Starting phenix.real_space_refine on Mon Jun 23 13:48:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a8v_15241/06_2025/8a8v_15241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8v_15241/06_2025/8a8v_15241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a8v_15241/06_2025/8a8v_15241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8v_15241/06_2025/8a8v_15241.map" model { file = "/net/cci-nas-00/data/ceres_data/8a8v_15241/06_2025/8a8v_15241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8v_15241/06_2025/8a8v_15241.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.073 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 20 5.49 5 S 66 5.16 5 C 17044 2.51 5 N 4838 2.21 5 O 5196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27164 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4403 Classifications: {'peptide': 558} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 540} Chain breaks: 4 Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4483 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 548} Chain breaks: 3 Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4510 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 553} Chain breaks: 2 Chain: "D" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4530 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 555} Chain breaks: 2 Chain: "E" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4490 Classifications: {'peptide': 569} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 548} Chain breaks: 3 Chain: "F" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4364 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 532} Chain breaks: 5 Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 114 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.86, per 1000 atoms: 0.69 Number of scatterers: 27164 At special positions: 0 Unit cell: (123.12, 139.365, 148.77, 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 66 16.00 P 20 15.00 O 5196 8.00 N 4838 7.00 C 17044 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: 6.50 Conformation dependent library (CDL) restraints added in 3.3 seconds 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6310 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 28 sheets defined 59.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.511A pdb=" N LYS A 243 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.440A pdb=" N GLY A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 371 removed outlier: 4.663A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 4.280A pdb=" N ARG A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 415 removed outlier: 3.960A pdb=" N MET A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 493 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 502 through 509 removed outlier: 3.555A pdb=" N ARG A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 558 through 572 Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.632A pdb=" N ARG A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.622A pdb=" N LYS A 694 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 702 " --> pdb=" O ASN A 698 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 4.142A pdb=" N LEU A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 743 Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 772 through 780 removed outlier: 3.906A pdb=" N GLN A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.673A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 221 through 236 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 262 through 280 removed outlier: 4.743A pdb=" N GLU B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.572A pdb=" N VAL B 293 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.601A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Proline residue: B 310 - end of helix removed outlier: 3.750A pdb=" N ARG B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.849A pdb=" N ARG B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 371 removed outlier: 4.669A pdb=" N ASP B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 Processing helix chain 'B' and resid 396 through 415 Processing helix chain 'B' and resid 480 through 493 Processing helix chain 'B' and resid 500 through 509 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 521 through 538 removed outlier: 3.599A pdb=" N GLY B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 572 removed outlier: 3.939A pdb=" N SER B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 575 No H-bonds generated for 'chain 'B' and resid 573 through 575' Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 590 through 596 removed outlier: 3.574A pdb=" N LEU B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.705A pdb=" N LYS B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 removed outlier: 3.620A pdb=" N LYS B 629 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA B 630 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N HIS B 631 " --> pdb=" O GLU B 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 626 through 631' Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.973A pdb=" N ASN B 636 " --> pdb=" O GLN B 632 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 705 Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 723 through 743 removed outlier: 3.845A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 746 No H-bonds generated for 'chain 'B' and resid 744 through 746' Processing helix chain 'B' and resid 752 through 763 Processing helix chain 'B' and resid 770 through 780 Processing helix chain 'B' and resid 781 through 791 Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.765A pdb=" N PHE C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 174' Processing helix chain 'C' and resid 178 through 184 removed outlier: 4.063A pdb=" N GLU C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.557A pdb=" N VAL C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.561A pdb=" N LYS C 243 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 280 Processing helix chain 'C' and resid 289 through 292 Processing helix chain 'C' and resid 303 through 314 Proline residue: C 310 - end of helix removed outlier: 3.559A pdb=" N ARG C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 371 removed outlier: 3.693A pdb=" N TYR C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 Processing helix chain 'C' and resid 396 through 415 removed outlier: 3.563A pdb=" N MET C 415 " --> pdb=" O ARG C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 493 removed outlier: 3.531A pdb=" N ILE C 484 " --> pdb=" O ASP C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 509 through 516 removed outlier: 3.508A pdb=" N GLU C 513 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 537 Processing helix chain 'C' and resid 558 through 572 removed outlier: 3.923A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 590 Processing helix chain 'C' and resid 591 through 596 removed outlier: 4.315A pdb=" N PHE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 617 removed outlier: 3.760A pdb=" N GLU C 612 " --> pdb=" O GLY C 608 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 630 Processing helix chain 'C' and resid 631 through 645 removed outlier: 4.108A pdb=" N TYR C 635 " --> pdb=" O HIS C 631 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLN C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 705 Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.561A pdb=" N LEU C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 743 Processing helix chain 'C' and resid 744 through 746 No H-bonds generated for 'chain 'C' and resid 744 through 746' Processing helix chain 'C' and resid 752 through 762 Processing helix chain 'C' and resid 773 through 781 removed outlier: 3.552A pdb=" N ILE C 777 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 791 Processing helix chain 'D' and resid 170 through 174 Processing helix chain 'D' and resid 178 through 184 removed outlier: 3.925A pdb=" N GLU D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 221 through 236 removed outlier: 3.898A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 263 through 280 Processing helix chain 'D' and resid 289 through 293 removed outlier: 3.909A pdb=" N VAL D 293 " --> pdb=" O HIS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 removed outlier: 3.589A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Proline residue: D 310 - end of helix removed outlier: 3.790A pdb=" N ARG D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 335 through 342 removed outlier: 3.590A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 371 removed outlier: 4.694A pdb=" N ASP D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 390 removed outlier: 3.665A pdb=" N MET D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 380 " --> pdb=" O ASP D 376 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 415 removed outlier: 3.548A pdb=" N MET D 415 " --> pdb=" O ARG D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 493 Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 509 through 516 Processing helix chain 'D' and resid 521 through 537 Processing helix chain 'D' and resid 558 through 572 removed outlier: 3.657A pdb=" N SER D 563 " --> pdb=" O LYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.579A pdb=" N ALA D 576 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 585 No H-bonds generated for 'chain 'D' and resid 583 through 585' Processing helix chain 'D' and resid 587 through 590 Processing helix chain 'D' and resid 591 through 596 removed outlier: 3.731A pdb=" N PHE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 617 Processing helix chain 'D' and resid 632 through 644 removed outlier: 3.784A pdb=" N ASN D 636 " --> pdb=" O GLN D 632 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 638 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 641 " --> pdb=" O SER D 637 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 705 Processing helix chain 'D' and resid 706 through 711 Processing helix chain 'D' and resid 723 through 744 removed outlier: 3.726A pdb=" N ASP D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER D 744 " --> pdb=" O GLY D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 763 Processing helix chain 'D' and resid 770 through 781 removed outlier: 3.624A pdb=" N ARG D 774 " --> pdb=" O ALA D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 791 Processing helix chain 'E' and resid 169 through 174 removed outlier: 3.505A pdb=" N PHE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 193 through 204 Processing helix chain 'E' and resid 221 through 236 removed outlier: 3.745A pdb=" N VAL E 226 " --> pdb=" O LYS E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 263 through 280 Processing helix chain 'E' and resid 289 through 293 removed outlier: 4.058A pdb=" N VAL E 293 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 315 removed outlier: 3.581A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 324 through 332 removed outlier: 3.586A pdb=" N ARG E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 332 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.988A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 362 Processing helix chain 'E' and resid 362 through 371 removed outlier: 3.546A pdb=" N TYR E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 390 removed outlier: 3.547A pdb=" N THR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 415 removed outlier: 3.961A pdb=" N LEU E 402 " --> pdb=" O LYS E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 493 removed outlier: 3.822A pdb=" N ILE E 484 " --> pdb=" O ASP E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 509 removed outlier: 3.537A pdb=" N ARG E 509 " --> pdb=" O THR E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 516 Processing helix chain 'E' and resid 521 through 537 Processing helix chain 'E' and resid 558 through 572 removed outlier: 3.570A pdb=" N SER E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 577 removed outlier: 3.660A pdb=" N ALA E 576 " --> pdb=" O ASP E 573 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 577 " --> pdb=" O ASP E 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 573 through 577' Processing helix chain 'E' and resid 591 through 596 removed outlier: 3.637A pdb=" N PHE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 617 Processing helix chain 'E' and resid 626 through 630 Processing helix chain 'E' and resid 631 through 645 removed outlier: 4.076A pdb=" N TYR E 635 " --> pdb=" O HIS E 631 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN E 640 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL E 641 " --> pdb=" O SER E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 705 Processing helix chain 'E' and resid 706 through 711 removed outlier: 3.521A pdb=" N LEU E 710 " --> pdb=" O ARG E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 743 Processing helix chain 'E' and resid 744 through 746 No H-bonds generated for 'chain 'E' and resid 744 through 746' Processing helix chain 'E' and resid 752 through 763 Processing helix chain 'E' and resid 770 through 781 removed outlier: 3.975A pdb=" N ARG E 774 " --> pdb=" O ALA E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 791 removed outlier: 3.696A pdb=" N LEU E 790 " --> pdb=" O SER E 786 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 791 " --> pdb=" O GLU E 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 174 No H-bonds generated for 'chain 'F' and resid 171 through 174' Processing helix chain 'F' and resid 178 through 185 removed outlier: 4.107A pdb=" N MET F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 221 through 236 removed outlier: 3.802A pdb=" N VAL F 226 " --> pdb=" O LYS F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 280 Processing helix chain 'F' and resid 289 through 292 Processing helix chain 'F' and resid 304 through 314 removed outlier: 3.627A pdb=" N LYS F 309 " --> pdb=" O ALA F 305 " (cutoff:3.500A) Proline residue: F 310 - end of helix Processing helix chain 'F' and resid 324 through 331 Processing helix chain 'F' and resid 351 through 371 removed outlier: 4.723A pdb=" N ASP F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 390 removed outlier: 3.668A pdb=" N ILE F 390 " --> pdb=" O ALA F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 415 removed outlier: 3.851A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 493 Processing helix chain 'F' and resid 502 through 509 Processing helix chain 'F' and resid 509 through 516 removed outlier: 3.971A pdb=" N GLU F 513 " --> pdb=" O ARG F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 537 removed outlier: 3.704A pdb=" N ALA F 537 " --> pdb=" O ARG F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 571 Processing helix chain 'F' and resid 587 through 592 Processing helix chain 'F' and resid 610 through 617 removed outlier: 3.531A pdb=" N LYS F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 630 removed outlier: 3.633A pdb=" N ALA F 630 " --> pdb=" O ILE F 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 627 through 630' Processing helix chain 'F' and resid 631 through 645 Processing helix chain 'F' and resid 688 through 704 Processing helix chain 'F' and resid 706 through 712 removed outlier: 3.838A pdb=" N LEU F 710 " --> pdb=" O ARG F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 744 removed outlier: 3.720A pdb=" N LEU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL F 738 " --> pdb=" O MET F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 770 through 781 removed outlier: 3.685A pdb=" N ARG F 774 " --> pdb=" O ALA F 770 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG F 775 " --> pdb=" O ARG F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 792 removed outlier: 3.552A pdb=" N LEU F 790 " --> pdb=" O SER F 786 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 250 removed outlier: 8.108A pdb=" N ILE A 320 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 284 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA A 322 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 286 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.630A pdb=" N SER A 373 " --> pdb=" O VAL A 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 581 removed outlier: 3.625A pdb=" N ILE A 580 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 625 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY A 547 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE A 664 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE A 549 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER A 548 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 717 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 550 " --> pdb=" O ILE A 717 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 Processing sheet with id=AA5, first strand: chain 'A' and resid 748 through 751 Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 removed outlier: 5.142A pdb=" N ASP B 287 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 374 removed outlier: 6.281A pdb=" N SER B 373 " --> pdb=" O VAL B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 577 through 581 removed outlier: 6.293A pdb=" N ILE B 578 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP B 625 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 580 " --> pdb=" O ASP B 625 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 622 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR B 665 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 624 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY B 547 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE B 664 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE B 549 " --> pdb=" O PHE B 664 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 548 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE B 717 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE B 550 " --> pdb=" O ILE B 717 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AB1, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.444A pdb=" N ALA B 748 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL B 802 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 750 " --> pdb=" O VAL B 802 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N VAL B 804 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 175 through 177 removed outlier: 5.178A pdb=" N ASP C 287 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 578 through 581 removed outlier: 6.391A pdb=" N VAL C 622 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR C 665 " --> pdb=" O VAL C 622 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE C 624 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLY C 547 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE C 664 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE C 549 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N SER C 666 " --> pdb=" O PHE C 549 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 551 " --> pdb=" O SER C 666 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER C 548 " --> pdb=" O ASP C 715 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE C 717 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE C 550 " --> pdb=" O ILE C 717 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 646 through 648 Processing sheet with id=AB5, first strand: chain 'C' and resid 749 through 751 removed outlier: 7.024A pdb=" N VAL C 750 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N VAL C 804 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.072A pdb=" N GLN D 246 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE D 285 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR D 248 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP D 287 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU D 250 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL D 213 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 373 through 374 removed outlier: 6.658A pdb=" N SER D 373 " --> pdb=" O VAL D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 578 through 581 removed outlier: 6.714A pdb=" N ILE D 578 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP D 625 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE D 580 " --> pdb=" O ASP D 625 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D 622 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR D 665 " --> pdb=" O VAL D 622 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE D 624 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER D 548 " --> pdb=" O ASP D 715 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE D 717 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE D 550 " --> pdb=" O ILE D 717 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 648 Processing sheet with id=AC1, first strand: chain 'D' and resid 748 through 751 Processing sheet with id=AC2, first strand: chain 'E' and resid 175 through 177 removed outlier: 5.000A pdb=" N ASP E 287 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA E 322 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN E 211 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL E 345 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL E 213 " --> pdb=" O VAL E 345 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 373 through 374 removed outlier: 6.700A pdb=" N SER E 373 " --> pdb=" O VAL E 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 578 through 581 removed outlier: 6.098A pdb=" N GLY E 547 " --> pdb=" O LEU E 662 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE E 664 " --> pdb=" O GLY E 547 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE E 549 " --> pdb=" O PHE E 664 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N SER E 666 " --> pdb=" O PHE E 549 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE E 551 " --> pdb=" O SER E 666 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER E 548 " --> pdb=" O ASP E 715 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE E 717 " --> pdb=" O SER E 548 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE E 550 " --> pdb=" O ILE E 717 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 646 through 648 Processing sheet with id=AC6, first strand: chain 'E' and resid 749 through 751 Processing sheet with id=AC7, first strand: chain 'F' and resid 175 through 177 removed outlier: 6.020A pdb=" N GLN F 246 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE F 285 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR F 248 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP F 287 " --> pdb=" O TYR F 248 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU F 250 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE F 282 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE F 320 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU F 284 " --> pdb=" O ILE F 320 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA F 322 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE F 286 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN F 211 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL F 345 " --> pdb=" O ASN F 211 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL F 213 " --> pdb=" O VAL F 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 578 through 581 removed outlier: 6.962A pdb=" N ILE F 578 " --> pdb=" O LEU F 623 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP F 625 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE F 580 " --> pdb=" O ASP F 625 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY F 547 " --> pdb=" O LEU F 662 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE F 664 " --> pdb=" O GLY F 547 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE F 549 " --> pdb=" O PHE F 664 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER F 666 " --> pdb=" O PHE F 549 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE F 551 " --> pdb=" O SER F 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 646 through 648 Processing sheet with id=AD1, first strand: chain 'F' and resid 748 through 751 removed outlier: 6.153A pdb=" N ALA F 748 " --> pdb=" O VAL F 800 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL F 802 " --> pdb=" O ALA F 748 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL F 750 " --> pdb=" O VAL F 802 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N VAL F 804 " --> pdb=" O VAL F 750 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR F 801 " --> pdb=" O THR F 821 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR F 821 " --> pdb=" O THR F 801 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3885 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: 10.34 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9245 1.34 - 1.46: 4452 1.46 - 1.58: 13693 1.58 - 1.70: 31 1.70 - 1.82: 132 Bond restraints: 27553 Sorted by residual: bond pdb=" N ASP E 732 " pdb=" CA ASP E 732 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.09e+00 bond pdb=" N MET E 734 " pdb=" CA MET E 734 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.30e-02 5.92e+03 3.75e+00 bond pdb=" N LEU E 733 " pdb=" CA LEU E 733 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.64e+00 bond pdb=" CA ARG F 712 " pdb=" C ARG F 712 " ideal model delta sigma weight residual 1.522 1.549 -0.026 1.43e-02 4.89e+03 3.35e+00 bond pdb=" CB PRO C 495 " pdb=" CG PRO C 495 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.13e+00 ... (remaining 27548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 36287 2.26 - 4.52: 716 4.52 - 6.78: 141 6.78 - 9.04: 17 9.04 - 11.30: 8 Bond angle restraints: 37169 Sorted by residual: angle pdb=" CA ARG F 509 " pdb=" CB ARG F 509 " pdb=" CG ARG F 509 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 angle pdb=" CA PRO C 495 " pdb=" N PRO C 495 " pdb=" CD PRO C 495 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" N VAL C 220 " pdb=" CA VAL C 220 " pdb=" C VAL C 220 " ideal model delta sigma weight residual 113.47 109.15 4.32 1.01e+00 9.80e-01 1.83e+01 angle pdb=" N LYS E 543 " pdb=" CA LYS E 543 " pdb=" C LYS E 543 " ideal model delta sigma weight residual 114.64 108.47 6.17 1.52e+00 4.33e-01 1.65e+01 angle pdb=" CB MET E 183 " pdb=" CG MET E 183 " pdb=" SD MET E 183 " ideal model delta sigma weight residual 112.70 124.00 -11.30 3.00e+00 1.11e-01 1.42e+01 ... (remaining 37164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.02: 16247 32.02 - 64.05: 565 64.05 - 96.07: 36 96.07 - 128.09: 7 128.09 - 160.11: 5 Dihedral angle restraints: 16860 sinusoidal: 7103 harmonic: 9757 Sorted by residual: dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 100.12 -160.11 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O2A ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PA ADP D 902 " pdb=" PB ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 99.29 -159.29 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 83.19 -143.18 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 16857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3646 0.066 - 0.133: 563 0.133 - 0.199: 24 0.199 - 0.266: 2 0.266 - 0.332: 4 Chirality restraints: 4239 Sorted by residual: chirality pdb=" CB ILE B 716 " pdb=" CA ILE B 716 " pdb=" CG1 ILE B 716 " pdb=" CG2 ILE B 716 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE B 550 " pdb=" CA ILE B 550 " pdb=" CG1 ILE B 550 " pdb=" CG2 ILE B 550 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL C 767 " pdb=" CA VAL C 767 " pdb=" CG1 VAL C 767 " pdb=" CG2 VAL C 767 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4236 not shown) Planarity restraints: 4820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 706 " -0.059 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO C 707 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 707 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 707 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 771 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO E 772 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO E 772 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 772 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 811 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO F 812 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 812 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 812 " -0.038 5.00e-02 4.00e+02 ... (remaining 4817 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2768 2.75 - 3.28: 27148 3.28 - 3.82: 45235 3.82 - 4.36: 53876 4.36 - 4.90: 92572 Nonbonded interactions: 221599 Sorted by model distance: nonbonded pdb=" O ILE D 627 " pdb=" OH TYR D 635 " model vdw 2.208 3.040 nonbonded pdb=" NH2 ARG A 775 " pdb=" O LEU F 710 " model vdw 2.212 3.120 nonbonded pdb=" O ILE E 627 " pdb=" OH TYR E 635 " model vdw 2.227 3.040 nonbonded pdb=" NH1 ARG B 262 " pdb=" O UNK G 7 " model vdw 2.241 3.120 nonbonded pdb=" O THR F 560 " pdb=" OG SER F 563 " model vdw 2.242 3.040 ... (remaining 221594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 594 or resid 609 through 668 or resid 691 through 808 or resid 815 through 8 \ 21 or resid 901)) selection = (chain 'B' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'C' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'D' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'E' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'F' and (resid 170 through 415 or resid 477 through 668 or resid 691 thro \ ugh 808 or resid 815 through 821 or resid 901)) } 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=0.00 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: 50.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 63.230 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.110 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 27553 Z= 0.173 Angle : 0.791 11.301 37169 Z= 0.406 Chirality : 0.047 0.332 4239 Planarity : 0.006 0.091 4820 Dihedral : 15.570 160.114 10550 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.11 % Allowed : 0.35 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3346 helix: -0.33 (0.11), residues: 1801 sheet: -0.44 (0.24), residues: 389 loop : -0.11 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 807 HIS 0.005 0.001 HIS D 720 PHE 0.030 0.002 PHE A 265 TYR 0.040 0.002 TYR F 389 ARG 0.018 0.001 ARG F 729 Details of bonding type rmsd hydrogen bonds : bond 0.13675 ( 1320) hydrogen bonds : angle 6.71170 ( 3885) covalent geometry : bond 0.00391 (27553) covalent geometry : angle 0.79101 (37169) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 370 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 MET cc_start: 0.4675 (ppp) cc_final: 0.4459 (mmt) REVERT: A 779 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7229 (mmm160) REVERT: B 415 MET cc_start: 0.3682 (mmm) cc_final: 0.3198 (mtt) REVERT: B 606 GLU cc_start: 0.7438 (pp20) cc_final: 0.7172 (pt0) REVERT: B 774 ARG cc_start: 0.6169 (mmm-85) cc_final: 0.5875 (mtp85) REVERT: D 331 TYR cc_start: 0.8320 (m-10) cc_final: 0.8090 (m-10) REVERT: D 518 ILE cc_start: 0.8666 (mm) cc_final: 0.8444 (mm) REVERT: D 695 GLN cc_start: 0.7710 (tp40) cc_final: 0.7477 (tp-100) REVERT: E 582 MET cc_start: 0.8037 (mmm) cc_final: 0.7805 (mmt) REVERT: E 589 PHE cc_start: 0.5554 (m-10) cc_final: 0.5033 (m-10) REVERT: E 727 ILE cc_start: 0.7575 (mm) cc_final: 0.7337 (mm) REVERT: E 734 MET cc_start: 0.8235 (mtt) cc_final: 0.7976 (mtt) outliers start: 3 outliers final: 1 residues processed: 372 average time/residue: 0.4483 time to fit residues: 253.8636 Evaluate side-chains 285 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 568 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 chunk 306 optimal weight: 0.0570 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 235 HIS ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 667 ASN B 211 ASN B 391 ASN B 490 ASN C 343 GLN C 391 ASN C 640 GLN C 651 GLN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.179922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143614 restraints weight = 34602.418| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.90 r_work: 0.3662 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27553 Z= 0.120 Angle : 0.595 8.111 37169 Z= 0.285 Chirality : 0.042 0.145 4239 Planarity : 0.005 0.069 4820 Dihedral : 8.598 177.991 3833 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.98 % Allowed : 7.23 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3346 helix: 0.49 (0.12), residues: 1835 sheet: -0.49 (0.24), residues: 386 loop : 0.07 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 807 HIS 0.011 0.001 HIS D 290 PHE 0.021 0.001 PHE C 497 TYR 0.017 0.001 TYR A 635 ARG 0.007 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 1320) hydrogen bonds : angle 5.00731 ( 3885) covalent geometry : bond 0.00271 (27553) covalent geometry : angle 0.59493 (37169) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 317 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.6997 (m110) cc_final: 0.6669 (m110) REVERT: A 779 ARG cc_start: 0.7531 (mmt180) cc_final: 0.6830 (tmm-80) REVERT: B 339 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8279 (tt0) REVERT: B 415 MET cc_start: 0.3703 (mmm) cc_final: 0.3112 (mtt) REVERT: B 595 PHE cc_start: 0.6743 (m-80) cc_final: 0.6323 (m-10) REVERT: B 667 ASN cc_start: 0.7721 (t0) cc_final: 0.7464 (t0) REVERT: B 774 ARG cc_start: 0.6460 (mmm-85) cc_final: 0.6196 (mtp85) REVERT: D 695 GLN cc_start: 0.7945 (tp40) cc_final: 0.7464 (tp-100) REVERT: E 589 PHE cc_start: 0.6032 (m-10) cc_final: 0.5352 (m-10) REVERT: E 732 ASP cc_start: 0.8327 (t0) cc_final: 0.7770 (m-30) REVERT: F 623 LEU cc_start: 0.7564 (tt) cc_final: 0.7291 (tt) outliers start: 28 outliers final: 14 residues processed: 337 average time/residue: 0.4690 time to fit residues: 242.2776 Evaluate side-chains 295 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 281 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 733 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 326 optimal weight: 0.9980 chunk 251 optimal weight: 0.7980 chunk 284 optimal weight: 0.3980 chunk 239 optimal weight: 0.9980 chunk 322 optimal weight: 5.9990 chunk 220 optimal weight: 0.0670 chunk 316 optimal weight: 8.9990 chunk 180 optimal weight: 0.0770 chunk 50 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 667 ASN C 290 HIS C 568 ASN C 651 GLN D 631 HIS E 640 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.181277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144807 restraints weight = 34820.388| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.86 r_work: 0.3639 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27553 Z= 0.107 Angle : 0.563 8.405 37169 Z= 0.268 Chirality : 0.041 0.138 4239 Planarity : 0.004 0.071 4820 Dihedral : 8.132 176.917 3831 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.16 % Allowed : 10.21 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3346 helix: 0.84 (0.12), residues: 1832 sheet: -0.49 (0.24), residues: 386 loop : 0.12 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.010 0.001 HIS D 290 PHE 0.018 0.001 PHE C 497 TYR 0.031 0.001 TYR F 635 ARG 0.009 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 1320) hydrogen bonds : angle 4.74275 ( 3885) covalent geometry : bond 0.00241 (27553) covalent geometry : angle 0.56341 (37169) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 319 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7800 (t0) cc_final: 0.7449 (m-30) REVERT: A 391 ASN cc_start: 0.6980 (m110) cc_final: 0.6638 (m110) REVERT: A 510 MET cc_start: 0.7860 (ptm) cc_final: 0.7652 (ptm) REVERT: A 779 ARG cc_start: 0.7690 (mmt180) cc_final: 0.6887 (tmm-80) REVERT: B 339 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8377 (tt0) REVERT: B 415 MET cc_start: 0.3523 (mmm) cc_final: 0.3143 (mtt) REVERT: B 595 PHE cc_start: 0.6743 (m-80) cc_final: 0.6403 (m-10) REVERT: B 606 GLU cc_start: 0.7783 (pp20) cc_final: 0.7132 (pp20) REVERT: B 774 ARG cc_start: 0.6530 (mmm-85) cc_final: 0.6303 (mtp85) REVERT: D 581 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6973 (p0) REVERT: D 695 GLN cc_start: 0.7912 (tp40) cc_final: 0.7447 (tp-100) REVERT: E 589 PHE cc_start: 0.6052 (m-10) cc_final: 0.5307 (m-10) REVERT: E 732 ASP cc_start: 0.8297 (t0) cc_final: 0.7734 (m-30) REVERT: F 215 ILE cc_start: 0.9011 (mm) cc_final: 0.8811 (mt) REVERT: F 623 LEU cc_start: 0.7399 (tt) cc_final: 0.7093 (tt) REVERT: F 783 ASP cc_start: 0.6973 (t70) cc_final: 0.6585 (t0) outliers start: 33 outliers final: 15 residues processed: 344 average time/residue: 0.4230 time to fit residues: 224.7451 Evaluate side-chains 303 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 287 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 733 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 301 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 169 optimal weight: 0.0970 chunk 319 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 327 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 667 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 391 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN E 640 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.178444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140647 restraints weight = 34972.554| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.89 r_work: 0.3628 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27553 Z= 0.118 Angle : 0.566 7.522 37169 Z= 0.268 Chirality : 0.041 0.157 4239 Planarity : 0.004 0.072 4820 Dihedral : 7.902 178.853 3831 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.07 % Allowed : 11.48 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3346 helix: 0.90 (0.12), residues: 1849 sheet: -0.54 (0.24), residues: 391 loop : 0.11 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 807 HIS 0.010 0.001 HIS D 290 PHE 0.021 0.001 PHE C 497 TYR 0.031 0.001 TYR F 635 ARG 0.009 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 1320) hydrogen bonds : angle 4.65571 ( 3885) covalent geometry : bond 0.00276 (27553) covalent geometry : angle 0.56632 (37169) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 305 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 ARG cc_start: 0.7673 (mmt180) cc_final: 0.6827 (tmm-80) REVERT: B 339 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8379 (tt0) REVERT: B 415 MET cc_start: 0.3485 (mmm) cc_final: 0.3048 (mtt) REVERT: B 595 PHE cc_start: 0.6756 (m-80) cc_final: 0.6403 (m-10) REVERT: B 606 GLU cc_start: 0.7796 (pp20) cc_final: 0.7199 (pp20) REVERT: B 626 GLU cc_start: 0.8300 (tp30) cc_final: 0.8049 (tp30) REVERT: B 667 ASN cc_start: 0.7570 (t0) cc_final: 0.7318 (t0) REVERT: B 774 ARG cc_start: 0.6610 (mmm-85) cc_final: 0.6322 (mtp85) REVERT: D 581 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7084 (p0) REVERT: D 695 GLN cc_start: 0.7921 (tp40) cc_final: 0.7395 (tp-100) REVERT: E 201 MET cc_start: 0.7729 (mmt) cc_final: 0.7461 (mmt) REVERT: E 339 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7956 (tp30) REVERT: E 589 PHE cc_start: 0.6040 (m-10) cc_final: 0.5290 (m-10) REVERT: E 715 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: E 732 ASP cc_start: 0.8225 (t0) cc_final: 0.7671 (m-30) REVERT: F 623 LEU cc_start: 0.7362 (tt) cc_final: 0.7046 (tt) outliers start: 59 outliers final: 31 residues processed: 349 average time/residue: 0.4460 time to fit residues: 238.5230 Evaluate side-chains 312 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 230 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 254 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN C 343 GLN C 391 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN F 586 HIS F 720 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.177297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139492 restraints weight = 34990.544| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.02 r_work: 0.3600 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27553 Z= 0.135 Angle : 0.581 7.552 37169 Z= 0.275 Chirality : 0.042 0.159 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.684 179.675 3831 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.18 % Allowed : 13.02 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3346 helix: 0.89 (0.12), residues: 1857 sheet: -0.60 (0.24), residues: 391 loop : 0.14 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 491 HIS 0.005 0.001 HIS C 290 PHE 0.027 0.001 PHE C 497 TYR 0.038 0.001 TYR F 635 ARG 0.007 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 1320) hydrogen bonds : angle 4.65318 ( 3885) covalent geometry : bond 0.00320 (27553) covalent geometry : angle 0.58053 (37169) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7782 (t0) cc_final: 0.7400 (m-30) REVERT: A 490 ASN cc_start: 0.7750 (t0) cc_final: 0.7501 (t0) REVERT: A 582 MET cc_start: 0.5013 (ppp) cc_final: 0.4061 (mpp) REVERT: B 171 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8025 (tp) REVERT: B 339 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8368 (tt0) REVERT: B 415 MET cc_start: 0.3342 (mmm) cc_final: 0.2912 (mtt) REVERT: B 595 PHE cc_start: 0.6834 (m-80) cc_final: 0.6515 (m-10) REVERT: B 606 GLU cc_start: 0.7787 (pp20) cc_final: 0.7411 (pp20) REVERT: B 667 ASN cc_start: 0.7589 (t0) cc_final: 0.7372 (t0) REVERT: B 787 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: D 695 GLN cc_start: 0.7927 (tp40) cc_final: 0.7343 (tp-100) REVERT: E 201 MET cc_start: 0.7786 (mmt) cc_final: 0.7528 (mmt) REVERT: E 339 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8034 (tp30) REVERT: E 715 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: E 732 ASP cc_start: 0.8348 (t0) cc_final: 0.7747 (m-30) REVERT: F 585 PHE cc_start: 0.5951 (m-80) cc_final: 0.5673 (m-80) outliers start: 62 outliers final: 33 residues processed: 342 average time/residue: 0.4185 time to fit residues: 221.0145 Evaluate side-chains 317 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 281 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 310 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN C 343 GLN C 391 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN F 720 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.176699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139206 restraints weight = 34913.890| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.95 r_work: 0.3594 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27553 Z= 0.138 Angle : 0.588 7.632 37169 Z= 0.280 Chirality : 0.042 0.170 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.460 179.245 3831 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.07 % Allowed : 13.97 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3346 helix: 0.93 (0.12), residues: 1851 sheet: -0.68 (0.24), residues: 391 loop : 0.10 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 807 HIS 0.005 0.001 HIS D 290 PHE 0.023 0.001 PHE C 497 TYR 0.039 0.001 TYR F 635 ARG 0.009 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 1320) hydrogen bonds : angle 4.67409 ( 3885) covalent geometry : bond 0.00328 (27553) covalent geometry : angle 0.58825 (37169) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 301 time to evaluate : 3.319 Fit side-chains revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7916 (t0) cc_final: 0.7429 (m-30) REVERT: A 490 ASN cc_start: 0.7785 (t0) cc_final: 0.7526 (t0) REVERT: A 582 MET cc_start: 0.5148 (ppp) cc_final: 0.4159 (mpp) REVERT: B 171 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7978 (tp) REVERT: B 339 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8361 (tt0) REVERT: B 415 MET cc_start: 0.3392 (mmm) cc_final: 0.3077 (mtt) REVERT: B 575 ASP cc_start: 0.6973 (m-30) cc_final: 0.6270 (p0) REVERT: B 595 PHE cc_start: 0.6895 (m-80) cc_final: 0.6561 (m-10) REVERT: B 606 GLU cc_start: 0.7776 (pp20) cc_final: 0.7447 (pp20) REVERT: B 626 GLU cc_start: 0.8378 (tp30) cc_final: 0.8026 (tp30) REVERT: B 628 GLU cc_start: 0.8185 (pt0) cc_final: 0.7953 (pt0) REVERT: B 667 ASN cc_start: 0.7483 (t0) cc_final: 0.7181 (t0) REVERT: B 774 ARG cc_start: 0.6699 (mmm-85) cc_final: 0.6258 (mtp85) REVERT: B 787 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: D 695 GLN cc_start: 0.7929 (tp40) cc_final: 0.7320 (tp-100) REVERT: E 201 MET cc_start: 0.7813 (mmt) cc_final: 0.7518 (mmt) REVERT: E 339 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7995 (tp30) REVERT: E 715 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: E 732 ASP cc_start: 0.8375 (t0) cc_final: 0.7759 (m-30) REVERT: F 585 PHE cc_start: 0.6015 (m-80) cc_final: 0.5708 (m-80) REVERT: F 623 LEU cc_start: 0.7468 (tt) cc_final: 0.7171 (tt) REVERT: F 646 ARG cc_start: 0.7602 (tpp80) cc_final: 0.7261 (tpp80) REVERT: F 747 MET cc_start: 0.7889 (mmt) cc_final: 0.7559 (mmt) outliers start: 59 outliers final: 45 residues processed: 343 average time/residue: 0.4247 time to fit residues: 226.2781 Evaluate side-chains 328 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 720 HIS Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 777 ILE Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 206 optimal weight: 0.5980 chunk 199 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 290 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 331 optimal weight: 0.0770 chunk 100 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 267 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 640 GLN C 343 GLN C 391 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN F 720 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.177750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140881 restraints weight = 35094.440| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.07 r_work: 0.3613 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27553 Z= 0.116 Angle : 0.574 7.629 37169 Z= 0.273 Chirality : 0.042 0.181 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.238 178.098 3831 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.21 % Allowed : 14.46 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3346 helix: 1.02 (0.12), residues: 1850 sheet: -0.70 (0.24), residues: 397 loop : 0.13 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 491 HIS 0.012 0.001 HIS F 720 PHE 0.025 0.001 PHE C 497 TYR 0.039 0.001 TYR F 635 ARG 0.008 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 1320) hydrogen bonds : angle 4.60020 ( 3885) covalent geometry : bond 0.00272 (27553) covalent geometry : angle 0.57397 (37169) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 297 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 490 ASN cc_start: 0.7712 (t0) cc_final: 0.7452 (t0) REVERT: A 534 ARG cc_start: 0.7798 (ptp-110) cc_final: 0.7501 (ptp-110) REVERT: A 582 MET cc_start: 0.5069 (ppp) cc_final: 0.4235 (mpp) REVERT: B 339 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8360 (tt0) REVERT: B 415 MET cc_start: 0.3280 (mmm) cc_final: 0.2998 (mtt) REVERT: B 575 ASP cc_start: 0.6889 (m-30) cc_final: 0.6229 (p0) REVERT: B 595 PHE cc_start: 0.6835 (m-80) cc_final: 0.6524 (m-10) REVERT: B 606 GLU cc_start: 0.7786 (pp20) cc_final: 0.7440 (pp20) REVERT: B 626 GLU cc_start: 0.8391 (tp30) cc_final: 0.8061 (tp30) REVERT: B 628 GLU cc_start: 0.8190 (pt0) cc_final: 0.7834 (pt0) REVERT: B 667 ASN cc_start: 0.7443 (t0) cc_final: 0.7175 (t0) REVERT: B 774 ARG cc_start: 0.6603 (mmm-85) cc_final: 0.6202 (mtp85) REVERT: B 787 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: D 695 GLN cc_start: 0.7925 (tp40) cc_final: 0.7335 (tp-100) REVERT: E 201 MET cc_start: 0.7820 (mmt) cc_final: 0.7515 (mmt) REVERT: E 339 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7984 (tp30) REVERT: E 732 ASP cc_start: 0.8392 (t0) cc_final: 0.7795 (m-30) REVERT: F 410 MET cc_start: 0.7293 (mmm) cc_final: 0.7055 (tpp) REVERT: F 509 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.5381 (pmt-80) REVERT: F 582 MET cc_start: 0.5183 (mmm) cc_final: 0.4719 (mmm) REVERT: F 585 PHE cc_start: 0.6027 (m-80) cc_final: 0.5644 (m-80) REVERT: F 623 LEU cc_start: 0.7423 (tt) cc_final: 0.7093 (tt) REVERT: F 646 ARG cc_start: 0.7612 (tpp80) cc_final: 0.7385 (tpp80) REVERT: F 747 MET cc_start: 0.7934 (mmt) cc_final: 0.7623 (mmt) outliers start: 63 outliers final: 45 residues processed: 345 average time/residue: 0.4218 time to fit residues: 224.4882 Evaluate side-chains 329 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 509 ARG Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 777 ILE Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 124 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 290 optimal weight: 0.8980 chunk 295 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN C 343 GLN C 391 ASN C 568 ASN C 651 GLN D 391 ASN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.176061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136378 restraints weight = 34912.575| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.84 r_work: 0.3592 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27553 Z= 0.138 Angle : 0.589 8.270 37169 Z= 0.281 Chirality : 0.042 0.182 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.242 179.446 3831 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.11 % Allowed : 14.95 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3346 helix: 0.97 (0.12), residues: 1850 sheet: -0.74 (0.24), residues: 396 loop : 0.11 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 491 HIS 0.005 0.001 HIS D 290 PHE 0.042 0.001 PHE E 791 TYR 0.039 0.001 TYR F 635 ARG 0.008 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 1320) hydrogen bonds : angle 4.64404 ( 3885) covalent geometry : bond 0.00332 (27553) covalent geometry : angle 0.58871 (37169) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 3.327 Fit side-chains revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7570 (t0) cc_final: 0.7299 (m-30) REVERT: A 490 ASN cc_start: 0.7706 (t0) cc_final: 0.7449 (t0) REVERT: A 534 ARG cc_start: 0.7778 (ptp-110) cc_final: 0.7475 (ptp-110) REVERT: A 582 MET cc_start: 0.5068 (ppp) cc_final: 0.4229 (mpp) REVERT: B 171 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8014 (tp) REVERT: B 267 GLU cc_start: 0.8381 (tp30) cc_final: 0.8069 (tt0) REVERT: B 339 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8350 (tt0) REVERT: B 415 MET cc_start: 0.3388 (mmm) cc_final: 0.3167 (mtt) REVERT: B 575 ASP cc_start: 0.6945 (m-30) cc_final: 0.6251 (p0) REVERT: B 606 GLU cc_start: 0.7767 (pp20) cc_final: 0.7438 (pp20) REVERT: B 626 GLU cc_start: 0.8343 (tp30) cc_final: 0.7976 (tp30) REVERT: B 628 GLU cc_start: 0.8170 (pt0) cc_final: 0.7772 (pt0) REVERT: B 667 ASN cc_start: 0.7504 (t0) cc_final: 0.7232 (t0) REVERT: B 774 ARG cc_start: 0.6557 (mmm-85) cc_final: 0.6215 (mtp85) REVERT: B 787 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: C 201 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7504 (mmt) REVERT: D 695 GLN cc_start: 0.7932 (tp40) cc_final: 0.7294 (tp-100) REVERT: E 201 MET cc_start: 0.7820 (mmt) cc_final: 0.7545 (mmt) REVERT: E 339 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7969 (tp30) REVERT: E 589 PHE cc_start: 0.6181 (m-10) cc_final: 0.5603 (m-80) REVERT: E 732 ASP cc_start: 0.8393 (t0) cc_final: 0.7771 (m-30) REVERT: F 585 PHE cc_start: 0.5983 (m-80) cc_final: 0.5563 (m-80) REVERT: F 623 LEU cc_start: 0.7434 (tt) cc_final: 0.7151 (tt) REVERT: F 646 ARG cc_start: 0.7617 (tpp80) cc_final: 0.7362 (tpp80) REVERT: F 747 MET cc_start: 0.7964 (mmt) cc_final: 0.7672 (mmt) outliers start: 60 outliers final: 48 residues processed: 336 average time/residue: 0.4472 time to fit residues: 232.9863 Evaluate side-chains 330 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 777 ILE Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 21 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 chunk 282 optimal weight: 0.4980 chunk 287 optimal weight: 0.7980 chunk 270 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN C 391 ASN C 568 ASN C 651 GLN E 202 GLN E 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.176384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136338 restraints weight = 35147.096| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.87 r_work: 0.3593 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27553 Z= 0.137 Angle : 0.598 8.065 37169 Z= 0.286 Chirality : 0.042 0.227 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.228 179.398 3831 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.04 % Allowed : 15.30 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3346 helix: 0.98 (0.12), residues: 1849 sheet: -0.79 (0.24), residues: 397 loop : 0.14 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 491 HIS 0.005 0.001 HIS D 290 PHE 0.030 0.001 PHE E 791 TYR 0.040 0.001 TYR F 635 ARG 0.008 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 1320) hydrogen bonds : angle 4.64142 ( 3885) covalent geometry : bond 0.00329 (27553) covalent geometry : angle 0.59793 (37169) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 298 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7672 (t0) cc_final: 0.7361 (m-30) REVERT: A 490 ASN cc_start: 0.7725 (t0) cc_final: 0.7457 (t0) REVERT: A 534 ARG cc_start: 0.7764 (ptp-110) cc_final: 0.7443 (ptp-110) REVERT: A 582 MET cc_start: 0.5089 (ppp) cc_final: 0.4228 (mpp) REVERT: A 644 ASP cc_start: 0.4289 (m-30) cc_final: 0.4014 (m-30) REVERT: A 734 MET cc_start: 0.8436 (ptm) cc_final: 0.8133 (ptp) REVERT: B 171 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8044 (tp) REVERT: B 267 GLU cc_start: 0.8370 (tp30) cc_final: 0.8055 (tt0) REVERT: B 339 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8356 (tt0) REVERT: B 575 ASP cc_start: 0.6930 (m-30) cc_final: 0.6223 (p0) REVERT: B 606 GLU cc_start: 0.7754 (pp20) cc_final: 0.7435 (pp20) REVERT: B 626 GLU cc_start: 0.8286 (tp30) cc_final: 0.7937 (tp30) REVERT: B 628 GLU cc_start: 0.8178 (pt0) cc_final: 0.7791 (pt0) REVERT: B 667 ASN cc_start: 0.7509 (t0) cc_final: 0.7261 (t0) REVERT: B 774 ARG cc_start: 0.6572 (mmm-85) cc_final: 0.6219 (mtp85) REVERT: B 787 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: C 201 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7505 (mmt) REVERT: D 695 GLN cc_start: 0.7926 (tp40) cc_final: 0.7288 (tp-100) REVERT: E 201 MET cc_start: 0.7806 (mmt) cc_final: 0.7532 (mmt) REVERT: E 339 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7944 (tp30) REVERT: E 507 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8189 (tt) REVERT: E 582 MET cc_start: 0.8589 (mmm) cc_final: 0.8331 (mmm) REVERT: E 589 PHE cc_start: 0.6184 (m-10) cc_final: 0.5615 (m-80) REVERT: E 732 ASP cc_start: 0.8414 (t0) cc_final: 0.7802 (m-30) REVERT: F 410 MET cc_start: 0.7354 (mmm) cc_final: 0.7084 (tpp) REVERT: F 582 MET cc_start: 0.5151 (mmm) cc_final: 0.4695 (mmm) REVERT: F 585 PHE cc_start: 0.6008 (m-80) cc_final: 0.5470 (m-80) REVERT: F 623 LEU cc_start: 0.7397 (tt) cc_final: 0.7036 (tt) REVERT: F 646 ARG cc_start: 0.7621 (tpp80) cc_final: 0.7361 (tpp80) REVERT: F 747 MET cc_start: 0.7986 (mmt) cc_final: 0.7648 (mmt) outliers start: 58 outliers final: 47 residues processed: 339 average time/residue: 0.4209 time to fit residues: 222.4547 Evaluate side-chains 334 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 283 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 777 ILE Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 4 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 266 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 318 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN C 343 GLN C 391 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN D 391 ASN E 640 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.172482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135559 restraints weight = 35060.070| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.11 r_work: 0.3524 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27553 Z= 0.204 Angle : 0.661 10.010 37169 Z= 0.318 Chirality : 0.044 0.184 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.479 178.682 3831 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.11 % Allowed : 15.41 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3346 helix: 0.73 (0.12), residues: 1857 sheet: -0.95 (0.24), residues: 399 loop : -0.01 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 807 HIS 0.006 0.001 HIS D 290 PHE 0.023 0.002 PHE E 791 TYR 0.039 0.002 TYR F 635 ARG 0.010 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1320) hydrogen bonds : angle 4.83691 ( 3885) covalent geometry : bond 0.00499 (27553) covalent geometry : angle 0.66066 (37169) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 287 time to evaluate : 2.980 Fit side-chains revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7952 (t0) cc_final: 0.7516 (m-30) REVERT: A 534 ARG cc_start: 0.7783 (ptp-110) cc_final: 0.7448 (ptp-110) REVERT: A 582 MET cc_start: 0.5112 (ppp) cc_final: 0.3985 (mpp) REVERT: A 644 ASP cc_start: 0.4323 (m-30) cc_final: 0.4005 (m-30) REVERT: A 734 MET cc_start: 0.8495 (ptm) cc_final: 0.8179 (ptp) REVERT: B 171 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7824 (tp) REVERT: B 267 GLU cc_start: 0.8545 (tp30) cc_final: 0.8131 (tt0) REVERT: B 339 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8395 (tt0) REVERT: B 606 GLU cc_start: 0.7833 (pp20) cc_final: 0.7475 (pp20) REVERT: B 774 ARG cc_start: 0.6650 (mmm-85) cc_final: 0.6277 (mtp85) REVERT: B 787 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: C 201 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7649 (mmt) REVERT: C 267 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8252 (tt0) REVERT: C 753 ASP cc_start: 0.7972 (t0) cc_final: 0.7692 (m-30) REVERT: D 695 GLN cc_start: 0.7984 (tp40) cc_final: 0.7263 (tp-100) REVERT: E 339 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8036 (tp30) REVERT: E 510 MET cc_start: 0.7781 (ptm) cc_final: 0.7494 (ptt) REVERT: E 589 PHE cc_start: 0.6290 (m-10) cc_final: 0.5731 (m-80) REVERT: E 732 ASP cc_start: 0.8472 (t0) cc_final: 0.7800 (m-30) REVERT: F 582 MET cc_start: 0.5149 (mmm) cc_final: 0.4746 (mmm) REVERT: F 585 PHE cc_start: 0.6144 (m-80) cc_final: 0.5604 (m-80) REVERT: F 623 LEU cc_start: 0.7392 (tt) cc_final: 0.7051 (tt) REVERT: F 624 PHE cc_start: 0.7911 (m-80) cc_final: 0.7593 (m-80) REVERT: F 646 ARG cc_start: 0.7696 (tpp80) cc_final: 0.7431 (tpp80) REVERT: F 747 MET cc_start: 0.8143 (mmt) cc_final: 0.7748 (mmt) outliers start: 60 outliers final: 45 residues processed: 331 average time/residue: 0.4121 time to fit residues: 211.3373 Evaluate side-chains 316 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 268 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 747 MET Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 777 ILE Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 178 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 291 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 282 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 667 ASN C 343 GLN C 391 ASN C 568 ASN C 651 GLN D 391 ASN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.175811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137524 restraints weight = 35283.695| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.01 r_work: 0.3567 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27553 Z= 0.149 Angle : 0.633 10.730 37169 Z= 0.303 Chirality : 0.043 0.219 4239 Planarity : 0.004 0.070 4820 Dihedral : 7.324 178.028 3831 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.00 % Allowed : 15.87 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3346 helix: 0.82 (0.12), residues: 1854 sheet: -0.99 (0.25), residues: 380 loop : 0.04 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 491 HIS 0.005 0.001 HIS D 290 PHE 0.023 0.001 PHE E 791 TYR 0.040 0.002 TYR F 635 ARG 0.010 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1320) hydrogen bonds : angle 4.73486 ( 3885) covalent geometry : bond 0.00359 (27553) covalent geometry : angle 0.63253 (37169) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16167.88 seconds wall clock time: 282 minutes 56.83 seconds (16976.83 seconds total)