Starting phenix.real_space_refine on Tue Aug 26 09:34:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fp6_50637/08_2025/9fp6_50637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fp6_50637/08_2025/9fp6_50637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fp6_50637/08_2025/9fp6_50637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fp6_50637/08_2025/9fp6_50637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fp6_50637/08_2025/9fp6_50637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fp6_50637/08_2025/9fp6_50637.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.056 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 156 5.16 5 C 22794 2.51 5 N 6126 2.21 5 O 6498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35592 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5901 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 26, 'TRANS': 705} Chain breaks: 13 Chain: "B" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5901 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 26, 'TRANS': 705} Chain breaks: 13 Chain: "C" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5901 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 26, 'TRANS': 705} Chain breaks: 13 Chain: "D" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5901 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 26, 'TRANS': 705} Chain breaks: 13 Chain: "E" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5901 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 26, 'TRANS': 705} Chain breaks: 13 Chain: "F" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5901 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 26, 'TRANS': 705} Chain breaks: 13 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.01, per 1000 atoms: 0.23 Number of scatterers: 35592 At special positions: 0 Unit cell: (194.58, 187.956, 100.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 18 15.00 O 6498 8.00 N 6126 7.00 C 22794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8352 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 30 sheets defined 47.2% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 27 through 49 Processing helix chain 'A' and resid 55 through 85 Processing helix chain 'A' and resid 104 through 124 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.604A pdb=" N ASP A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.678A pdb=" N LYS A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.973A pdb=" N GLN A 236 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 256 removed outlier: 4.051A pdb=" N GLY A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 351 through 365 removed outlier: 4.016A pdb=" N GLY A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 393 through 401 removed outlier: 4.093A pdb=" N SER A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.625A pdb=" N ALA A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS A 414 " --> pdb=" O CYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 446 through 460 Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.522A pdb=" N ALA A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.552A pdb=" N THR A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 675 through 678 Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.552A pdb=" N ARG A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.966A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.559A pdb=" N ALA A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 49 Processing helix chain 'B' and resid 55 through 85 Processing helix chain 'B' and resid 104 through 124 Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 157 through 170 removed outlier: 3.608A pdb=" N ASP B 162 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 218 through 229 removed outlier: 3.689A pdb=" N LYS B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 4.003A pdb=" N GLN B 236 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS B 238 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 256 removed outlier: 4.062A pdb=" N GLY B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 351 through 365 removed outlier: 3.989A pdb=" N GLY B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 Processing helix chain 'B' and resid 393 through 401 removed outlier: 4.137A pdb=" N SER B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 removed outlier: 3.614A pdb=" N ALA B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS B 414 " --> pdb=" O CYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 446 through 460 Processing helix chain 'B' and resid 480 through 494 Processing helix chain 'B' and resid 511 through 516 removed outlier: 3.508A pdb=" N ALA B 516 " --> pdb=" O LYS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 533 removed outlier: 3.542A pdb=" N THR B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 605 through 611 Processing helix chain 'B' and resid 675 through 678 Processing helix chain 'B' and resid 679 through 685 removed outlier: 3.560A pdb=" N ARG B 685 " --> pdb=" O GLU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 701 Processing helix chain 'B' and resid 760 through 766 removed outlier: 4.032A pdb=" N LEU B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 766 " --> pdb=" O SER B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 863 removed outlier: 3.568A pdb=" N ALA B 854 " --> pdb=" O THR B 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 49 Processing helix chain 'C' and resid 55 through 85 Processing helix chain 'C' and resid 104 through 124 Processing helix chain 'C' and resid 124 through 131 Processing helix chain 'C' and resid 157 through 170 removed outlier: 3.698A pdb=" N ASP C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 218 through 229 removed outlier: 3.685A pdb=" N LYS C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 4.024A pdb=" N GLN C 236 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 256 removed outlier: 4.044A pdb=" N GLY C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 276 Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 351 through 365 removed outlier: 4.000A pdb=" N GLY C 364 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 374 Processing helix chain 'C' and resid 393 through 401 removed outlier: 4.099A pdb=" N SER C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 414 removed outlier: 3.634A pdb=" N ALA C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS C 414 " --> pdb=" O CYS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 446 through 460 Processing helix chain 'C' and resid 480 through 494 Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.512A pdb=" N ALA C 516 " --> pdb=" O LYS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 533 removed outlier: 3.507A pdb=" N THR C 533 " --> pdb=" O GLU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 558 Processing helix chain 'C' and resid 559 through 565 Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 605 through 611 Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'C' and resid 675 through 678 Processing helix chain 'C' and resid 679 through 685 removed outlier: 3.561A pdb=" N ARG C 685 " --> pdb=" O GLU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 701 Processing helix chain 'C' and resid 760 through 766 removed outlier: 4.060A pdb=" N LEU C 764 " --> pdb=" O ASP C 760 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 766 " --> pdb=" O SER C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 863 removed outlier: 3.562A pdb=" N ALA C 854 " --> pdb=" O THR C 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 49 Processing helix chain 'D' and resid 55 through 85 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.626A pdb=" N ASP D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 229 removed outlier: 3.685A pdb=" N LYS D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.942A pdb=" N GLN D 236 " --> pdb=" O ASN D 233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 237 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS D 238 " --> pdb=" O LYS D 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 238' Processing helix chain 'D' and resid 241 through 256 removed outlier: 4.201A pdb=" N GLY D 256 " --> pdb=" O PHE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 276 Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 315 through 328 Processing helix chain 'D' and resid 339 through 347 Processing helix chain 'D' and resid 351 through 365 removed outlier: 3.996A pdb=" N GLY D 364 " --> pdb=" O GLY D 360 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.507A pdb=" N GLN D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 401 removed outlier: 4.126A pdb=" N SER D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 414 removed outlier: 3.626A pdb=" N ALA D 409 " --> pdb=" O TYR D 405 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS D 414 " --> pdb=" O CYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 435 Processing helix chain 'D' and resid 446 through 460 Processing helix chain 'D' and resid 480 through 494 Processing helix chain 'D' and resid 511 through 516 removed outlier: 3.526A pdb=" N ALA D 516 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 533 removed outlier: 3.533A pdb=" N THR D 533 " --> pdb=" O GLU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 558 Processing helix chain 'D' and resid 559 through 565 Processing helix chain 'D' and resid 584 through 588 Processing helix chain 'D' and resid 605 through 611 Processing helix chain 'D' and resid 631 through 635 Processing helix chain 'D' and resid 675 through 678 Processing helix chain 'D' and resid 679 through 685 removed outlier: 3.525A pdb=" N ARG D 685 " --> pdb=" O GLU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 701 Processing helix chain 'D' and resid 760 through 766 removed outlier: 3.990A pdb=" N LEU D 764 " --> pdb=" O ASP D 760 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D 766 " --> pdb=" O SER D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 863 removed outlier: 3.557A pdb=" N ALA D 854 " --> pdb=" O THR D 850 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 49 Processing helix chain 'E' and resid 55 through 85 Processing helix chain 'E' and resid 104 through 124 Processing helix chain 'E' and resid 124 through 131 Processing helix chain 'E' and resid 157 through 170 removed outlier: 3.550A pdb=" N ASP E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 197 Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 218 through 229 removed outlier: 3.692A pdb=" N LYS E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 removed outlier: 3.977A pdb=" N GLN E 236 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS E 238 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 256 removed outlier: 4.073A pdb=" N GLY E 256 " --> pdb=" O PHE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 276 Processing helix chain 'E' and resid 277 through 279 No H-bonds generated for 'chain 'E' and resid 277 through 279' Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 339 through 347 Processing helix chain 'E' and resid 351 through 365 removed outlier: 4.011A pdb=" N GLY E 364 " --> pdb=" O GLY E 360 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS E 365 " --> pdb=" O ALA E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 374 Processing helix chain 'E' and resid 393 through 401 removed outlier: 4.144A pdb=" N SER E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 414 removed outlier: 3.613A pdb=" N ALA E 409 " --> pdb=" O TYR E 405 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS E 414 " --> pdb=" O CYS E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 435 Processing helix chain 'E' and resid 446 through 460 Processing helix chain 'E' and resid 480 through 494 Processing helix chain 'E' and resid 511 through 516 removed outlier: 3.508A pdb=" N ALA E 516 " --> pdb=" O LYS E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 533 removed outlier: 3.503A pdb=" N THR E 533 " --> pdb=" O GLU E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 558 Processing helix chain 'E' and resid 559 through 565 Processing helix chain 'E' and resid 584 through 588 Processing helix chain 'E' and resid 605 through 611 Processing helix chain 'E' and resid 675 through 678 Processing helix chain 'E' and resid 679 through 685 removed outlier: 3.519A pdb=" N ARG E 685 " --> pdb=" O GLU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 701 Processing helix chain 'E' and resid 760 through 766 removed outlier: 4.050A pdb=" N LEU E 764 " --> pdb=" O ASP E 760 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN E 766 " --> pdb=" O SER E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 863 removed outlier: 3.565A pdb=" N ALA E 854 " --> pdb=" O THR E 850 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 49 Processing helix chain 'F' and resid 55 through 85 Processing helix chain 'F' and resid 104 through 124 Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 157 through 170 removed outlier: 3.610A pdb=" N ASP F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.683A pdb=" N LYS F 229 " --> pdb=" O ASN F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 removed outlier: 4.043A pdb=" N GLN F 236 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR F 237 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS F 238 " --> pdb=" O LYS F 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 233 through 238' Processing helix chain 'F' and resid 241 through 256 removed outlier: 4.172A pdb=" N GLY F 256 " --> pdb=" O PHE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 276 Processing helix chain 'F' and resid 277 through 279 No H-bonds generated for 'chain 'F' and resid 277 through 279' Processing helix chain 'F' and resid 315 through 328 Processing helix chain 'F' and resid 339 through 347 Processing helix chain 'F' and resid 351 through 365 removed outlier: 3.999A pdb=" N GLY F 364 " --> pdb=" O GLY F 360 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS F 365 " --> pdb=" O ALA F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 374 Processing helix chain 'F' and resid 393 through 401 removed outlier: 4.139A pdb=" N SER F 399 " --> pdb=" O LEU F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 414 removed outlier: 3.636A pdb=" N ALA F 409 " --> pdb=" O TYR F 405 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS F 414 " --> pdb=" O CYS F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 435 Processing helix chain 'F' and resid 446 through 460 Processing helix chain 'F' and resid 480 through 494 Processing helix chain 'F' and resid 511 through 516 Processing helix chain 'F' and resid 526 through 533 removed outlier: 3.557A pdb=" N THR F 533 " --> pdb=" O GLU F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 558 Processing helix chain 'F' and resid 559 through 565 Processing helix chain 'F' and resid 584 through 588 Processing helix chain 'F' and resid 605 through 611 Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 675 through 678 Processing helix chain 'F' and resid 679 through 685 removed outlier: 3.539A pdb=" N ARG F 685 " --> pdb=" O GLU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 701 Processing helix chain 'F' and resid 760 through 766 removed outlier: 4.027A pdb=" N LEU F 764 " --> pdb=" O ASP F 760 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN F 766 " --> pdb=" O SER F 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 863 removed outlier: 3.576A pdb=" N ALA F 854 " --> pdb=" O THR F 850 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 212 removed outlier: 6.398A pdb=" N THR A 207 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL A 262 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 209 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP A 264 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A 211 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR A 259 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU A 289 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 261 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR A 291 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 263 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS A 309 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 423 through 424 removed outlier: 6.708A pdb=" N GLN A 467 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYS A 477 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 465 " --> pdb=" O CYS A 477 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 500 removed outlier: 6.249A pdb=" N LEU A 521 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 597 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER A 575 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 644 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR A 621 " --> pdb=" O ASN A 644 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER A 646 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 551 through 552 removed outlier: 6.925A pdb=" N ILE A 551 " --> pdb=" O ASN A 577 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 597 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER A 575 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 644 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR A 621 " --> pdb=" O ASN A 644 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER A 646 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 641 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE A 673 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N THR A 643 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS A 691 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER A 671 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLY A 693 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU A 692 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE A 724 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 694 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 721 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL A 752 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 723 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU A 820 " --> pdb=" O GLU A 845 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 784 through 786 Processing sheet with id=AA6, first strand: chain 'B' and resid 207 through 212 removed outlier: 6.402A pdb=" N THR B 207 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL B 262 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 209 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP B 264 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL B 211 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 259 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 289 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 261 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR B 291 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 263 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS B 309 " --> pdb=" O VAL B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 423 through 424 removed outlier: 6.725A pdb=" N GLN B 467 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS B 477 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 465 " --> pdb=" O CYS B 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 499 through 500 removed outlier: 6.246A pdb=" N LEU B 521 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 597 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER B 575 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 594 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASN B 620 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 596 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 644 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 621 " --> pdb=" O ASN B 644 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N SER B 646 " --> pdb=" O THR B 621 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 551 through 552 removed outlier: 6.926A pdb=" N ILE B 551 " --> pdb=" O ASN B 577 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 597 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER B 575 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 594 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASN B 620 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 596 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 644 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 621 " --> pdb=" O ASN B 644 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N SER B 646 " --> pdb=" O THR B 621 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU B 641 " --> pdb=" O SER B 671 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE B 673 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N THR B 643 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS B 691 " --> pdb=" O THR B 669 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N SER B 671 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLY B 693 " --> pdb=" O SER B 671 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU B 692 " --> pdb=" O LYS B 722 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE B 724 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 694 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 721 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL B 752 " --> pdb=" O LEU B 721 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 723 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 797 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE B 823 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 799 " --> pdb=" O ILE B 823 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 820 " --> pdb=" O GLU B 845 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 784 through 786 Processing sheet with id=AB2, first strand: chain 'C' and resid 207 through 212 removed outlier: 6.408A pdb=" N THR C 207 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL C 262 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 209 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASP C 264 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 211 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR C 259 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 289 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE C 261 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR C 291 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU C 263 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N HIS C 309 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 423 through 424 removed outlier: 6.692A pdb=" N GLN C 467 " --> pdb=" O LYS C 475 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS C 477 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 465 " --> pdb=" O CYS C 477 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 499 through 500 removed outlier: 6.248A pdb=" N LEU C 521 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER C 597 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER C 575 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 644 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR C 621 " --> pdb=" O ASN C 644 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER C 646 " --> pdb=" O THR C 621 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 551 through 552 removed outlier: 6.961A pdb=" N ILE C 551 " --> pdb=" O ASN C 577 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER C 597 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER C 575 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 644 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR C 621 " --> pdb=" O ASN C 644 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER C 646 " --> pdb=" O THR C 621 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 641 " --> pdb=" O SER C 671 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 673 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N THR C 643 " --> pdb=" O ILE C 673 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS C 691 " --> pdb=" O THR C 669 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER C 671 " --> pdb=" O LYS C 691 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY C 693 " --> pdb=" O SER C 671 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU C 692 " --> pdb=" O LYS C 722 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE C 724 " --> pdb=" O LEU C 692 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE C 694 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 721 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL C 752 " --> pdb=" O LEU C 721 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU C 723 " --> pdb=" O VAL C 752 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 797 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE C 823 " --> pdb=" O LEU C 797 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C 799 " --> pdb=" O ILE C 823 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 820 " --> pdb=" O GLU C 845 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 784 through 786 Processing sheet with id=AB7, first strand: chain 'D' and resid 207 through 212 removed outlier: 6.400A pdb=" N THR D 207 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL D 262 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 209 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP D 264 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL D 211 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR D 259 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU D 289 " --> pdb=" O TYR D 259 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE D 261 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR D 291 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU D 263 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N HIS D 309 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 423 through 424 removed outlier: 6.700A pdb=" N GLN D 467 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N CYS D 477 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL D 465 " --> pdb=" O CYS D 477 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 499 through 500 removed outlier: 6.259A pdb=" N LEU D 521 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER D 597 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER D 575 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN D 644 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR D 621 " --> pdb=" O ASN D 644 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER D 646 " --> pdb=" O THR D 621 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 551 through 552 removed outlier: 6.968A pdb=" N ILE D 551 " --> pdb=" O ASN D 577 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER D 597 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER D 575 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN D 644 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR D 621 " --> pdb=" O ASN D 644 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER D 646 " --> pdb=" O THR D 621 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU D 641 " --> pdb=" O SER D 671 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE D 673 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N THR D 643 " --> pdb=" O ILE D 673 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS D 691 " --> pdb=" O THR D 669 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER D 671 " --> pdb=" O LYS D 691 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY D 693 " --> pdb=" O SER D 671 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU D 692 " --> pdb=" O LYS D 722 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE D 724 " --> pdb=" O LEU D 692 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE D 694 " --> pdb=" O ILE D 724 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU D 721 " --> pdb=" O SER D 750 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL D 752 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU D 723 " --> pdb=" O VAL D 752 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU D 797 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE D 823 " --> pdb=" O LEU D 797 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE D 799 " --> pdb=" O ILE D 823 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU D 820 " --> pdb=" O GLU D 845 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 784 through 786 Processing sheet with id=AC3, first strand: chain 'E' and resid 207 through 212 removed outlier: 6.396A pdb=" N THR E 207 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL E 262 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE E 209 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP E 264 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL E 211 " --> pdb=" O ASP E 264 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR E 259 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU E 289 " --> pdb=" O TYR E 259 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE E 261 " --> pdb=" O LEU E 289 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR E 291 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU E 263 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N HIS E 309 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 423 through 424 removed outlier: 6.722A pdb=" N GLN E 467 " --> pdb=" O LYS E 475 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N CYS E 477 " --> pdb=" O VAL E 465 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL E 465 " --> pdb=" O CYS E 477 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 499 through 500 removed outlier: 6.250A pdb=" N LEU E 521 " --> pdb=" O LEU E 544 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER E 597 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER E 575 " --> pdb=" O SER E 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE E 594 " --> pdb=" O ILE E 618 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASN E 620 " --> pdb=" O ILE E 594 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE E 596 " --> pdb=" O ASN E 620 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN E 644 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR E 621 " --> pdb=" O ASN E 644 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER E 646 " --> pdb=" O THR E 621 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 551 through 552 removed outlier: 6.957A pdb=" N ILE E 551 " --> pdb=" O ASN E 577 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER E 597 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER E 575 " --> pdb=" O SER E 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE E 594 " --> pdb=" O ILE E 618 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASN E 620 " --> pdb=" O ILE E 594 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE E 596 " --> pdb=" O ASN E 620 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN E 644 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR E 621 " --> pdb=" O ASN E 644 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER E 646 " --> pdb=" O THR E 621 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU E 641 " --> pdb=" O SER E 671 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE E 673 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N THR E 643 " --> pdb=" O ILE E 673 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS E 691 " --> pdb=" O THR E 669 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER E 671 " --> pdb=" O LYS E 691 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY E 693 " --> pdb=" O SER E 671 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU E 692 " --> pdb=" O LYS E 722 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE E 724 " --> pdb=" O LEU E 692 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE E 694 " --> pdb=" O ILE E 724 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU E 721 " --> pdb=" O SER E 750 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL E 752 " --> pdb=" O LEU E 721 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU E 723 " --> pdb=" O VAL E 752 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU E 797 " --> pdb=" O VAL E 821 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE E 823 " --> pdb=" O LEU E 797 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE E 799 " --> pdb=" O ILE E 823 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU E 820 " --> pdb=" O GLU E 845 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 784 through 786 Processing sheet with id=AC8, first strand: chain 'F' and resid 207 through 212 removed outlier: 6.091A pdb=" N TYR F 259 " --> pdb=" O ARG F 287 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU F 289 " --> pdb=" O TYR F 259 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE F 261 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR F 291 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU F 263 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N HIS F 309 " --> pdb=" O VAL F 177 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 423 through 424 removed outlier: 6.741A pdb=" N GLN F 467 " --> pdb=" O LYS F 475 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS F 477 " --> pdb=" O VAL F 465 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL F 465 " --> pdb=" O CYS F 477 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 499 through 500 removed outlier: 6.240A pdb=" N LEU F 521 " --> pdb=" O LEU F 544 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER F 597 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER F 575 " --> pdb=" O SER F 597 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE F 594 " --> pdb=" O ILE F 618 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASN F 620 " --> pdb=" O ILE F 594 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE F 596 " --> pdb=" O ASN F 620 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN F 644 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR F 621 " --> pdb=" O ASN F 644 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER F 646 " --> pdb=" O THR F 621 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 551 through 552 removed outlier: 6.922A pdb=" N ILE F 551 " --> pdb=" O ASN F 577 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER F 597 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER F 575 " --> pdb=" O SER F 597 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE F 594 " --> pdb=" O ILE F 618 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASN F 620 " --> pdb=" O ILE F 594 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE F 596 " --> pdb=" O ASN F 620 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN F 644 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR F 621 " --> pdb=" O ASN F 644 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER F 646 " --> pdb=" O THR F 621 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU F 641 " --> pdb=" O SER F 671 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE F 673 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N THR F 643 " --> pdb=" O ILE F 673 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS F 691 " --> pdb=" O THR F 669 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER F 671 " --> pdb=" O LYS F 691 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY F 693 " --> pdb=" O SER F 671 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU F 692 " --> pdb=" O LYS F 722 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE F 724 " --> pdb=" O LEU F 692 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE F 694 " --> pdb=" O ILE F 724 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU F 721 " --> pdb=" O SER F 750 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL F 752 " --> pdb=" O LEU F 721 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU F 723 " --> pdb=" O VAL F 752 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU F 797 " --> pdb=" O VAL F 821 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE F 823 " --> pdb=" O LEU F 797 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE F 799 " --> pdb=" O ILE F 823 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU F 820 " --> pdb=" O GLU F 845 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 784 through 786 1529 hydrogen bonds defined for protein. 4317 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: 10.03 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11423 1.34 - 1.46: 7135 1.46 - 1.58: 17418 1.58 - 1.69: 30 1.69 - 1.81: 228 Bond restraints: 36234 Sorted by residual: bond pdb=" C ILE C 558 " pdb=" N PRO C 559 " ideal model delta sigma weight residual 1.331 1.353 -0.021 7.90e-03 1.60e+04 7.32e+00 bond pdb=" C ILE E 558 " pdb=" N PRO E 559 " ideal model delta sigma weight residual 1.331 1.352 -0.021 7.90e-03 1.60e+04 7.01e+00 bond pdb=" C ILE D 558 " pdb=" N PRO D 559 " ideal model delta sigma weight residual 1.331 1.352 -0.021 7.90e-03 1.60e+04 6.78e+00 bond pdb=" C ILE B 558 " pdb=" N PRO B 559 " ideal model delta sigma weight residual 1.331 1.352 -0.020 7.90e-03 1.60e+04 6.43e+00 bond pdb=" C ILE F 558 " pdb=" N PRO F 559 " ideal model delta sigma weight residual 1.331 1.350 -0.018 7.90e-03 1.60e+04 5.30e+00 ... (remaining 36229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 48366 1.79 - 3.58: 347 3.58 - 5.36: 82 5.36 - 7.15: 4 7.15 - 8.94: 5 Bond angle restraints: 48804 Sorted by residual: angle pdb=" CB LYS F 235 " pdb=" CG LYS F 235 " pdb=" CD LYS F 235 " ideal model delta sigma weight residual 111.30 120.24 -8.94 2.30e+00 1.89e-01 1.51e+01 angle pdb=" CB LYS A 235 " pdb=" CG LYS A 235 " pdb=" CD LYS A 235 " ideal model delta sigma weight residual 111.30 120.15 -8.85 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CB LYS E 235 " pdb=" CG LYS E 235 " pdb=" CD LYS E 235 " ideal model delta sigma weight residual 111.30 118.60 -7.30 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CB LYS B 235 " pdb=" CG LYS B 235 " pdb=" CD LYS B 235 " ideal model delta sigma weight residual 111.30 118.50 -7.20 2.30e+00 1.89e-01 9.80e+00 angle pdb=" CB LYS D 235 " pdb=" CG LYS D 235 " pdb=" CD LYS D 235 " ideal model delta sigma weight residual 111.30 118.18 -6.88 2.30e+00 1.89e-01 8.96e+00 ... (remaining 48799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 18692 17.97 - 35.95: 2424 35.95 - 53.92: 780 53.92 - 71.90: 201 71.90 - 89.87: 55 Dihedral angle restraints: 22152 sinusoidal: 9408 harmonic: 12744 Sorted by residual: dihedral pdb=" CA ASP E 471 " pdb=" CB ASP E 471 " pdb=" CG ASP E 471 " pdb=" OD1 ASP E 471 " ideal model delta sinusoidal sigma weight residual -30.00 -87.27 57.27 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP F 471 " pdb=" CB ASP F 471 " pdb=" CG ASP F 471 " pdb=" OD1 ASP F 471 " ideal model delta sinusoidal sigma weight residual -30.00 -87.21 57.21 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP B 471 " pdb=" CB ASP B 471 " pdb=" CG ASP B 471 " pdb=" OD1 ASP B 471 " ideal model delta sinusoidal sigma weight residual -30.00 -87.09 57.09 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 22149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4146 0.042 - 0.083: 1072 0.083 - 0.125: 311 0.125 - 0.167: 7 0.167 - 0.208: 2 Chirality restraints: 5538 Sorted by residual: chirality pdb=" CB ILE D 594 " pdb=" CA ILE D 594 " pdb=" CG1 ILE D 594 " pdb=" CG2 ILE D 594 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE A 594 " pdb=" CA ILE A 594 " pdb=" CG1 ILE A 594 " pdb=" CG2 ILE A 594 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL F 181 " pdb=" N VAL F 181 " pdb=" C VAL F 181 " pdb=" CB VAL F 181 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 5535 not shown) Planarity restraints: 6078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET F 553 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO F 554 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO F 554 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 554 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 737 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO B 738 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 738 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 738 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 553 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO E 554 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 554 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 554 " 0.029 5.00e-02 4.00e+02 ... (remaining 6075 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5994 2.77 - 3.30: 32469 3.30 - 3.83: 58309 3.83 - 4.37: 72035 4.37 - 4.90: 124055 Nonbonded interactions: 292862 Sorted by model distance: nonbonded pdb=" OG SER F 30 " pdb=" NZ LYS F 111 " model vdw 2.236 3.120 nonbonded pdb=" O THR E 643 " pdb=" OG1 THR E 672 " model vdw 2.238 3.040 nonbonded pdb=" O THR D 643 " pdb=" OG1 THR D 672 " model vdw 2.248 3.040 nonbonded pdb=" O THR B 643 " pdb=" OG1 THR B 672 " model vdw 2.250 3.040 nonbonded pdb=" O THR C 643 " pdb=" OG1 THR C 672 " model vdw 2.257 3.040 ... (remaining 292857 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 9.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 32.320 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.002 0.039 36234 Z= 0.104 Angle : 0.452 8.940 48804 Z= 0.240 Chirality : 0.039 0.208 5538 Planarity : 0.004 0.062 6078 Dihedral : 18.367 89.874 13800 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.39 % Allowed : 27.20 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.14), residues: 4224 helix: 1.31 (0.13), residues: 1830 sheet: 0.06 (0.23), residues: 738 loop : 0.47 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 121 TYR 0.008 0.001 TYR C 196 PHE 0.008 0.001 PHE F 486 TRP 0.010 0.001 TRP B 633 HIS 0.004 0.001 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00221 (36234) covalent geometry : angle 0.45206 (48804) hydrogen bonds : bond 0.14717 ( 1478) hydrogen bonds : angle 5.72499 ( 4317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 475 time to evaluate : 1.531 Fit side-chains REVERT: A 111 LYS cc_start: 0.8010 (mppt) cc_final: 0.6887 (ttpp) REVERT: A 251 ASP cc_start: 0.7900 (m-30) cc_final: 0.7561 (m-30) REVERT: A 492 MET cc_start: 0.8927 (mtp) cc_final: 0.8565 (mtt) REVERT: A 587 GLN cc_start: 0.7585 (mt0) cc_final: 0.7380 (mt0) REVERT: A 745 LYS cc_start: 0.7725 (mttt) cc_final: 0.7339 (tptp) REVERT: B 41 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: B 77 ASP cc_start: 0.7656 (m-30) cc_final: 0.7435 (m-30) REVERT: B 109 GLU cc_start: 0.7749 (tt0) cc_final: 0.7107 (tt0) REVERT: B 116 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7418 (tppt) REVERT: B 150 GLU cc_start: 0.8276 (tp30) cc_final: 0.8027 (tp30) REVERT: B 492 MET cc_start: 0.8855 (mtp) cc_final: 0.8545 (mtm) REVERT: B 745 LYS cc_start: 0.7920 (tptp) cc_final: 0.7463 (tptp) REVERT: B 845 GLU cc_start: 0.7625 (tt0) cc_final: 0.7086 (mt-10) REVERT: C 36 GLN cc_start: 0.6906 (mm-40) cc_final: 0.6211 (mm-40) REVERT: C 77 ASP cc_start: 0.7746 (m-30) cc_final: 0.7442 (m-30) REVERT: C 111 LYS cc_start: 0.7853 (mppt) cc_final: 0.6944 (ttpp) REVERT: C 118 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7497 (mttp) REVERT: C 488 ARG cc_start: 0.8025 (ttp80) cc_final: 0.6727 (ttm170) REVERT: C 492 MET cc_start: 0.8888 (mtp) cc_final: 0.8661 (mtm) REVERT: D 111 LYS cc_start: 0.7893 (mppt) cc_final: 0.6794 (ttpp) REVERT: D 116 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7282 (tttt) REVERT: D 121 ARG cc_start: 0.7851 (mmt90) cc_final: 0.7477 (mmt90) REVERT: D 492 MET cc_start: 0.8881 (mtp) cc_final: 0.8597 (mtt) REVERT: D 745 LYS cc_start: 0.7587 (mttt) cc_final: 0.7321 (tptp) REVERT: D 818 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8131 (mtpm) REVERT: E 111 LYS cc_start: 0.7966 (mppt) cc_final: 0.6874 (ttpp) REVERT: E 121 ARG cc_start: 0.7925 (mmt90) cc_final: 0.7552 (mmt90) REVERT: E 492 MET cc_start: 0.8882 (mtp) cc_final: 0.8581 (mtm) REVERT: E 745 LYS cc_start: 0.7722 (mttt) cc_final: 0.7465 (tptp) REVERT: E 844 MET cc_start: 0.8466 (ttt) cc_final: 0.8147 (ttt) REVERT: F 77 ASP cc_start: 0.7637 (m-30) cc_final: 0.7265 (m-30) REVERT: F 492 MET cc_start: 0.8892 (mtp) cc_final: 0.8636 (mtm) REVERT: F 685 ARG cc_start: 0.6525 (mtt180) cc_final: 0.6045 (mtt180) REVERT: F 745 LYS cc_start: 0.7615 (mttt) cc_final: 0.7195 (tptp) outliers start: 55 outliers final: 18 residues processed: 521 average time/residue: 0.7117 time to fit residues: 436.8221 Evaluate side-chains 471 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 452 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 343 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 343 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 401 optimal weight: 0.6980 chunk 424 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN A 848 ASN B 720 ASN B 848 ASN C 720 ASN C 848 ASN D 720 ASN E 720 ASN E 848 ASN F 720 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.165044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125206 restraints weight = 37092.556| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.76 r_work: 0.3249 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36234 Z= 0.173 Angle : 0.503 6.174 48804 Z= 0.260 Chirality : 0.042 0.169 5538 Planarity : 0.004 0.053 6078 Dihedral : 8.875 79.198 4861 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.65 % Allowed : 24.06 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.14), residues: 4224 helix: 1.39 (0.12), residues: 1854 sheet: 0.01 (0.23), residues: 726 loop : 0.36 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 639 TYR 0.014 0.001 TYR C 196 PHE 0.009 0.001 PHE A 586 TRP 0.008 0.001 TRP E 633 HIS 0.003 0.001 HIS E 642 Details of bonding type rmsd covalent geometry : bond 0.00425 (36234) covalent geometry : angle 0.50314 (48804) hydrogen bonds : bond 0.03908 ( 1478) hydrogen bonds : angle 4.26043 ( 4317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 476 time to evaluate : 1.526 Fit side-chains REVERT: A 32 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 251 ASP cc_start: 0.7997 (m-30) cc_final: 0.7642 (m-30) REVERT: A 276 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8615 (ttm170) REVERT: A 492 MET cc_start: 0.8952 (mtp) cc_final: 0.8657 (mtm) REVERT: A 602 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7935 (mtpt) REVERT: A 680 GLU cc_start: 0.7292 (tt0) cc_final: 0.7042 (mp0) REVERT: A 745 LYS cc_start: 0.7762 (mttt) cc_final: 0.7217 (tptp) REVERT: B 35 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8077 (tt) REVERT: B 36 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6343 (mm-40) REVERT: B 77 ASP cc_start: 0.7664 (m-30) cc_final: 0.7377 (m-30) REVERT: B 109 GLU cc_start: 0.7963 (tt0) cc_final: 0.7355 (tt0) REVERT: B 118 LYS cc_start: 0.8116 (mppt) cc_final: 0.7765 (mmtm) REVERT: B 467 GLN cc_start: 0.8678 (mt0) cc_final: 0.8403 (mt0) REVERT: B 475 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8943 (ttmm) REVERT: B 492 MET cc_start: 0.8883 (mtp) cc_final: 0.8598 (mtm) REVERT: B 603 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8161 (mt) REVERT: B 680 GLU cc_start: 0.7128 (tt0) cc_final: 0.6824 (mp0) REVERT: B 745 LYS cc_start: 0.7923 (tptp) cc_final: 0.7542 (tmtt) REVERT: B 808 LYS cc_start: 0.7736 (mttt) cc_final: 0.7160 (mttt) REVERT: B 845 GLU cc_start: 0.7800 (tt0) cc_final: 0.7321 (mt-10) REVERT: C 36 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6234 (mm-40) REVERT: C 41 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8751 (m-10) REVERT: C 77 ASP cc_start: 0.7828 (m-30) cc_final: 0.7288 (m-30) REVERT: C 118 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7561 (mttp) REVERT: C 488 ARG cc_start: 0.8236 (ttp80) cc_final: 0.6863 (ttm170) REVERT: C 492 MET cc_start: 0.8927 (mtp) cc_final: 0.8668 (mtm) REVERT: C 635 MET cc_start: 0.8156 (mtt) cc_final: 0.7935 (mtt) REVERT: C 680 GLU cc_start: 0.7288 (tt0) cc_final: 0.6931 (mp0) REVERT: C 808 LYS cc_start: 0.7837 (mttt) cc_final: 0.7237 (mttt) REVERT: C 844 MET cc_start: 0.8295 (ttt) cc_final: 0.7977 (ttt) REVERT: C 845 GLU cc_start: 0.7744 (tt0) cc_final: 0.7189 (mt-10) REVERT: D 32 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7720 (mm-30) REVERT: D 35 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8223 (tt) REVERT: D 121 ARG cc_start: 0.7933 (mmt90) cc_final: 0.7569 (mmt90) REVERT: D 251 ASP cc_start: 0.7950 (m-30) cc_final: 0.7713 (m-30) REVERT: D 492 MET cc_start: 0.8933 (mtp) cc_final: 0.8597 (mtt) REVERT: D 680 GLU cc_start: 0.7307 (tt0) cc_final: 0.6970 (mp0) REVERT: D 745 LYS cc_start: 0.7703 (mttt) cc_final: 0.7230 (tptp) REVERT: E 35 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8072 (tt) REVERT: E 36 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6286 (mm-40) REVERT: E 68 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8506 (t) REVERT: E 77 ASP cc_start: 0.7733 (m-30) cc_final: 0.7505 (m-30) REVERT: E 467 GLN cc_start: 0.8689 (mt0) cc_final: 0.8411 (mt0) REVERT: E 475 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8945 (ttmm) REVERT: E 492 MET cc_start: 0.8909 (mtp) cc_final: 0.8615 (mtm) REVERT: E 680 GLU cc_start: 0.7076 (tt0) cc_final: 0.6733 (mp0) REVERT: E 745 LYS cc_start: 0.7679 (mttt) cc_final: 0.7300 (tptp) REVERT: E 845 GLU cc_start: 0.7847 (tt0) cc_final: 0.7351 (mt-10) REVERT: F 36 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6107 (mm-40) REVERT: F 41 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8684 (m-10) REVERT: F 77 ASP cc_start: 0.7805 (m-30) cc_final: 0.7358 (m-30) REVERT: F 81 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8309 (mm) REVERT: F 251 ASP cc_start: 0.7913 (m-30) cc_final: 0.7505 (m-30) REVERT: F 492 MET cc_start: 0.8943 (mtp) cc_final: 0.8691 (mtm) REVERT: F 624 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7769 (tpt-90) REVERT: F 680 GLU cc_start: 0.7274 (tt0) cc_final: 0.6899 (mp0) REVERT: F 745 LYS cc_start: 0.7717 (mttt) cc_final: 0.7079 (tptp) REVERT: F 845 GLU cc_start: 0.7646 (tt0) cc_final: 0.7094 (mt-10) outliers start: 144 outliers final: 50 residues processed: 563 average time/residue: 0.6824 time to fit residues: 454.9164 Evaluate side-chains 523 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 457 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 606 LYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain C residue 41 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 606 LYS Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 677 SER Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 406 ASP Chi-restraints excluded: chain F residue 466 MET Chi-restraints excluded: chain F residue 624 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 177 optimal weight: 0.8980 chunk 414 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 389 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 315 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN B 123 ASN B 720 ASN C 539 HIS C 720 ASN D 720 ASN E 720 ASN F 720 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.166518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126812 restraints weight = 36922.861| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.77 r_work: 0.3269 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36234 Z= 0.114 Angle : 0.447 6.399 48804 Z= 0.233 Chirality : 0.040 0.142 5538 Planarity : 0.004 0.053 6078 Dihedral : 8.451 77.781 4843 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.27 % Allowed : 24.04 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.14), residues: 4224 helix: 1.59 (0.12), residues: 1854 sheet: -0.23 (0.22), residues: 738 loop : 0.40 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 121 TYR 0.011 0.001 TYR A 196 PHE 0.005 0.001 PHE C 79 TRP 0.008 0.001 TRP B 633 HIS 0.003 0.001 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00275 (36234) covalent geometry : angle 0.44745 (48804) hydrogen bonds : bond 0.03270 ( 1478) hydrogen bonds : angle 3.91513 ( 4317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 478 time to evaluate : 1.170 Fit side-chains REVERT: A 118 LYS cc_start: 0.8267 (mppt) cc_final: 0.7883 (mmtm) REVERT: A 251 ASP cc_start: 0.7982 (m-30) cc_final: 0.7618 (m-30) REVERT: A 467 GLN cc_start: 0.8628 (mt0) cc_final: 0.8406 (mt0) REVERT: A 492 MET cc_start: 0.8930 (mtp) cc_final: 0.8617 (mtm) REVERT: A 602 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7890 (mtpt) REVERT: A 637 ARG cc_start: 0.8050 (mtp-110) cc_final: 0.7825 (mtp-110) REVERT: A 680 GLU cc_start: 0.7282 (tt0) cc_final: 0.7029 (mp0) REVERT: A 745 LYS cc_start: 0.7746 (mttt) cc_final: 0.7181 (tptp) REVERT: B 35 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8083 (tt) REVERT: B 41 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8245 (m-10) REVERT: B 77 ASP cc_start: 0.7724 (m-30) cc_final: 0.7390 (m-30) REVERT: B 81 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8254 (mp) REVERT: B 109 GLU cc_start: 0.7964 (tt0) cc_final: 0.7303 (tt0) REVERT: B 118 LYS cc_start: 0.8160 (mppt) cc_final: 0.7734 (mmtm) REVERT: B 123 ASN cc_start: 0.7629 (t0) cc_final: 0.7218 (m110) REVERT: B 492 MET cc_start: 0.8853 (mtp) cc_final: 0.8564 (mtm) REVERT: B 680 GLU cc_start: 0.7129 (tt0) cc_final: 0.6824 (mp0) REVERT: B 808 LYS cc_start: 0.7792 (mttt) cc_final: 0.7203 (mttt) REVERT: B 845 GLU cc_start: 0.7682 (tt0) cc_final: 0.7243 (mt-10) REVERT: C 36 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6192 (mm-40) REVERT: C 41 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8746 (m-10) REVERT: C 77 ASP cc_start: 0.7779 (m-30) cc_final: 0.7205 (m-30) REVERT: C 118 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7501 (mttp) REVERT: C 183 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8072 (ttt) REVERT: C 483 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8457 (mt) REVERT: C 488 ARG cc_start: 0.8178 (ttp80) cc_final: 0.6823 (ttm170) REVERT: C 492 MET cc_start: 0.8915 (mtp) cc_final: 0.8642 (mtm) REVERT: C 635 MET cc_start: 0.8119 (mtt) cc_final: 0.7907 (mtt) REVERT: C 680 GLU cc_start: 0.7286 (tt0) cc_final: 0.6946 (mp0) REVERT: C 808 LYS cc_start: 0.7871 (mttt) cc_final: 0.7214 (mttt) REVERT: C 844 MET cc_start: 0.8287 (ttt) cc_final: 0.7935 (ttt) REVERT: C 845 GLU cc_start: 0.7730 (tt0) cc_final: 0.7212 (mt-10) REVERT: D 35 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8150 (tt) REVERT: D 118 LYS cc_start: 0.8243 (mppt) cc_final: 0.7846 (mmtm) REVERT: D 251 ASP cc_start: 0.7908 (m-30) cc_final: 0.7553 (m-30) REVERT: D 492 MET cc_start: 0.8905 (mtp) cc_final: 0.8579 (mtm) REVERT: D 513 ARG cc_start: 0.7450 (mtt180) cc_final: 0.6950 (mtp-110) REVERT: D 637 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7877 (mtp-110) REVERT: D 680 GLU cc_start: 0.7316 (tt0) cc_final: 0.6978 (mp0) REVERT: D 745 LYS cc_start: 0.7682 (mttt) cc_final: 0.7210 (tptp) REVERT: E 35 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8116 (tt) REVERT: E 36 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6189 (mm-40) REVERT: E 41 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8211 (m-10) REVERT: E 77 ASP cc_start: 0.7753 (m-30) cc_final: 0.7473 (m-30) REVERT: E 81 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8219 (mp) REVERT: E 467 GLN cc_start: 0.8661 (mt0) cc_final: 0.8404 (mt0) REVERT: E 492 MET cc_start: 0.8887 (mtp) cc_final: 0.8600 (mtm) REVERT: E 677 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7879 (p) REVERT: E 680 GLU cc_start: 0.7114 (tt0) cc_final: 0.6767 (mp0) REVERT: E 745 LYS cc_start: 0.7670 (mttt) cc_final: 0.7293 (tptp) REVERT: E 845 GLU cc_start: 0.7745 (tt0) cc_final: 0.7265 (mt-10) REVERT: F 41 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8676 (m-10) REVERT: F 77 ASP cc_start: 0.7788 (m-30) cc_final: 0.7264 (m-30) REVERT: F 81 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8300 (mm) REVERT: F 251 ASP cc_start: 0.7888 (m-30) cc_final: 0.7475 (m-30) REVERT: F 624 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7819 (tpt-90) REVERT: F 680 GLU cc_start: 0.7275 (tt0) cc_final: 0.6894 (mp0) REVERT: F 745 LYS cc_start: 0.7698 (mttt) cc_final: 0.7094 (tptp) REVERT: F 767 MET cc_start: 0.8186 (mtt) cc_final: 0.7749 (mtt) REVERT: F 845 GLU cc_start: 0.7655 (tt0) cc_final: 0.7215 (mt-10) outliers start: 129 outliers final: 49 residues processed: 558 average time/residue: 0.7144 time to fit residues: 469.9252 Evaluate side-chains 527 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 461 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 677 SER Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 392 CYS Chi-restraints excluded: chain F residue 406 ASP Chi-restraints excluded: chain F residue 624 ARG Chi-restraints excluded: chain F residue 643 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 12 optimal weight: 0.1980 chunk 362 optimal weight: 8.9990 chunk 390 optimal weight: 1.9990 chunk 350 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 364 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 284 optimal weight: 0.4980 chunk 430 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN A 720 ASN B 720 ASN C 123 ASN C 539 HIS C 720 ASN D 720 ASN E 720 ASN F 720 ASN F 848 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.165684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127525 restraints weight = 36884.800| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.81 r_work: 0.3279 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36234 Z= 0.141 Angle : 0.466 6.315 48804 Z= 0.240 Chirality : 0.041 0.128 5538 Planarity : 0.004 0.054 6078 Dihedral : 8.475 79.194 4840 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.24 % Allowed : 24.59 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.14), residues: 4224 helix: 1.60 (0.12), residues: 1854 sheet: -0.22 (0.22), residues: 732 loop : 0.35 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 121 TYR 0.013 0.001 TYR B 196 PHE 0.006 0.001 PHE A 586 TRP 0.008 0.001 TRP B 633 HIS 0.003 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00348 (36234) covalent geometry : angle 0.46637 (48804) hydrogen bonds : bond 0.03308 ( 1478) hydrogen bonds : angle 3.81719 ( 4317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 486 time to evaluate : 1.212 Fit side-chains REVERT: A 251 ASP cc_start: 0.7928 (m-30) cc_final: 0.7556 (m-30) REVERT: A 492 MET cc_start: 0.8914 (mtp) cc_final: 0.8596 (mtm) REVERT: A 602 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: A 637 ARG cc_start: 0.8019 (mtp-110) cc_final: 0.7806 (mtp-110) REVERT: A 680 GLU cc_start: 0.7255 (tt0) cc_final: 0.7023 (mp0) REVERT: A 745 LYS cc_start: 0.7759 (mttt) cc_final: 0.7202 (tptp) REVERT: A 845 GLU cc_start: 0.7883 (tt0) cc_final: 0.7385 (mt-10) REVERT: B 35 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7988 (tt) REVERT: B 41 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: B 77 ASP cc_start: 0.7732 (m-30) cc_final: 0.7405 (m-30) REVERT: B 81 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8213 (mp) REVERT: B 109 GLU cc_start: 0.7862 (tt0) cc_final: 0.7231 (tt0) REVERT: B 123 ASN cc_start: 0.7616 (t0) cc_final: 0.7200 (m110) REVERT: B 367 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7902 (mmtt) REVERT: B 467 GLN cc_start: 0.8629 (mt0) cc_final: 0.8386 (mt0) REVERT: B 492 MET cc_start: 0.8851 (mtp) cc_final: 0.8553 (mtm) REVERT: B 680 GLU cc_start: 0.7095 (tt0) cc_final: 0.6804 (mp0) REVERT: B 808 LYS cc_start: 0.7765 (mttt) cc_final: 0.7140 (mttt) REVERT: B 845 GLU cc_start: 0.7671 (tt0) cc_final: 0.7261 (mt-10) REVERT: C 36 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6121 (mm-40) REVERT: C 41 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8712 (m-10) REVERT: C 77 ASP cc_start: 0.7709 (m-30) cc_final: 0.7155 (m-30) REVERT: C 118 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7463 (mttp) REVERT: C 123 ASN cc_start: 0.7613 (t0) cc_final: 0.7391 (m110) REVERT: C 183 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8134 (ttt) REVERT: C 483 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8422 (mt) REVERT: C 488 ARG cc_start: 0.8117 (ttp80) cc_final: 0.6756 (ttm170) REVERT: C 492 MET cc_start: 0.8900 (mtp) cc_final: 0.8618 (mtm) REVERT: C 680 GLU cc_start: 0.7221 (tt0) cc_final: 0.6895 (mp0) REVERT: C 808 LYS cc_start: 0.7903 (mttt) cc_final: 0.7219 (mttt) REVERT: C 844 MET cc_start: 0.8275 (ttt) cc_final: 0.7883 (ttt) REVERT: C 845 GLU cc_start: 0.7705 (tt0) cc_final: 0.7181 (mt-10) REVERT: D 35 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8084 (tt) REVERT: D 251 ASP cc_start: 0.7828 (m-30) cc_final: 0.7445 (m-30) REVERT: D 492 MET cc_start: 0.8884 (mtp) cc_final: 0.8546 (mtm) REVERT: D 513 ARG cc_start: 0.7402 (mtt180) cc_final: 0.6913 (mtp-110) REVERT: D 602 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8029 (mtpt) REVERT: D 680 GLU cc_start: 0.7287 (tt0) cc_final: 0.6969 (mp0) REVERT: D 745 LYS cc_start: 0.7681 (mttt) cc_final: 0.7192 (tptp) REVERT: D 845 GLU cc_start: 0.7890 (tt0) cc_final: 0.7410 (mt-10) REVERT: E 35 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8049 (tt) REVERT: E 36 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6170 (mm-40) REVERT: E 77 ASP cc_start: 0.7708 (m-30) cc_final: 0.7389 (m-30) REVERT: E 81 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8195 (mp) REVERT: E 492 MET cc_start: 0.8874 (mtp) cc_final: 0.8573 (mtm) REVERT: E 680 GLU cc_start: 0.7077 (tt0) cc_final: 0.6758 (mp0) REVERT: E 745 LYS cc_start: 0.7646 (mttt) cc_final: 0.7253 (tptp) REVERT: E 845 GLU cc_start: 0.7837 (tt0) cc_final: 0.7337 (mt-10) REVERT: F 41 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8625 (m-10) REVERT: F 77 ASP cc_start: 0.7718 (m-30) cc_final: 0.7078 (m-30) REVERT: F 81 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8286 (mm) REVERT: F 624 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7897 (tpt-90) REVERT: F 680 GLU cc_start: 0.7251 (tt0) cc_final: 0.6884 (mp0) REVERT: F 745 LYS cc_start: 0.7710 (mttt) cc_final: 0.7108 (tptp) REVERT: F 767 MET cc_start: 0.8318 (mtt) cc_final: 0.7873 (mtt) REVERT: F 845 GLU cc_start: 0.7673 (tt0) cc_final: 0.7258 (mt-10) outliers start: 128 outliers final: 71 residues processed: 561 average time/residue: 0.6837 time to fit residues: 453.0912 Evaluate side-chains 559 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 471 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 602 LYS Chi-restraints excluded: chain D residue 606 LYS Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 392 CYS Chi-restraints excluded: chain F residue 406 ASP Chi-restraints excluded: chain F residue 466 MET Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 624 ARG Chi-restraints excluded: chain F residue 643 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 190 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 385 optimal weight: 0.2980 chunk 129 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 369 optimal weight: 1.9990 chunk 413 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN B 720 ASN C 539 HIS C 720 ASN D 720 ASN E 720 ASN F 720 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.166113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125621 restraints weight = 36802.640| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.70 r_work: 0.3275 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36234 Z= 0.124 Angle : 0.453 6.808 48804 Z= 0.234 Chirality : 0.040 0.127 5538 Planarity : 0.004 0.054 6078 Dihedral : 8.367 82.465 4840 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.72 % Allowed : 24.32 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.13), residues: 4224 helix: 1.68 (0.12), residues: 1854 sheet: -0.24 (0.22), residues: 732 loop : 0.36 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 121 TYR 0.012 0.001 TYR B 196 PHE 0.010 0.001 PHE A 586 TRP 0.008 0.001 TRP B 633 HIS 0.002 0.001 HIS E 642 Details of bonding type rmsd covalent geometry : bond 0.00304 (36234) covalent geometry : angle 0.45333 (48804) hydrogen bonds : bond 0.03132 ( 1478) hydrogen bonds : angle 3.72218 ( 4317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 486 time to evaluate : 1.049 Fit side-chains REVERT: A 118 LYS cc_start: 0.8217 (mppt) cc_final: 0.7795 (mmtm) REVERT: A 251 ASP cc_start: 0.7931 (m-30) cc_final: 0.7557 (m-30) REVERT: A 492 MET cc_start: 0.8896 (mtp) cc_final: 0.8585 (mtm) REVERT: A 602 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7891 (mtpt) REVERT: A 637 ARG cc_start: 0.8025 (mtp-110) cc_final: 0.7792 (mtp-110) REVERT: A 680 GLU cc_start: 0.7260 (tt0) cc_final: 0.7019 (mp0) REVERT: A 745 LYS cc_start: 0.7732 (mttt) cc_final: 0.7166 (tptp) REVERT: A 845 GLU cc_start: 0.7916 (tt0) cc_final: 0.7445 (mt-10) REVERT: B 35 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8027 (tt) REVERT: B 41 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: B 77 ASP cc_start: 0.7797 (m-30) cc_final: 0.7457 (m-30) REVERT: B 81 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8210 (mp) REVERT: B 109 GLU cc_start: 0.7865 (tt0) cc_final: 0.7229 (tt0) REVERT: B 118 LYS cc_start: 0.8087 (mppt) cc_final: 0.7783 (mmtm) REVERT: B 123 ASN cc_start: 0.7616 (t0) cc_final: 0.7263 (m110) REVERT: B 367 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8144 (mptp) REVERT: B 475 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8855 (ttmm) REVERT: B 492 MET cc_start: 0.8852 (mtp) cc_final: 0.8558 (mtm) REVERT: B 680 GLU cc_start: 0.7060 (tt0) cc_final: 0.6769 (mp0) REVERT: B 808 LYS cc_start: 0.7751 (mttt) cc_final: 0.7125 (mttt) REVERT: B 845 GLU cc_start: 0.7701 (tt0) cc_final: 0.7315 (mt-10) REVERT: C 36 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6109 (mm-40) REVERT: C 41 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8665 (m-10) REVERT: C 77 ASP cc_start: 0.7739 (m-30) cc_final: 0.7161 (m-30) REVERT: C 118 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7508 (mttp) REVERT: C 123 ASN cc_start: 0.7598 (t0) cc_final: 0.7370 (m110) REVERT: C 183 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8132 (ttt) REVERT: C 483 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8444 (mt) REVERT: C 488 ARG cc_start: 0.8111 (ttp80) cc_final: 0.6805 (ttm170) REVERT: C 492 MET cc_start: 0.8901 (mtp) cc_final: 0.8614 (mtm) REVERT: C 680 GLU cc_start: 0.7226 (tt0) cc_final: 0.6879 (mp0) REVERT: C 808 LYS cc_start: 0.7866 (mttt) cc_final: 0.7154 (mttt) REVERT: C 844 MET cc_start: 0.8297 (ttt) cc_final: 0.7910 (ttt) REVERT: C 845 GLU cc_start: 0.7736 (tt0) cc_final: 0.7241 (mt-10) REVERT: D 35 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8110 (tt) REVERT: D 118 LYS cc_start: 0.8222 (mppt) cc_final: 0.7793 (mmtm) REVERT: D 251 ASP cc_start: 0.7878 (m-30) cc_final: 0.7479 (m-30) REVERT: D 429 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8440 (mm) REVERT: D 492 MET cc_start: 0.8881 (mtp) cc_final: 0.8529 (mtm) REVERT: D 513 ARG cc_start: 0.7407 (mtt180) cc_final: 0.6914 (mtp-110) REVERT: D 680 GLU cc_start: 0.7319 (tt0) cc_final: 0.7011 (mp0) REVERT: D 745 LYS cc_start: 0.7687 (mttt) cc_final: 0.7192 (tptp) REVERT: D 845 GLU cc_start: 0.7914 (tt0) cc_final: 0.7450 (mt-10) REVERT: E 35 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8057 (tt) REVERT: E 36 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6166 (mm-40) REVERT: E 77 ASP cc_start: 0.7754 (m-30) cc_final: 0.7416 (m-30) REVERT: E 81 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8202 (mp) REVERT: E 467 GLN cc_start: 0.8629 (mt0) cc_final: 0.8376 (mt0) REVERT: E 492 MET cc_start: 0.8875 (mtp) cc_final: 0.8576 (mtm) REVERT: E 680 GLU cc_start: 0.7100 (tt0) cc_final: 0.6771 (mp0) REVERT: E 745 LYS cc_start: 0.7616 (mttt) cc_final: 0.7231 (tptp) REVERT: E 845 GLU cc_start: 0.7867 (tt0) cc_final: 0.7373 (mt-10) REVERT: F 36 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.5980 (mm-40) REVERT: F 41 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: F 77 ASP cc_start: 0.7752 (m-30) cc_final: 0.7108 (m-30) REVERT: F 81 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8282 (mm) REVERT: F 488 ARG cc_start: 0.8073 (ttp80) cc_final: 0.6821 (ttm170) REVERT: F 624 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7827 (tpt-90) REVERT: F 680 GLU cc_start: 0.7262 (tt0) cc_final: 0.6894 (mp0) REVERT: F 745 LYS cc_start: 0.7712 (mttt) cc_final: 0.7111 (tptp) REVERT: F 767 MET cc_start: 0.8340 (mtt) cc_final: 0.7921 (mtt) REVERT: F 845 GLU cc_start: 0.7666 (tt0) cc_final: 0.7256 (mt-10) outliers start: 147 outliers final: 73 residues processed: 575 average time/residue: 0.6681 time to fit residues: 456.5622 Evaluate side-chains 562 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 470 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 606 LYS Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 677 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 392 CYS Chi-restraints excluded: chain F residue 406 ASP Chi-restraints excluded: chain F residue 466 MET Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 624 ARG Chi-restraints excluded: chain F residue 643 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 357 optimal weight: 0.2980 chunk 404 optimal weight: 0.8980 chunk 247 optimal weight: 0.6980 chunk 377 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 57 optimal weight: 0.0370 chunk 33 optimal weight: 0.0070 chunk 250 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN B 720 ASN C 539 HIS C 720 ASN D 720 ASN E 720 ASN F 720 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130216 restraints weight = 36899.440| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.72 r_work: 0.3328 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36234 Z= 0.085 Angle : 0.423 7.344 48804 Z= 0.220 Chirality : 0.039 0.125 5538 Planarity : 0.003 0.054 6078 Dihedral : 7.977 87.750 4840 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.22 % Allowed : 24.95 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.14), residues: 4224 helix: 1.92 (0.12), residues: 1854 sheet: -0.20 (0.22), residues: 732 loop : 0.46 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 121 TYR 0.009 0.001 TYR B 196 PHE 0.007 0.001 PHE C 486 TRP 0.007 0.001 TRP E 633 HIS 0.002 0.000 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00202 (36234) covalent geometry : angle 0.42290 (48804) hydrogen bonds : bond 0.02673 ( 1478) hydrogen bonds : angle 3.53069 ( 4317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 488 time to evaluate : 1.499 Fit side-chains REVERT: A 118 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7810 (mmtm) REVERT: A 251 ASP cc_start: 0.7834 (m-30) cc_final: 0.7429 (m-30) REVERT: A 492 MET cc_start: 0.8826 (mtp) cc_final: 0.8425 (mtt) REVERT: A 602 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7897 (mtpt) REVERT: A 637 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7726 (mtp-110) REVERT: A 677 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7773 (p) REVERT: A 680 GLU cc_start: 0.7240 (tt0) cc_final: 0.7027 (mp0) REVERT: A 745 LYS cc_start: 0.7710 (mttt) cc_final: 0.7236 (tptp) REVERT: A 845 GLU cc_start: 0.7908 (tt0) cc_final: 0.7445 (mt-10) REVERT: B 77 ASP cc_start: 0.7734 (m-30) cc_final: 0.7392 (m-30) REVERT: B 118 LYS cc_start: 0.8112 (mppt) cc_final: 0.7769 (mmtm) REVERT: B 123 ASN cc_start: 0.7592 (t0) cc_final: 0.7281 (m110) REVERT: B 150 GLU cc_start: 0.8290 (tp30) cc_final: 0.7980 (tp30) REVERT: B 367 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8152 (mptp) REVERT: B 492 MET cc_start: 0.8811 (mtp) cc_final: 0.8495 (mtm) REVERT: B 677 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7948 (p) REVERT: B 680 GLU cc_start: 0.7059 (tt0) cc_final: 0.6802 (mp0) REVERT: B 808 LYS cc_start: 0.7753 (mttt) cc_final: 0.7130 (mttt) REVERT: B 845 GLU cc_start: 0.7702 (tt0) cc_final: 0.7335 (mt-10) REVERT: C 36 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.5930 (mm-40) REVERT: C 41 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8721 (m-10) REVERT: C 77 ASP cc_start: 0.7685 (m-30) cc_final: 0.7107 (m-30) REVERT: C 111 LYS cc_start: 0.7783 (mppt) cc_final: 0.6814 (ttpp) REVERT: C 118 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7534 (mttp) REVERT: C 123 ASN cc_start: 0.7608 (t0) cc_final: 0.7398 (m110) REVERT: C 251 ASP cc_start: 0.7758 (m-30) cc_final: 0.7382 (m-30) REVERT: C 483 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8446 (mt) REVERT: C 488 ARG cc_start: 0.8060 (ttp80) cc_final: 0.6782 (ttm170) REVERT: C 680 GLU cc_start: 0.7231 (tt0) cc_final: 0.6896 (mp0) REVERT: C 808 LYS cc_start: 0.7906 (mttt) cc_final: 0.7196 (mttt) REVERT: C 844 MET cc_start: 0.8257 (ttt) cc_final: 0.7842 (ttt) REVERT: C 845 GLU cc_start: 0.7747 (tt0) cc_final: 0.7254 (mt-10) REVERT: D 216 SER cc_start: 0.8374 (m) cc_final: 0.8170 (m) REVERT: D 251 ASP cc_start: 0.7830 (m-30) cc_final: 0.7442 (m-30) REVERT: D 429 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8478 (mm) REVERT: D 492 MET cc_start: 0.8813 (mtp) cc_final: 0.8471 (mtt) REVERT: D 513 ARG cc_start: 0.7333 (mtt180) cc_final: 0.6839 (mtp-110) REVERT: D 601 ILE cc_start: 0.8033 (mt) cc_final: 0.7832 (mt) REVERT: D 677 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7829 (p) REVERT: D 680 GLU cc_start: 0.7276 (tt0) cc_final: 0.7014 (mp0) REVERT: D 745 LYS cc_start: 0.7655 (mttt) cc_final: 0.7148 (tptp) REVERT: D 845 GLU cc_start: 0.7900 (tt0) cc_final: 0.7450 (mt-10) REVERT: E 35 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8059 (tt) REVERT: E 36 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.6168 (mm-40) REVERT: E 41 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8193 (m-10) REVERT: E 77 ASP cc_start: 0.7689 (m-30) cc_final: 0.7411 (m-30) REVERT: E 118 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7938 (mmtm) REVERT: E 150 GLU cc_start: 0.8259 (tp30) cc_final: 0.7939 (tp30) REVERT: E 467 GLN cc_start: 0.8564 (mt0) cc_final: 0.8330 (mt0) REVERT: E 492 MET cc_start: 0.8812 (mtp) cc_final: 0.8510 (mtm) REVERT: E 677 SER cc_start: 0.8134 (OUTLIER) cc_final: 0.7871 (p) REVERT: E 680 GLU cc_start: 0.7060 (tt0) cc_final: 0.6752 (mp0) REVERT: E 745 LYS cc_start: 0.7540 (mttt) cc_final: 0.7058 (tptp) REVERT: E 845 GLU cc_start: 0.7863 (tt0) cc_final: 0.7391 (mt-10) REVERT: F 36 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.5909 (mm-40) REVERT: F 41 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8699 (m-10) REVERT: F 77 ASP cc_start: 0.7730 (m-30) cc_final: 0.7124 (m-30) REVERT: F 488 ARG cc_start: 0.8025 (ttp80) cc_final: 0.6813 (ttm170) REVERT: F 624 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7785 (tpt-90) REVERT: F 680 GLU cc_start: 0.7273 (tt0) cc_final: 0.6927 (mp0) REVERT: F 745 LYS cc_start: 0.7699 (mttt) cc_final: 0.6845 (tptp) REVERT: F 767 MET cc_start: 0.8335 (mtt) cc_final: 0.7864 (mtt) REVERT: F 845 GLU cc_start: 0.7703 (tt0) cc_final: 0.7289 (mt-10) outliers start: 127 outliers final: 47 residues processed: 570 average time/residue: 0.7915 time to fit residues: 533.1186 Evaluate side-chains 529 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 465 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 606 LYS Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 677 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 406 ASP Chi-restraints excluded: chain F residue 466 MET Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 624 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 303 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 349 optimal weight: 4.9990 chunk 281 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 363 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 364 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN B 720 ASN C 539 HIS C 720 ASN D 720 ASN E 720 ASN F 720 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123996 restraints weight = 37032.856| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.71 r_work: 0.3251 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 36234 Z= 0.192 Angle : 0.515 7.728 48804 Z= 0.262 Chirality : 0.042 0.163 5538 Planarity : 0.004 0.054 6078 Dihedral : 8.551 79.816 4838 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.39 % Allowed : 24.54 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.13), residues: 4224 helix: 1.58 (0.12), residues: 1854 sheet: -0.20 (0.22), residues: 720 loop : 0.36 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 639 TYR 0.017 0.002 TYR A 196 PHE 0.012 0.001 PHE A 586 TRP 0.007 0.001 TRP B 633 HIS 0.004 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00477 (36234) covalent geometry : angle 0.51538 (48804) hydrogen bonds : bond 0.03541 ( 1478) hydrogen bonds : angle 3.73470 ( 4317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 487 time to evaluate : 1.867 Fit side-chains REVERT: A 35 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8118 (tt) REVERT: A 118 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7544 (mtmm) REVERT: A 251 ASP cc_start: 0.7936 (m-30) cc_final: 0.7550 (m-30) REVERT: A 492 MET cc_start: 0.8920 (mtp) cc_final: 0.8610 (mtm) REVERT: A 680 GLU cc_start: 0.7266 (tt0) cc_final: 0.7006 (mp0) REVERT: A 745 LYS cc_start: 0.7739 (mttt) cc_final: 0.7216 (tptp) REVERT: A 845 GLU cc_start: 0.7843 (tt0) cc_final: 0.7371 (mt-10) REVERT: B 77 ASP cc_start: 0.7778 (m-30) cc_final: 0.7476 (m-30) REVERT: B 109 GLU cc_start: 0.7861 (tt0) cc_final: 0.7223 (tt0) REVERT: B 123 ASN cc_start: 0.7619 (t0) cc_final: 0.7269 (m110) REVERT: B 367 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7819 (mttp) REVERT: B 492 MET cc_start: 0.8890 (mtp) cc_final: 0.8580 (mtm) REVERT: B 680 GLU cc_start: 0.7046 (tt0) cc_final: 0.6778 (mp0) REVERT: B 808 LYS cc_start: 0.7742 (mttt) cc_final: 0.7046 (mttt) REVERT: B 845 GLU cc_start: 0.7751 (tt0) cc_final: 0.7390 (mt-10) REVERT: C 36 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6216 (mm-40) REVERT: C 41 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8737 (m-10) REVERT: C 77 ASP cc_start: 0.7733 (m-30) cc_final: 0.7040 (m-30) REVERT: C 118 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7491 (mttp) REVERT: C 123 ASN cc_start: 0.7632 (t0) cc_final: 0.7400 (m110) REVERT: C 251 ASP cc_start: 0.7860 (m-30) cc_final: 0.7469 (m-30) REVERT: C 483 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8477 (mt) REVERT: C 492 MET cc_start: 0.8914 (mtp) cc_final: 0.8632 (mtm) REVERT: C 680 GLU cc_start: 0.7224 (tt0) cc_final: 0.6881 (mp0) REVERT: C 808 LYS cc_start: 0.7934 (mttt) cc_final: 0.7146 (mttt) REVERT: C 844 MET cc_start: 0.8273 (ttt) cc_final: 0.7891 (ttt) REVERT: C 845 GLU cc_start: 0.7740 (tt0) cc_final: 0.7314 (mt-10) REVERT: D 35 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8135 (tt) REVERT: D 251 ASP cc_start: 0.7869 (m-30) cc_final: 0.7509 (m-30) REVERT: D 492 MET cc_start: 0.8919 (mtp) cc_final: 0.8591 (mtm) REVERT: D 513 ARG cc_start: 0.7440 (mtt180) cc_final: 0.6975 (mtp-110) REVERT: D 680 GLU cc_start: 0.7310 (tt0) cc_final: 0.7007 (mp0) REVERT: D 745 LYS cc_start: 0.7706 (mttt) cc_final: 0.7185 (tptp) REVERT: D 845 GLU cc_start: 0.7865 (tt0) cc_final: 0.7392 (mt-10) REVERT: E 35 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8035 (tt) REVERT: E 36 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6342 (mm-40) REVERT: E 41 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8280 (m-10) REVERT: E 77 ASP cc_start: 0.7739 (m-30) cc_final: 0.7468 (m-30) REVERT: E 492 MET cc_start: 0.8899 (mtp) cc_final: 0.8587 (mtm) REVERT: E 680 GLU cc_start: 0.7036 (tt0) cc_final: 0.6732 (mp0) REVERT: E 745 LYS cc_start: 0.7610 (mttt) cc_final: 0.7197 (tptp) REVERT: E 845 GLU cc_start: 0.7885 (tt0) cc_final: 0.7411 (mt-10) REVERT: F 36 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6044 (mm-40) REVERT: F 41 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8716 (m-10) REVERT: F 77 ASP cc_start: 0.7749 (m-30) cc_final: 0.7028 (m-30) REVERT: F 81 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8304 (mm) REVERT: F 488 ARG cc_start: 0.8160 (ttp80) cc_final: 0.6881 (ttm170) REVERT: F 492 MET cc_start: 0.8916 (mtp) cc_final: 0.8636 (mtm) REVERT: F 624 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7959 (tpt-90) REVERT: F 680 GLU cc_start: 0.7285 (tt0) cc_final: 0.6914 (mp0) REVERT: F 745 LYS cc_start: 0.7735 (mttt) cc_final: 0.7104 (tptp) REVERT: F 767 MET cc_start: 0.8344 (mtt) cc_final: 0.7947 (mtt) REVERT: F 845 GLU cc_start: 0.7732 (tt0) cc_final: 0.7331 (mt-10) outliers start: 134 outliers final: 70 residues processed: 570 average time/residue: 0.8077 time to fit residues: 546.1411 Evaluate side-chains 557 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 473 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 624 ARG Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 392 CYS Chi-restraints excluded: chain F residue 406 ASP Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 624 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 380 optimal weight: 0.5980 chunk 402 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 310 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 265 optimal weight: 0.4980 chunk 418 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN B 720 ASN C 539 HIS C 720 ASN D 720 ASN E 467 GLN E 720 ASN F 720 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.167012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126783 restraints weight = 36889.587| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.70 r_work: 0.3290 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36234 Z= 0.102 Angle : 0.453 8.401 48804 Z= 0.233 Chirality : 0.040 0.224 5538 Planarity : 0.003 0.054 6078 Dihedral : 8.087 88.972 4838 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.30 % Allowed : 25.99 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.14), residues: 4224 helix: 1.78 (0.12), residues: 1854 sheet: -0.25 (0.22), residues: 732 loop : 0.45 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 639 TYR 0.011 0.001 TYR B 196 PHE 0.007 0.001 PHE A 585 TRP 0.008 0.001 TRP E 633 HIS 0.002 0.000 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00248 (36234) covalent geometry : angle 0.45255 (48804) hydrogen bonds : bond 0.02853 ( 1478) hydrogen bonds : angle 3.56982 ( 4317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 484 time to evaluate : 1.553 Fit side-chains REVERT: A 118 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7801 (mmtm) REVERT: A 251 ASP cc_start: 0.7898 (m-30) cc_final: 0.7517 (m-30) REVERT: A 464 MET cc_start: 0.9118 (mtm) cc_final: 0.8861 (mtp) REVERT: A 492 MET cc_start: 0.8867 (mtp) cc_final: 0.8545 (mtm) REVERT: A 680 GLU cc_start: 0.7280 (tt0) cc_final: 0.7033 (mp0) REVERT: A 745 LYS cc_start: 0.7691 (mttt) cc_final: 0.7197 (tptp) REVERT: A 845 GLU cc_start: 0.7843 (tt0) cc_final: 0.7391 (mt-10) REVERT: B 77 ASP cc_start: 0.7747 (m-30) cc_final: 0.7428 (m-30) REVERT: B 109 GLU cc_start: 0.7846 (tt0) cc_final: 0.7211 (tt0) REVERT: B 118 LYS cc_start: 0.8101 (mppt) cc_final: 0.7724 (mmtm) REVERT: B 123 ASN cc_start: 0.7564 (t0) cc_final: 0.7270 (m110) REVERT: B 150 GLU cc_start: 0.8281 (tp30) cc_final: 0.8012 (tp30) REVERT: B 367 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7823 (mttp) REVERT: B 492 MET cc_start: 0.8859 (mtp) cc_final: 0.8562 (mtm) REVERT: B 677 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7968 (p) REVERT: B 680 GLU cc_start: 0.7038 (tt0) cc_final: 0.6791 (mp0) REVERT: B 808 LYS cc_start: 0.7759 (mttt) cc_final: 0.7059 (mttt) REVERT: B 845 GLU cc_start: 0.7762 (tt0) cc_final: 0.7383 (mt-10) REVERT: C 36 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.5854 (mm-40) REVERT: C 41 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8733 (m-10) REVERT: C 77 ASP cc_start: 0.7679 (m-30) cc_final: 0.7036 (m-30) REVERT: C 111 LYS cc_start: 0.7772 (mppt) cc_final: 0.6750 (ttpp) REVERT: C 118 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7524 (mttp) REVERT: C 123 ASN cc_start: 0.7651 (t0) cc_final: 0.7418 (m110) REVERT: C 251 ASP cc_start: 0.7813 (m-30) cc_final: 0.7438 (m-30) REVERT: C 488 ARG cc_start: 0.8125 (ttp80) cc_final: 0.6736 (ttm170) REVERT: C 492 MET cc_start: 0.8890 (mtp) cc_final: 0.8605 (mtm) REVERT: C 680 GLU cc_start: 0.7244 (tt0) cc_final: 0.6905 (mp0) REVERT: C 767 MET cc_start: 0.8257 (mtt) cc_final: 0.7867 (mtt) REVERT: C 808 LYS cc_start: 0.7942 (mttt) cc_final: 0.7154 (mttt) REVERT: C 844 MET cc_start: 0.8249 (ttt) cc_final: 0.7856 (ttt) REVERT: C 845 GLU cc_start: 0.7786 (tt0) cc_final: 0.7338 (mt-10) REVERT: D 35 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8061 (tt) REVERT: D 116 LYS cc_start: 0.7839 (ttpt) cc_final: 0.7294 (ttmt) REVERT: D 118 LYS cc_start: 0.8170 (mppt) cc_final: 0.7522 (mttp) REVERT: D 251 ASP cc_start: 0.7867 (m-30) cc_final: 0.7458 (m-30) REVERT: D 492 MET cc_start: 0.8862 (mtp) cc_final: 0.8515 (mtm) REVERT: D 513 ARG cc_start: 0.7370 (mtt180) cc_final: 0.6828 (mtp-110) REVERT: D 677 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7820 (p) REVERT: D 680 GLU cc_start: 0.7277 (tt0) cc_final: 0.7003 (mp0) REVERT: D 745 LYS cc_start: 0.7713 (mttt) cc_final: 0.7155 (tptp) REVERT: D 845 GLU cc_start: 0.7847 (tt0) cc_final: 0.7392 (mt-10) REVERT: E 35 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8033 (tt) REVERT: E 36 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6235 (mm-40) REVERT: E 41 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: E 77 ASP cc_start: 0.7671 (m-30) cc_final: 0.7385 (m-30) REVERT: E 150 GLU cc_start: 0.8277 (tp30) cc_final: 0.7992 (tp30) REVERT: E 492 MET cc_start: 0.8865 (mtp) cc_final: 0.8567 (mtm) REVERT: E 677 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7875 (p) REVERT: E 680 GLU cc_start: 0.7038 (tt0) cc_final: 0.6739 (mp0) REVERT: E 745 LYS cc_start: 0.7536 (mttt) cc_final: 0.7035 (tptp) REVERT: E 845 GLU cc_start: 0.7873 (tt0) cc_final: 0.7402 (mt-10) REVERT: F 36 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.5974 (mm-40) REVERT: F 41 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8701 (m-10) REVERT: F 77 ASP cc_start: 0.7759 (m-30) cc_final: 0.7117 (m-30) REVERT: F 81 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8269 (mm) REVERT: F 488 ARG cc_start: 0.8066 (ttp80) cc_final: 0.6842 (ttm170) REVERT: F 624 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7802 (tpt-90) REVERT: F 680 GLU cc_start: 0.7273 (tt0) cc_final: 0.6916 (mp0) REVERT: F 745 LYS cc_start: 0.7724 (mttt) cc_final: 0.7037 (tptp) REVERT: F 767 MET cc_start: 0.8344 (mtt) cc_final: 0.7944 (mtt) REVERT: F 845 GLU cc_start: 0.7759 (tt0) cc_final: 0.7331 (mt-10) outliers start: 91 outliers final: 53 residues processed: 539 average time/residue: 0.7944 time to fit residues: 505.7235 Evaluate side-chains 539 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 471 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 606 LYS Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 677 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 406 ASP Chi-restraints excluded: chain F residue 466 MET Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 624 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 317 optimal weight: 0.9990 chunk 406 optimal weight: 0.6980 chunk 348 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 311 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 410 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN B 720 ASN C 720 ASN D 720 ASN E 467 GLN E 720 ASN F 720 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.166743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126410 restraints weight = 36728.662| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.70 r_work: 0.3285 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36234 Z= 0.114 Angle : 0.466 8.803 48804 Z= 0.239 Chirality : 0.040 0.202 5538 Planarity : 0.003 0.054 6078 Dihedral : 8.096 89.992 4838 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.23 % Allowed : 26.14 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.14), residues: 4224 helix: 1.81 (0.12), residues: 1854 sheet: -0.26 (0.22), residues: 732 loop : 0.46 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 488 TYR 0.012 0.001 TYR A 196 PHE 0.013 0.001 PHE A 586 TRP 0.007 0.001 TRP B 633 HIS 0.003 0.001 HIS D 238 Details of bonding type rmsd covalent geometry : bond 0.00280 (36234) covalent geometry : angle 0.46551 (48804) hydrogen bonds : bond 0.02908 ( 1478) hydrogen bonds : angle 3.54445 ( 4317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 470 time to evaluate : 1.328 Fit side-chains REVERT: A 35 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8142 (tt) REVERT: A 118 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7584 (mttp) REVERT: A 251 ASP cc_start: 0.7912 (m-30) cc_final: 0.7509 (m-30) REVERT: A 464 MET cc_start: 0.9098 (mtm) cc_final: 0.8890 (mtp) REVERT: A 492 MET cc_start: 0.8879 (mtp) cc_final: 0.8552 (mtm) REVERT: A 680 GLU cc_start: 0.7276 (tt0) cc_final: 0.7035 (mp0) REVERT: A 745 LYS cc_start: 0.7693 (mttt) cc_final: 0.7186 (tptp) REVERT: A 845 GLU cc_start: 0.7853 (tt0) cc_final: 0.7396 (mt-10) REVERT: B 77 ASP cc_start: 0.7721 (m-30) cc_final: 0.7399 (m-30) REVERT: B 118 LYS cc_start: 0.8081 (mppt) cc_final: 0.7795 (mmtm) REVERT: B 123 ASN cc_start: 0.7549 (t0) cc_final: 0.7293 (m110) REVERT: B 150 GLU cc_start: 0.8312 (tp30) cc_final: 0.7848 (tp30) REVERT: B 367 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7829 (mttp) REVERT: B 492 MET cc_start: 0.8828 (mtp) cc_final: 0.8527 (mtm) REVERT: B 677 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7967 (p) REVERT: B 680 GLU cc_start: 0.6988 (tt0) cc_final: 0.6745 (mp0) REVERT: B 808 LYS cc_start: 0.7783 (mttt) cc_final: 0.7077 (mttt) REVERT: B 845 GLU cc_start: 0.7749 (tt0) cc_final: 0.7389 (mt-10) REVERT: C 36 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.5955 (mm-40) REVERT: C 41 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8717 (m-10) REVERT: C 77 ASP cc_start: 0.7672 (m-30) cc_final: 0.7025 (m-30) REVERT: C 111 LYS cc_start: 0.7817 (mppt) cc_final: 0.6790 (ttpp) REVERT: C 118 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7513 (mttp) REVERT: C 123 ASN cc_start: 0.7645 (t0) cc_final: 0.7413 (m110) REVERT: C 251 ASP cc_start: 0.7823 (m-30) cc_final: 0.7434 (m-30) REVERT: C 488 ARG cc_start: 0.8115 (ttp80) cc_final: 0.6729 (ttm170) REVERT: C 492 MET cc_start: 0.8887 (mtp) cc_final: 0.8602 (mtm) REVERT: C 680 GLU cc_start: 0.7254 (tt0) cc_final: 0.6895 (mp0) REVERT: C 767 MET cc_start: 0.8337 (mtt) cc_final: 0.7933 (mtt) REVERT: C 808 LYS cc_start: 0.7963 (mttt) cc_final: 0.7147 (mttt) REVERT: C 845 GLU cc_start: 0.7788 (tt0) cc_final: 0.7396 (mt-10) REVERT: D 35 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8061 (tt) REVERT: D 116 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7274 (ttmt) REVERT: D 118 LYS cc_start: 0.8170 (mppt) cc_final: 0.7536 (mttp) REVERT: D 251 ASP cc_start: 0.7847 (m-30) cc_final: 0.7439 (m-30) REVERT: D 395 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8613 (mm) REVERT: D 492 MET cc_start: 0.8864 (mtp) cc_final: 0.8526 (mtm) REVERT: D 513 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6857 (mtp-110) REVERT: D 677 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7815 (p) REVERT: D 680 GLU cc_start: 0.7271 (tt0) cc_final: 0.7004 (mp0) REVERT: D 742 PHE cc_start: 0.8020 (m-80) cc_final: 0.7757 (m-80) REVERT: D 745 LYS cc_start: 0.7722 (mttt) cc_final: 0.7167 (tptp) REVERT: D 845 GLU cc_start: 0.7834 (tt0) cc_final: 0.7396 (mt-10) REVERT: E 35 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8040 (tt) REVERT: E 36 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6236 (mm-40) REVERT: E 77 ASP cc_start: 0.7686 (m-30) cc_final: 0.7391 (m-30) REVERT: E 150 GLU cc_start: 0.8274 (tp30) cc_final: 0.7792 (tp30) REVERT: E 492 MET cc_start: 0.8860 (mtp) cc_final: 0.8565 (mtm) REVERT: E 680 GLU cc_start: 0.7026 (tt0) cc_final: 0.6726 (mp0) REVERT: E 745 LYS cc_start: 0.7533 (mttt) cc_final: 0.7017 (tptp) REVERT: E 845 GLU cc_start: 0.7899 (tt0) cc_final: 0.7442 (mt-10) REVERT: F 36 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.5973 (mm-40) REVERT: F 41 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8696 (m-10) REVERT: F 77 ASP cc_start: 0.7745 (m-30) cc_final: 0.7047 (m-30) REVERT: F 81 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8270 (mm) REVERT: F 488 ARG cc_start: 0.8062 (ttp80) cc_final: 0.6834 (ttm170) REVERT: F 594 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8337 (tp) REVERT: F 624 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7931 (tpt-90) REVERT: F 680 GLU cc_start: 0.7279 (tt0) cc_final: 0.6919 (mp0) REVERT: F 745 LYS cc_start: 0.7726 (mttt) cc_final: 0.7037 (tptp) REVERT: F 767 MET cc_start: 0.8348 (mtt) cc_final: 0.7932 (mtt) REVERT: F 845 GLU cc_start: 0.7748 (tt0) cc_final: 0.7337 (mt-10) outliers start: 88 outliers final: 55 residues processed: 528 average time/residue: 0.6468 time to fit residues: 404.6072 Evaluate side-chains 537 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 466 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 624 ARG Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 392 CYS Chi-restraints excluded: chain F residue 406 ASP Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 624 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 397 optimal weight: 0.6980 chunk 291 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 385 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 65 optimal weight: 10.0000 chunk 301 optimal weight: 0.0870 chunk 266 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN B 720 ASN C 720 ASN D 238 HIS D 720 ASN E 720 ASN F 238 HIS F 720 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.168056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130017 restraints weight = 36889.712| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.69 r_work: 0.3326 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 36234 Z= 0.092 Angle : 0.447 9.210 48804 Z= 0.230 Chirality : 0.039 0.192 5538 Planarity : 0.003 0.054 6078 Dihedral : 7.840 85.965 4838 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.10 % Allowed : 26.24 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.14), residues: 4224 helix: 1.91 (0.12), residues: 1860 sheet: -0.23 (0.22), residues: 732 loop : 0.55 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 639 TYR 0.010 0.001 TYR B 196 PHE 0.006 0.001 PHE F 498 TRP 0.007 0.001 TRP E 633 HIS 0.003 0.000 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00221 (36234) covalent geometry : angle 0.44663 (48804) hydrogen bonds : bond 0.02675 ( 1478) hydrogen bonds : angle 3.46740 ( 4317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 472 time to evaluate : 1.280 Fit side-chains REVERT: A 35 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 118 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7846 (mmtm) REVERT: A 251 ASP cc_start: 0.7847 (m-30) cc_final: 0.7442 (m-30) REVERT: A 464 MET cc_start: 0.9080 (mtm) cc_final: 0.8859 (mtp) REVERT: A 492 MET cc_start: 0.8822 (mtp) cc_final: 0.8435 (mtm) REVERT: A 680 GLU cc_start: 0.7251 (tt0) cc_final: 0.7042 (mp0) REVERT: A 745 LYS cc_start: 0.7675 (mttt) cc_final: 0.7175 (tptp) REVERT: A 845 GLU cc_start: 0.7839 (tt0) cc_final: 0.7391 (mt-10) REVERT: B 77 ASP cc_start: 0.7705 (m-30) cc_final: 0.7405 (m-30) REVERT: B 111 LYS cc_start: 0.7980 (mppt) cc_final: 0.6723 (ttpp) REVERT: B 118 LYS cc_start: 0.8089 (mppt) cc_final: 0.7796 (mmtm) REVERT: B 123 ASN cc_start: 0.7530 (t0) cc_final: 0.7314 (m110) REVERT: B 150 GLU cc_start: 0.8304 (tp30) cc_final: 0.8021 (tp30) REVERT: B 367 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8119 (mptp) REVERT: B 492 MET cc_start: 0.8800 (mtp) cc_final: 0.8518 (mtm) REVERT: B 603 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 677 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7949 (p) REVERT: B 680 GLU cc_start: 0.6983 (tt0) cc_final: 0.6762 (mp0) REVERT: B 808 LYS cc_start: 0.7815 (mttt) cc_final: 0.7111 (mttt) REVERT: B 845 GLU cc_start: 0.7729 (tt0) cc_final: 0.7359 (mt-10) REVERT: C 36 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.5820 (mm-40) REVERT: C 77 ASP cc_start: 0.7691 (m-30) cc_final: 0.7048 (m-30) REVERT: C 111 LYS cc_start: 0.7856 (mppt) cc_final: 0.6860 (ttpp) REVERT: C 118 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7498 (mttp) REVERT: C 251 ASP cc_start: 0.7776 (m-30) cc_final: 0.7417 (m-30) REVERT: C 488 ARG cc_start: 0.8090 (ttp80) cc_final: 0.6748 (ttm170) REVERT: C 680 GLU cc_start: 0.7251 (tt0) cc_final: 0.6917 (mp0) REVERT: C 767 MET cc_start: 0.8400 (mtt) cc_final: 0.7987 (mtt) REVERT: C 808 LYS cc_start: 0.7977 (mttt) cc_final: 0.7191 (mttt) REVERT: C 844 MET cc_start: 0.8424 (ttt) cc_final: 0.8047 (ttt) REVERT: C 845 GLU cc_start: 0.7794 (tt0) cc_final: 0.7360 (mt-10) REVERT: D 35 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8088 (tt) REVERT: D 109 GLU cc_start: 0.7126 (tt0) cc_final: 0.6909 (tt0) REVERT: D 111 LYS cc_start: 0.7864 (mppt) cc_final: 0.6665 (ttpp) REVERT: D 116 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7287 (ttmt) REVERT: D 118 LYS cc_start: 0.8214 (mppt) cc_final: 0.7573 (mttt) REVERT: D 251 ASP cc_start: 0.7804 (m-30) cc_final: 0.7399 (m-30) REVERT: D 464 MET cc_start: 0.9184 (mtm) cc_final: 0.8877 (mtp) REVERT: D 492 MET cc_start: 0.8808 (mtp) cc_final: 0.8452 (mtm) REVERT: D 513 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6820 (mtp-110) REVERT: D 677 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7828 (p) REVERT: D 680 GLU cc_start: 0.7263 (tt0) cc_final: 0.7026 (mp0) REVERT: D 742 PHE cc_start: 0.8010 (m-80) cc_final: 0.7789 (m-80) REVERT: D 745 LYS cc_start: 0.7712 (mttt) cc_final: 0.7186 (tptp) REVERT: D 845 GLU cc_start: 0.7812 (tt0) cc_final: 0.7355 (mt-10) REVERT: E 35 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8068 (tt) REVERT: E 77 ASP cc_start: 0.7682 (m-30) cc_final: 0.7422 (m-30) REVERT: E 111 LYS cc_start: 0.7830 (mppt) cc_final: 0.6646 (ttpp) REVERT: E 150 GLU cc_start: 0.8268 (tp30) cc_final: 0.7953 (tp30) REVERT: E 492 MET cc_start: 0.8808 (mtp) cc_final: 0.8514 (mtm) REVERT: E 680 GLU cc_start: 0.7025 (tt0) cc_final: 0.6751 (mp0) REVERT: E 742 PHE cc_start: 0.8033 (m-80) cc_final: 0.7826 (m-80) REVERT: E 745 LYS cc_start: 0.7521 (mttt) cc_final: 0.7032 (tptp) REVERT: E 845 GLU cc_start: 0.7895 (tt0) cc_final: 0.7444 (mt-10) REVERT: F 36 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.5955 (mm-40) REVERT: F 41 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8677 (m-10) REVERT: F 77 ASP cc_start: 0.7778 (m-30) cc_final: 0.7118 (m-30) REVERT: F 81 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8270 (mm) REVERT: F 488 ARG cc_start: 0.8025 (ttp80) cc_final: 0.6821 (ttm170) REVERT: F 624 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7931 (tpt-90) REVERT: F 639 ARG cc_start: 0.8304 (mtp85) cc_final: 0.8009 (mtp85) REVERT: F 680 GLU cc_start: 0.7269 (tt0) cc_final: 0.6932 (mp0) REVERT: F 745 LYS cc_start: 0.7710 (mttt) cc_final: 0.6837 (tptp) REVERT: F 767 MET cc_start: 0.8373 (mtt) cc_final: 0.7942 (mtt) REVERT: F 845 GLU cc_start: 0.7753 (tt0) cc_final: 0.7357 (mt-10) outliers start: 83 outliers final: 46 residues processed: 528 average time/residue: 0.6941 time to fit residues: 434.3365 Evaluate side-chains 523 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 464 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 392 CYS Chi-restraints excluded: chain F residue 406 ASP Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 624 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 411 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 chunk 322 optimal weight: 1.9990 chunk 284 optimal weight: 9.9990 chunk 405 optimal weight: 1.9990 chunk 253 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 720 ASN B 720 ASN C 123 ASN C 720 ASN D 238 HIS D 720 ASN E 720 ASN F 238 HIS F 720 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.166337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126063 restraints weight = 36748.712| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.69 r_work: 0.3280 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36234 Z= 0.134 Angle : 0.481 9.067 48804 Z= 0.246 Chirality : 0.041 0.196 5538 Planarity : 0.004 0.054 6078 Dihedral : 8.123 87.550 4838 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.08 % Allowed : 26.32 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.14), residues: 4224 helix: 1.75 (0.12), residues: 1860 sheet: -0.28 (0.21), residues: 756 loop : 0.55 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 488 TYR 0.013 0.001 TYR B 196 PHE 0.013 0.001 PHE A 586 TRP 0.006 0.001 TRP E 633 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00330 (36234) covalent geometry : angle 0.48123 (48804) hydrogen bonds : bond 0.03043 ( 1478) hydrogen bonds : angle 3.54759 ( 4317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12655.61 seconds wall clock time: 216 minutes 9.73 seconds (12969.73 seconds total)