ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 424 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 47173 Z= 0.206 Angle : 0.626 14.102 63609 Z= 0.329 Chirality : 0.043 0.287 7056 Planarity : 0.005 0.139 8015 Dihedral : 5.505 39.043 6090 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 1.01 % Allowed : 7.29 % Favored : 91.70 % Rotamer: Outliers : 4.43 % Allowed : 15.48 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.12), residues: 5460 helix: 1.64 (0.09), residues: 3206 sheet: -1.06 (0.40), residues: 175 loop : -2.25 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 418 HIS 0.006 0.001 HIS A 432 PHE 0.014 0.002 PHE E 414 TYR 0.027 0.002 TYR E 651 ARG 0.003 0.000 ARG A 815 *********************** 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 825 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 599 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: A 282 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7165 (pp) REVERT: A 323 ASN cc_start: 0.7144 (p0) cc_final: 0.6879 (m-40) REVERT: A 350 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7443 (mm-30) REVERT: A 379 MET cc_start: 0.3260 (ppp) cc_final: 0.2501 (ppp) REVERT: A 424 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.5138 (t70) REVERT: A 533 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.5886 (p90) REVERT: A 574 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7372 (tp-100) REVERT: A 863 LYS cc_start: 0.7362 (mtmt) cc_final: 0.7090 (mtpt) REVERT: B 122 ASP cc_start: 0.7619 (m-30) cc_final: 0.7307 (m-30) REVERT: B 284 LYS cc_start: 0.7794 (pttt) cc_final: 0.7476 (mmtm) REVERT: B 299 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8370 (t) REVERT: B 412 MET cc_start: 0.8096 (mmm) cc_final: 0.7829 (mmm) REVERT: B 413 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: B 424 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.5980 (t70) REVERT: B 437 TYR cc_start: 0.8656 (m-80) cc_final: 0.8359 (m-80) REVERT: B 574 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: B 888 GLU cc_start: 0.7066 (mp0) cc_final: 0.6560 (pm20) REVERT: E 153 GLU cc_start: 0.7481 (mp0) cc_final: 0.7081 (mp0) REVERT: E 201 ASP cc_start: 0.7240 (m-30) cc_final: 0.6884 (m-30) REVERT: E 276 LEU cc_start: 0.8421 (pp) cc_final: 0.7947 (mp) REVERT: E 282 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7247 (pp) REVERT: E 308 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: E 362 MET cc_start: 0.8874 (tpt) cc_final: 0.8428 (tmm) REVERT: E 648 ARG cc_start: 0.6992 (mtm180) cc_final: 0.6464 (mmm-85) REVERT: E 755 THR cc_start: 0.8391 (m) cc_final: 0.8177 (p) REVERT: E 794 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8012 (tttp) REVERT: E 809 MET cc_start: 0.8513 (tpp) cc_final: 0.8292 (tpt) REVERT: E 822 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8568 (tp) REVERT: E 888 GLU cc_start: 0.7307 (mp0) cc_final: 0.6837 (pm20) REVERT: E 895 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.5679 (mp0) REVERT: F 75 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8658 (mt) REVERT: F 80 GLN cc_start: 0.8136 (mt0) cc_final: 0.7874 (mt0) REVERT: F 249 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7279 (tp30) REVERT: F 276 LEU cc_start: 0.8509 (pp) cc_final: 0.8010 (mp) REVERT: F 284 LYS cc_start: 0.8054 (ptmt) cc_final: 0.7457 (mmtm) REVERT: F 437 TYR cc_start: 0.8688 (m-80) cc_final: 0.8431 (m-80) REVERT: F 480 MET cc_start: 0.9135 (mtm) cc_final: 0.8863 (mtm) REVERT: F 557 LYS cc_start: 0.7825 (tmtm) cc_final: 0.7603 (tptp) REVERT: F 611 ASP cc_start: 0.7149 (t0) cc_final: 0.6929 (t0) REVERT: F 824 GLU cc_start: 0.6816 (pt0) cc_final: 0.6585 (pt0) REVERT: F 836 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8235 (m) REVERT: F 864 LYS cc_start: 0.7991 (tttt) cc_final: 0.7759 (ttmm) REVERT: G 68 SER cc_start: 0.7819 (m) cc_final: 0.7581 (t) REVERT: G 282 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7382 (pp) REVERT: G 299 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8436 (t) REVERT: G 350 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: G 413 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: G 424 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.5864 (t70) REVERT: G 475 ASP cc_start: 0.7813 (m-30) cc_final: 0.7576 (m-30) REVERT: G 533 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6334 (p90) REVERT: G 558 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: G 648 ARG cc_start: 0.7035 (mtm180) cc_final: 0.6313 (mmm-85) REVERT: G 795 LYS cc_start: 0.7805 (mttp) cc_final: 0.7558 (mmpt) REVERT: G 880 HIS cc_start: 0.6590 (t-90) cc_final: 0.6336 (t-170) REVERT: D 284 LYS cc_start: 0.8074 (pttt) cc_final: 0.7436 (mmtm) REVERT: D 379 MET cc_start: 0.2005 (OUTLIER) cc_final: 0.1375 (ppp) REVERT: D 413 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: D 424 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.5004 (t70) REVERT: D 648 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6756 (mtp180) REVERT: D 659 THR cc_start: 0.7922 (p) cc_final: 0.7679 (t) REVERT: D 755 THR cc_start: 0.8511 (m) cc_final: 0.8213 (p) REVERT: D 888 GLU cc_start: 0.7314 (mp0) cc_final: 0.6723 (pm20) REVERT: C 40 LEU cc_start: 0.8494 (mt) cc_final: 0.8130 (tt) REVERT: C 276 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7656 (mp) REVERT: C 291 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7738 (ptpt) REVERT: C 350 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6225 (mm-30) REVERT: C 362 MET cc_start: 0.8960 (tpt) cc_final: 0.8724 (mmm) REVERT: C 368 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6557 (mm-30) REVERT: C 416 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7734 (tm130) REVERT: C 424 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.5111 (t70) REVERT: C 558 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: C 648 ARG cc_start: 0.7160 (mtm180) cc_final: 0.6701 (mtp180) REVERT: C 659 THR cc_start: 0.8109 (p) cc_final: 0.7812 (t) outliers start: 226 outliers final: 106 residues processed: 762 average time/residue: 1.4676 time to fit residues: 1371.5217 Evaluate side-chains 707 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 568 time to evaluate : 4.286 ------------------------------------------------------------------------------- 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 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 533 TYR Chi-restraints excluded: chain A residue 574 GLN 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 61 ASP 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 413 GLU Chi-restraints excluded: chain B residue 424 HIS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 569 LYS Chi-restraints excluded: chain B residue 574 GLN Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 123 ARG 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 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 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 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 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 209 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 249 GLU 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 406 TYR Chi-restraints excluded: chain F residue 424 HIS Chi-restraints excluded: chain F residue 534 MET Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 756 LYS Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain F residue 794 LYS 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 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 350 GLU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 406 TYR Chi-restraints excluded: chain G residue 413 GLU Chi-restraints excluded: chain G residue 424 HIS 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 610 ASP Chi-restraints excluded: chain G residue 657 GLN Chi-restraints excluded: chain G residue 659 THR Chi-restraints excluded: chain G residue 769 GLN 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 175 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 282 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 413 GLU 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 580 VAL Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 648 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 756 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 68 SER 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 277 SER Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 424 HIS Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 836 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 515 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 390 optimal weight: 0.0170 chunk 302 optimal weight: 0.8980 chunk 450 optimal weight: 0.5980 chunk 298 optimal weight: 0.0060 chunk 533 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 overall best weight: 0.5034 ------------------------------------------------------------------------------- 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 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN E 712 ASN ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 HIS ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 424 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN C 712 ASN C 769 GLN C 806 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4037 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= 0.165 Angle : 0.584 12.131 63609 Z= 0.305 Chirality : 0.041 0.229 7056 Planarity : 0.004 0.128 8015 Dihedral : 5.259 38.296 6090 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.93 % Allowed : 7.07 % Favored : 92.00 % Rotamer: Outliers : 3.59 % Allowed : 16.72 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.12), residues: 5460 helix: 1.79 (0.09), residues: 3199 sheet: -1.00 (0.40), residues: 175 loop : -2.31 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 418 HIS 0.007 0.001 HIS F 424 PHE 0.013 0.001 PHE G 433 TYR 0.023 0.001 TYR C 651 ARG 0.005 0.000 ARG G 389 *********************** 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 791 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 608 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7169 (pp) REVERT: A 323 ASN cc_start: 0.7229 (p0) cc_final: 0.6984 (m-40) REVERT: A 350 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: A 406 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.4077 (p90) REVERT: A 424 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.5120 (t70) REVERT: A 574 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7509 (tp40) REVERT: A 822 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8263 (pp) REVERT: A 863 LYS cc_start: 0.7308 (mtmt) cc_final: 0.7046 (mtpt) REVERT: B 140 GLU cc_start: 0.8041 (tt0) cc_final: 0.7719 (tt0) REVERT: B 284 LYS cc_start: 0.7706 (pttt) cc_final: 0.7380 (mmtm) REVERT: B 379 MET cc_start: 0.2659 (ppp) cc_final: 0.2361 (ppp) REVERT: B 413 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: B 424 HIS cc_start: 0.6995 (OUTLIER) cc_final: 0.5847 (t70) REVERT: B 533 TYR cc_start: 0.6068 (p90) cc_final: 0.5413 (p90) REVERT: B 688 GLU cc_start: 0.6572 (mm-30) cc_final: 0.6256 (mp0) REVERT: B 725 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8129 (tptm) REVERT: B 888 GLU cc_start: 0.7116 (mp0) cc_final: 0.6589 (pm20) REVERT: E 40 LEU cc_start: 0.8597 (mt) cc_final: 0.8275 (mm) REVERT: E 153 GLU cc_start: 0.7521 (mp0) cc_final: 0.7156 (mp0) REVERT: E 201 ASP cc_start: 0.7017 (m-30) cc_final: 0.6697 (m-30) REVERT: E 276 LEU cc_start: 0.8204 (pp) cc_final: 0.7766 (mp) REVERT: E 308 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7160 (pp20) REVERT: E 534 MET cc_start: 0.7434 (mmm) cc_final: 0.7144 (tpt) REVERT: E 755 THR cc_start: 0.8369 (m) cc_final: 0.8149 (p) REVERT: E 794 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8040 (tttp) REVERT: E 809 MET cc_start: 0.8478 (tpp) cc_final: 0.8273 (tpt) REVERT: E 822 ILE cc_start: 0.8768 (tt) cc_final: 0.8537 (tp) REVERT: E 888 GLU cc_start: 0.7307 (mp0) cc_final: 0.6831 (pm20) REVERT: E 895 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5593 (mp0) REVERT: F 75 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8690 (mt) REVERT: F 249 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: F 276 LEU cc_start: 0.8488 (pp) cc_final: 0.8012 (mp) REVERT: F 284 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7434 (mmtm) REVERT: F 437 TYR cc_start: 0.8637 (m-80) cc_final: 0.8380 (m-80) REVERT: F 480 MET cc_start: 0.9101 (mtm) cc_final: 0.8836 (mtm) REVERT: F 557 LYS cc_start: 0.7743 (tmtm) cc_final: 0.7457 (tptp) REVERT: F 659 THR cc_start: 0.7933 (p) cc_final: 0.7627 (t) REVERT: F 688 GLU cc_start: 0.7152 (mp0) cc_final: 0.6891 (mp0) REVERT: F 864 LYS cc_start: 0.7988 (tttt) cc_final: 0.7758 (ttmm) REVERT: G 282 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7365 (pp) REVERT: G 299 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8506 (t) REVERT: G 424 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.5315 (t70) REVERT: G 533 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.6473 (p90) REVERT: G 648 ARG cc_start: 0.7019 (mtm180) cc_final: 0.6252 (mmm-85) REVERT: G 795 LYS cc_start: 0.7780 (mttp) cc_final: 0.7485 (mmpt) REVERT: G 880 HIS cc_start: 0.6577 (t-90) cc_final: 0.6320 (t-170) REVERT: D 123 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7417 (ttt-90) REVERT: D 201 ASP cc_start: 0.6868 (m-30) cc_final: 0.6599 (m-30) REVERT: D 284 LYS cc_start: 0.7969 (pttt) cc_final: 0.7374 (mmtm) REVERT: D 291 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7935 (ttpt) REVERT: D 379 MET cc_start: 0.2081 (OUTLIER) cc_final: 0.1494 (ppp) REVERT: D 424 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.4547 (t70) REVERT: D 557 LYS cc_start: 0.7755 (ttpp) cc_final: 0.7435 (tptp) REVERT: D 659 THR cc_start: 0.7800 (p) cc_final: 0.7577 (t) REVERT: D 755 THR cc_start: 0.8441 (m) cc_final: 0.8142 (p) REVERT: D 888 GLU cc_start: 0.7334 (mp0) cc_final: 0.6782 (pm20) REVERT: C 40 LEU cc_start: 0.8449 (mt) cc_final: 0.8129 (tt) REVERT: C 276 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7714 (mp) REVERT: C 325 THR cc_start: 0.7540 (p) cc_final: 0.7242 (m) REVERT: C 350 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6223 (mm-30) REVERT: C 362 MET cc_start: 0.8892 (tpt) cc_final: 0.8646 (mmm) REVERT: C 416 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7737 (tm130) REVERT: C 424 HIS cc_start: 0.6792 (OUTLIER) cc_final: 0.4997 (t70) REVERT: C 769 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7134 (mt0) outliers start: 183 outliers final: 88 residues processed: 739 average time/residue: 1.3547 time to fit residues: 1229.5426 Evaluate side-chains 697 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 583 time to evaluate : 3.941 ------------------------------------------------------------------------------- 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 210 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 350 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 574 GLN Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 836 SER 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 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 525 VAL Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain B residue 756 LYS 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 225 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 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 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 86 ASP Chi-restraints excluded: chain F residue 192 ILE 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 249 GLU 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 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 692 THR Chi-restraints excluded: chain F residue 756 LYS Chi-restraints excluded: chain F residue 769 GLN Chi-restraints excluded: chain F residue 794 LYS 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 424 HIS Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 610 ASP Chi-restraints excluded: chain G residue 659 THR Chi-restraints excluded: chain G residue 900 LEU 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 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 561 GLU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 756 LYS Chi-restraints excluded: chain C residue 79 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 277 SER 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 610 ASP Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 769 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 329 optimal weight: 0.5980 chunk 212 optimal weight: 2.9990 chunk 318 optimal weight: 0.0020 chunk 160 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 338 optimal weight: 0.9990 chunk 363 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 418 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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** A 806 HIS B 248 ASN B 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS E 248 ASN ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 HIS ** 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** D 248 ASN D 253 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 248 ASN C 769 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47173 Z= 0.168 Angle : 0.583 11.614 63609 Z= 0.304 Chirality : 0.041 0.189 7056 Planarity : 0.004 0.124 8015 Dihedral : 5.211 38.399 6090 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.93 % Allowed : 7.36 % Favored : 91.70 % Rotamer: Outliers : 3.61 % Allowed : 17.09 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 5460 helix: 1.82 (0.09), residues: 3206 sheet: -0.90 (0.40), residues: 175 loop : -2.31 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 418 HIS 0.006 0.001 HIS F 424 PHE 0.020 0.001 PHE B 433 TYR 0.023 0.001 TYR E 651 ARG 0.003 0.000 ARG A 815 *********************** 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 782 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 598 time to evaluate : 3.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: A 282 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7180 (pp) REVERT: A 323 ASN cc_start: 0.7319 (p0) cc_final: 0.7049 (m-40) REVERT: A 350 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: A 379 MET cc_start: 0.2817 (ppp) cc_final: 0.2164 (ppp) REVERT: A 424 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.5456 (t70) REVERT: A 533 TYR cc_start: 0.6618 (OUTLIER) cc_final: 0.5819 (p90) REVERT: A 574 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7502 (tp40) REVERT: A 822 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8270 (pp) REVERT: A 863 LYS cc_start: 0.7311 (mtmt) cc_final: 0.7035 (mtpt) REVERT: B 140 GLU cc_start: 0.8031 (tt0) cc_final: 0.7698 (tt0) REVERT: B 201 ASP cc_start: 0.6927 (m-30) cc_final: 0.6537 (m-30) REVERT: B 284 LYS cc_start: 0.7504 (pttt) cc_final: 0.7259 (mmtm) REVERT: B 424 HIS cc_start: 0.7037 (OUTLIER) cc_final: 0.5895 (t70) REVERT: B 574 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: B 688 GLU cc_start: 0.6518 (mm-30) cc_final: 0.6188 (mp0) REVERT: B 888 GLU cc_start: 0.7100 (mp0) cc_final: 0.6584 (pm20) REVERT: E 40 LEU cc_start: 0.8600 (mt) cc_final: 0.8290 (mm) REVERT: E 153 GLU cc_start: 0.7497 (mp0) cc_final: 0.7097 (mp0) REVERT: E 201 ASP cc_start: 0.6843 (m-30) cc_final: 0.6529 (m-30) REVERT: E 276 LEU cc_start: 0.8177 (pp) cc_final: 0.7740 (mp) REVERT: E 282 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7144 (pp) REVERT: E 308 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7161 (pp20) REVERT: E 362 MET cc_start: 0.8874 (tpt) cc_final: 0.8512 (tmm) REVERT: E 534 MET cc_start: 0.7256 (mmm) cc_final: 0.6820 (tpt) REVERT: E 755 THR cc_start: 0.8354 (m) cc_final: 0.8135 (p) REVERT: E 794 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8046 (tttp) REVERT: E 822 ILE cc_start: 0.8775 (tt) cc_final: 0.8544 (tp) REVERT: E 888 GLU cc_start: 0.7318 (mp0) cc_final: 0.6840 (pm20) REVERT: E 895 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5446 (mp0) REVERT: F 199 ILE cc_start: 0.8144 (mt) cc_final: 0.7803 (mp) REVERT: F 249 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: F 276 LEU cc_start: 0.8471 (pp) cc_final: 0.7983 (mp) REVERT: F 284 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7428 (mmtm) REVERT: F 437 TYR cc_start: 0.8659 (m-80) cc_final: 0.8393 (m-80) REVERT: F 480 MET cc_start: 0.9119 (mtm) cc_final: 0.8854 (mtm) REVERT: F 557 LYS cc_start: 0.7743 (tmtm) cc_final: 0.7533 (tptp) REVERT: F 659 THR cc_start: 0.7893 (p) cc_final: 0.7601 (t) REVERT: F 864 LYS cc_start: 0.7987 (tttt) cc_final: 0.7761 (ttmm) REVERT: G 282 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7373 (pp) REVERT: G 424 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.5625 (t70) REVERT: G 533 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6397 (p90) REVERT: G 557 LYS cc_start: 0.7504 (ttpp) cc_final: 0.7071 (tptp) REVERT: G 569 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8042 (mtpt) REVERT: G 648 ARG cc_start: 0.7032 (mtm180) cc_final: 0.6344 (mmm-85) REVERT: G 795 LYS cc_start: 0.7757 (mttp) cc_final: 0.7472 (mmpt) REVERT: G 880 HIS cc_start: 0.6540 (t-90) cc_final: 0.6294 (t-170) REVERT: D 123 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7433 (ttt-90) REVERT: D 201 ASP cc_start: 0.6883 (m-30) cc_final: 0.6604 (m-30) REVERT: D 284 LYS cc_start: 0.8026 (pttt) cc_final: 0.7475 (mmtm) REVERT: D 379 MET cc_start: 0.2215 (OUTLIER) cc_final: 0.1629 (ppp) REVERT: D 557 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7382 (tptp) REVERT: D 648 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6725 (mtp180) REVERT: D 659 THR cc_start: 0.7775 (p) cc_final: 0.7552 (t) REVERT: D 755 THR cc_start: 0.8442 (m) cc_final: 0.8136 (p) REVERT: D 888 GLU cc_start: 0.7323 (mp0) cc_final: 0.6794 (pm20) REVERT: C 40 LEU cc_start: 0.8448 (mt) cc_final: 0.8128 (tt) REVERT: C 276 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7721 (mp) REVERT: C 325 THR cc_start: 0.7474 (p) cc_final: 0.7224 (m) REVERT: C 350 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6229 (mm-30) REVERT: C 416 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7725 (tm130) REVERT: C 424 HIS cc_start: 0.6822 (OUTLIER) cc_final: 0.5536 (t-170) REVERT: C 534 MET cc_start: 0.7639 (tmm) cc_final: 0.7396 (tpp) REVERT: C 888 GLU cc_start: 0.6984 (mp0) cc_final: 0.6348 (pm20) outliers start: 184 outliers final: 104 residues processed: 727 average time/residue: 1.3267 time to fit residues: 1183.7684 Evaluate side-chains 693 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 564 time to evaluate : 3.846 ------------------------------------------------------------------------------- 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 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 350 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 LEU 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 756 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 249 GLU 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 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 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 895 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 192 ILE 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 249 GLU 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 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 406 TYR Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 610 ASP Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 769 GLN Chi-restraints excluded: chain F residue 794 LYS 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 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 569 LYS Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 610 ASP Chi-restraints excluded: chain G residue 618 LEU Chi-restraints excluded: chain G residue 659 THR Chi-restraints excluded: chain G residue 769 GLN Chi-restraints excluded: chain G residue 836 SER Chi-restraints excluded: chain G residue 900 LEU 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 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 525 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 648 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 756 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 409 LEU 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 836 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 484 optimal weight: 1.9990 chunk 510 optimal weight: 2.9990 chunk 465 optimal weight: 4.9990 chunk 496 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 390 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 448 optimal weight: 10.0000 chunk 469 optimal weight: 9.9990 chunk 494 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 320 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 403 ASN B 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 ASN ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 880 HIS F 80 GLN ** F 424 HIS ** 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 149 GLN ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 806 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 D 880 HIS C 248 ASN C 403 ASN C 769 GLN ** C 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 47173 Z= 0.278 Angle : 0.678 13.526 63609 Z= 0.357 Chirality : 0.046 0.201 7056 Planarity : 0.005 0.131 8015 Dihedral : 5.645 40.456 6090 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.86 % Favored : 91.10 % Rotamer: Outliers : 3.51 % Allowed : 17.33 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.12), residues: 5460 helix: 1.63 (0.09), residues: 3213 sheet: -0.71 (0.41), residues: 189 loop : -2.24 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 745 HIS 0.011 0.001 HIS D 424 PHE 0.017 0.002 PHE E 414 TYR 0.025 0.002 TYR E 651 ARG 0.005 0.001 ARG A 54 *********************** 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 779 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 600 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: A 282 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7389 (pp) REVERT: A 350 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: A 379 MET cc_start: 0.2893 (ppp) cc_final: 0.2180 (ppp) REVERT: A 406 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.4407 (p90) REVERT: A 424 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6585 (t70) REVERT: A 533 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.5863 (p90) REVERT: A 822 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8303 (pp) REVERT: A 863 LYS cc_start: 0.7414 (mtmt) cc_final: 0.7204 (mtpt) REVERT: B 276 LEU cc_start: 0.8202 (pp) cc_final: 0.7794 (mt) REVERT: B 379 MET cc_start: 0.2767 (ppp) cc_final: 0.2501 (ppp) REVERT: B 424 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6112 (t70) REVERT: B 574 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: B 888 GLU cc_start: 0.7103 (mp0) cc_final: 0.6606 (pm20) REVERT: E 153 GLU cc_start: 0.7546 (mp0) cc_final: 0.7179 (mp0) REVERT: E 201 ASP cc_start: 0.7219 (m-30) cc_final: 0.6875 (m-30) REVERT: E 282 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7305 (pp) REVERT: E 308 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7279 (pp20) REVERT: E 362 MET cc_start: 0.8936 (tpt) cc_final: 0.8610 (tmm) REVERT: E 534 MET cc_start: 0.7429 (mmm) cc_final: 0.7155 (tpt) REVERT: E 648 ARG cc_start: 0.7180 (mtm180) cc_final: 0.6588 (mmm-85) REVERT: E 794 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7982 (tttm) REVERT: E 822 ILE cc_start: 0.8823 (tt) cc_final: 0.8588 (tp) REVERT: E 888 GLU cc_start: 0.7301 (mp0) cc_final: 0.6817 (pm20) REVERT: E 895 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5623 (mp0) REVERT: F 168 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: F 199 ILE cc_start: 0.8445 (mt) cc_final: 0.8163 (mp) REVERT: F 276 LEU cc_start: 0.8545 (pp) cc_final: 0.8025 (mp) REVERT: F 284 LYS cc_start: 0.8023 (ptmt) cc_final: 0.7520 (mmtm) REVERT: F 424 HIS cc_start: 0.7138 (OUTLIER) cc_final: 0.6260 (t-90) REVERT: F 437 TYR cc_start: 0.8750 (m-80) cc_final: 0.8514 (m-80) REVERT: F 557 LYS cc_start: 0.7831 (tmtm) cc_final: 0.7526 (tptp) REVERT: F 864 LYS cc_start: 0.7979 (tttt) cc_final: 0.7745 (ttmm) REVERT: G 282 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7481 (pp) REVERT: G 350 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6834 (mt-10) REVERT: G 409 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6757 (tt) REVERT: G 424 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.6854 (t-170) REVERT: G 475 ASP cc_start: 0.7621 (m-30) cc_final: 0.7204 (m-30) REVERT: G 533 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6404 (p90) REVERT: G 569 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8043 (mtpt) REVERT: G 648 ARG cc_start: 0.7098 (mtm180) cc_final: 0.6361 (mmm-85) REVERT: G 795 LYS cc_start: 0.7824 (mttp) cc_final: 0.7511 (mmpt) REVERT: G 863 LYS cc_start: 0.7646 (mttt) cc_final: 0.7353 (mtpt) REVERT: G 880 HIS cc_start: 0.6792 (t-90) cc_final: 0.6506 (t-170) REVERT: D 123 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7486 (ttt-90) REVERT: D 284 LYS cc_start: 0.8112 (pttt) cc_final: 0.7498 (mmtm) REVERT: D 379 MET cc_start: 0.2233 (OUTLIER) cc_final: 0.1606 (ppp) REVERT: D 424 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6538 (t-90) REVERT: D 557 LYS cc_start: 0.7808 (ttpp) cc_final: 0.7461 (tptp) REVERT: D 648 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6885 (mtp180) REVERT: D 659 THR cc_start: 0.7977 (p) cc_final: 0.7751 (t) REVERT: C 209 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8030 (mm) REVERT: C 276 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7688 (mp) REVERT: C 350 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6230 (mm-30) REVERT: C 362 MET cc_start: 0.8980 (tpt) cc_final: 0.8703 (mmm) REVERT: C 379 MET cc_start: 0.2542 (ppp) cc_final: 0.2158 (pp-130) REVERT: C 412 MET cc_start: 0.8134 (mmm) cc_final: 0.7921 (mmt) REVERT: C 424 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.6802 (t-170) REVERT: C 558 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: C 648 ARG cc_start: 0.7207 (mtm180) cc_final: 0.6740 (mmm-85) outliers start: 179 outliers final: 108 residues processed: 725 average time/residue: 1.3120 time to fit residues: 1165.7094 Evaluate side-chains 715 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 577 time to evaluate : 3.855 ------------------------------------------------------------------------------- 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 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 350 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 409 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 825 ILE 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 61 ASP 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 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 569 LYS Chi-restraints excluded: chain B residue 574 GLN Chi-restraints excluded: chain B residue 756 LYS 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 249 GLU 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 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 610 ASP Chi-restraints excluded: chain E residue 794 LYS 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 168 GLU Chi-restraints excluded: chain F residue 192 ILE 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 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 769 GLN 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 350 GLU 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 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 569 LYS Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 618 LEU Chi-restraints excluded: chain G residue 659 THR 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 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 439 GLN Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 648 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 756 LYS Chi-restraints excluded: chain D residue 836 SER 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 277 SER 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 558 GLU 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 762 LEU Chi-restraints excluded: chain C residue 836 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 326 optimal weight: 2.9990 chunk 525 optimal weight: 0.9980 chunk 320 optimal weight: 0.5980 chunk 249 optimal weight: 0.0170 chunk 365 optimal weight: 4.9990 chunk 550 optimal weight: 5.9990 chunk 507 optimal weight: 0.9980 chunk 438 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 338 optimal weight: 5.9990 chunk 269 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 439 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** F 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 880 HIS G 80 GLN ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 253 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN C 769 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 47173 Z= 0.177 Angle : 0.595 11.851 63609 Z= 0.312 Chirality : 0.042 0.186 7056 Planarity : 0.004 0.122 8015 Dihedral : 5.349 40.098 6090 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.62 % Favored : 91.50 % Rotamer: Outliers : 2.81 % Allowed : 18.11 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.12), residues: 5460 helix: 1.77 (0.09), residues: 3206 sheet: -0.75 (0.40), residues: 175 loop : -2.31 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 418 HIS 0.007 0.001 HIS D 424 PHE 0.016 0.001 PHE B 433 TYR 0.026 0.002 TYR C 651 ARG 0.005 0.000 ARG B 268 ********************** 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 734 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 591 time to evaluate : 3.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7079 (tt0) REVERT: A 282 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7165 (pp) REVERT: A 350 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: A 379 MET cc_start: 0.2545 (OUTLIER) cc_final: 0.1868 (ppp) REVERT: A 406 TYR cc_start: 0.6083 (OUTLIER) cc_final: 0.4162 (p90) REVERT: A 424 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.5480 (t70) REVERT: A 533 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.5801 (p90) REVERT: A 822 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8273 (pp) REVERT: A 863 LYS cc_start: 0.7344 (mtmt) cc_final: 0.7099 (mtpt) REVERT: B 276 LEU cc_start: 0.8231 (pp) cc_final: 0.7766 (mt) REVERT: B 379 MET cc_start: 0.3013 (ppp) cc_final: 0.2747 (ppp) REVERT: B 424 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6050 (t70) REVERT: B 574 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: B 688 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6264 (mp0) REVERT: B 888 GLU cc_start: 0.7103 (mp0) cc_final: 0.6595 (pm20) REVERT: E 152 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7829 (Cg_endo) REVERT: E 153 GLU cc_start: 0.7468 (mp0) cc_final: 0.7137 (mp0) REVERT: E 201 ASP cc_start: 0.6940 (m-30) cc_final: 0.6610 (m-30) REVERT: E 276 LEU cc_start: 0.8576 (pp) cc_final: 0.8028 (mp) REVERT: E 282 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7115 (pp) REVERT: E 308 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7220 (pp20) REVERT: E 362 MET cc_start: 0.8883 (tpt) cc_final: 0.8466 (tmm) REVERT: E 379 MET cc_start: 0.2096 (ppp) cc_final: 0.1753 (ppp) REVERT: E 534 MET cc_start: 0.7226 (mmm) cc_final: 0.6978 (tpt) REVERT: E 794 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8104 (tttp) REVERT: E 822 ILE cc_start: 0.8793 (tt) cc_final: 0.8560 (tp) REVERT: E 888 GLU cc_start: 0.7306 (mp0) cc_final: 0.6815 (pm20) REVERT: E 895 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5572 (mp0) REVERT: F 168 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: F 199 ILE cc_start: 0.8380 (mt) cc_final: 0.8090 (mp) REVERT: F 276 LEU cc_start: 0.8519 (pp) cc_final: 0.8015 (mp) REVERT: F 284 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7455 (mmtm) REVERT: F 437 TYR cc_start: 0.8685 (m-80) cc_final: 0.8438 (m-80) REVERT: F 659 THR cc_start: 0.7988 (p) cc_final: 0.7686 (t) REVERT: F 864 LYS cc_start: 0.7977 (tttt) cc_final: 0.7746 (ttmm) REVERT: G 282 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7375 (pp) REVERT: G 409 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6458 (tt) REVERT: G 424 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6789 (t-170) REVERT: G 439 GLN cc_start: 0.7614 (mt0) cc_final: 0.7401 (mt0) REVERT: G 533 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6234 (p90) REVERT: G 557 LYS cc_start: 0.7543 (ttpp) cc_final: 0.7085 (tptp) REVERT: G 648 ARG cc_start: 0.7008 (mtm180) cc_final: 0.6325 (mmm-85) REVERT: G 795 LYS cc_start: 0.7776 (mttp) cc_final: 0.7504 (mmpt) REVERT: G 880 HIS cc_start: 0.6691 (t-90) cc_final: 0.6444 (t-170) REVERT: D 123 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7437 (ttt-90) REVERT: D 201 ASP cc_start: 0.6900 (m-30) cc_final: 0.6619 (m-30) REVERT: D 284 LYS cc_start: 0.7998 (pttt) cc_final: 0.7413 (mmtm) REVERT: D 379 MET cc_start: 0.2034 (OUTLIER) cc_final: 0.1392 (ppp) REVERT: D 557 LYS cc_start: 0.7674 (ttpp) cc_final: 0.7346 (tptp) REVERT: D 648 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6668 (mpp-170) REVERT: D 659 THR cc_start: 0.7852 (p) cc_final: 0.7626 (t) REVERT: D 888 GLU cc_start: 0.7253 (mp0) cc_final: 0.6948 (pp20) REVERT: C 40 LEU cc_start: 0.8564 (mt) cc_final: 0.8170 (tt) REVERT: C 276 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7733 (mp) REVERT: C 325 THR cc_start: 0.7561 (p) cc_final: 0.7278 (m) REVERT: C 350 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6285 (mm-30) REVERT: C 362 MET cc_start: 0.8901 (tpt) cc_final: 0.8635 (mmm) REVERT: C 379 MET cc_start: 0.2456 (ppp) cc_final: 0.2065 (pp-130) REVERT: C 416 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7718 (tm130) REVERT: C 424 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6071 (t-170) REVERT: C 659 THR cc_start: 0.8072 (p) cc_final: 0.7757 (t) REVERT: C 888 GLU cc_start: 0.6972 (mp0) cc_final: 0.6353 (pm20) outliers start: 143 outliers final: 95 residues processed: 689 average time/residue: 1.2145 time to fit residues: 1026.9068 Evaluate side-chains 699 residues out of total 5096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 578 time to evaluate : 3.974 ------------------------------------------------------------------------------- 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 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 350 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 MET 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 439 GLN Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 ASP 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 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 756 LYS 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 249 GLU 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 756 LYS Chi-restraints excluded: chain E residue 794 LYS 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 168 GLU Chi-restraints excluded: chain F residue 192 ILE 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 369 LEU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 406 TYR Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 769 GLN 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 525 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 618 LEU 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 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 525 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 648 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 756 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 424 HIS Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 836 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 348 optimal weight: 0.8980 chunk 467 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 404 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 121 optimal weight: 0.0770 chunk 439 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 451 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 149 GLN B 248 ASN B 439 GLN B 712 ASN E 248 ASN E 439 GLN E 806 HIS ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN F 657 GLN ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN ** G 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 253 ASN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144802 restraints weight = 44303.025| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.48 r_work: 0.3412 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4277 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= 0.170 Angle : 0.587 12.002 63609 Z= 0.306 Chirality : 0.041 0.174 7056 Planarity : 0.004 0.121 8015 Dihedral : 5.236 40.596 6090 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.64 % Favored : 91.52 % Rotamer: Outliers : 2.71 % Allowed : 18.35 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.12), residues: 5460 helix: 1.82 (0.09), residues: 3206 sheet: -0.67 (0.40), residues: 175 loop : -2.32 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 418 HIS 0.006 0.001 HIS F 424 PHE 0.015 0.001 PHE B 433 TYR 0.023 0.001 TYR E 651 ARG 0.004 0.000 ARG E 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18134.55 seconds wall clock time: 318 minutes 42.24 seconds (19122.24 seconds total)