Starting phenix.real_space_refine on Mon Apr 6 23:26:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqz_23492/04_2026/7lqz_23492_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqz_23492/04_2026/7lqz_23492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqz_23492/04_2026/7lqz_23492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqz_23492/04_2026/7lqz_23492.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqz_23492/04_2026/7lqz_23492_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqz_23492/04_2026/7lqz_23492_trim.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.092 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 S 124 5.16 5 Na 1 4.78 5 C 15024 2.51 5 N 3476 2.21 5 O 4108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22765 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "B" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "C" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "D" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "A" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 442 Unusual residues: {' NA': 1, '6EU': 1, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "B" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 441 Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 441 Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 441 Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Time building chain proxies: 5.05, per 1000 atoms: 0.22 Number of scatterers: 22765 At special positions: 0 Unit cell: (137.75, 137.75, 124.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 32 15.00 Na 1 11.00 O 4108 8.00 N 3476 7.00 C 15024 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: 1.67 Conformation dependent library (CDL) restraints added in 994.5 milliseconds 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4928 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 59.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 158 through 166 removed outlier: 3.512A pdb=" N LEU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.621A pdb=" N GLN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.693A pdb=" N ASN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.211A pdb=" N LYS A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 215 through 224 removed outlier: 3.505A pdb=" N VAL A 219 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 262 through 269 removed outlier: 3.667A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.868A pdb=" N VAL A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 322 removed outlier: 3.597A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 314 " --> pdb=" O MET A 310 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.672A pdb=" N GLU A 329 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 330 " --> pdb=" O LEU A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.562A pdb=" N ALA A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.772A pdb=" N ALA A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.807A pdb=" N LEU A 415 " --> pdb=" O HIS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.608A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 removed outlier: 3.549A pdb=" N ASP A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 456 removed outlier: 3.501A pdb=" N ILE A 448 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 499 removed outlier: 3.618A pdb=" N PHE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.962A pdb=" N PHE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 529 " --> pdb=" O MET A 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 533 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.752A pdb=" N TYR A 539 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.812A pdb=" N THR A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 557 Processing helix chain 'A' and resid 561 through 574 removed outlier: 4.118A pdb=" N TYR A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 568 " --> pdb=" O MET A 564 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 570 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 571 " --> pdb=" O TYR A 567 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 601 removed outlier: 3.971A pdb=" N PHE A 584 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 595 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 598 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 removed outlier: 3.609A pdb=" N THR A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.524A pdb=" N ILE A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 673 Processing helix chain 'A' and resid 675 through 713 removed outlier: 3.754A pdb=" N ILE A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 removed outlier: 3.511A pdb=" N ARG A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 125 Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 158 through 166 removed outlier: 3.512A pdb=" N LEU B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.620A pdb=" N GLN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.693A pdb=" N ASN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 4.211A pdb=" N LYS B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 215 through 224 removed outlier: 3.504A pdb=" N VAL B 219 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.666A pdb=" N LYS B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.868A pdb=" N VAL B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 322 removed outlier: 3.596A pdb=" N LYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 314 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.672A pdb=" N GLU B 329 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 330 " --> pdb=" O LEU B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 330' Processing helix chain 'B' and resid 337 through 345 removed outlier: 3.562A pdb=" N ALA B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.773A pdb=" N ALA B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.806A pdb=" N LEU B 415 " --> pdb=" O HIS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.609A pdb=" N ARG B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.549A pdb=" N ASP B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 456 removed outlier: 3.501A pdb=" N ILE B 448 " --> pdb=" O CYS B 444 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 499 removed outlier: 3.618A pdb=" N PHE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 499 " --> pdb=" O ILE B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 512 through 533 removed outlier: 3.963A pdb=" N PHE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 529 " --> pdb=" O MET B 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 533 " --> pdb=" O VAL B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.752A pdb=" N TYR B 539 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 540 " --> pdb=" O LYS B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 553 removed outlier: 3.810A pdb=" N THR B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 557 Processing helix chain 'B' and resid 561 through 574 removed outlier: 4.117A pdb=" N TYR B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 570 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 571 " --> pdb=" O TYR B 567 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 601 removed outlier: 3.971A pdb=" N PHE B 584 " --> pdb=" O CYS B 580 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 removed outlier: 3.609A pdb=" N THR B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.524A pdb=" N ILE B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 673 Processing helix chain 'B' and resid 675 through 713 removed outlier: 3.754A pdb=" N ILE B 681 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 682 " --> pdb=" O ASN B 678 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 694 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN B 697 " --> pdb=" O GLN B 693 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 719 removed outlier: 3.510A pdb=" N ARG B 719 " --> pdb=" O LEU B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 125 Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 158 through 166 removed outlier: 3.512A pdb=" N LEU C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.621A pdb=" N GLN C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.692A pdb=" N ASN C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 4.210A pdb=" N LYS C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 215 through 224 removed outlier: 3.504A pdb=" N VAL C 219 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 262 through 269 removed outlier: 3.666A pdb=" N LYS C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.869A pdb=" N VAL C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 322 removed outlier: 3.596A pdb=" N LYS C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 308 " --> pdb=" O THR C 304 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 314 " --> pdb=" O MET C 310 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 315 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 330 removed outlier: 3.671A pdb=" N GLU C 329 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 330 " --> pdb=" O LEU C 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 326 through 330' Processing helix chain 'C' and resid 337 through 345 removed outlier: 3.563A pdb=" N ALA C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.772A pdb=" N ALA C 402 " --> pdb=" O LEU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 removed outlier: 3.806A pdb=" N LEU C 415 " --> pdb=" O HIS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.609A pdb=" N ARG C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 429 removed outlier: 3.549A pdb=" N ASP C 429 " --> pdb=" O GLN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 456 removed outlier: 3.739A pdb=" N VAL C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 499 removed outlier: 3.617A pdb=" N PHE C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 497 " --> pdb=" O ARG C 493 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 499 " --> pdb=" O ILE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 509 Processing helix chain 'C' and resid 512 through 533 removed outlier: 3.963A pdb=" N PHE C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C 522 " --> pdb=" O PHE C 518 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 529 " --> pdb=" O MET C 525 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 533 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 541 removed outlier: 3.752A pdb=" N TYR C 539 " --> pdb=" O ARG C 536 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 540 " --> pdb=" O LYS C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 553 removed outlier: 3.811A pdb=" N THR C 552 " --> pdb=" O ALA C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 557 Processing helix chain 'C' and resid 561 through 574 removed outlier: 4.117A pdb=" N TYR C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 568 " --> pdb=" O MET C 564 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C 570 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 601 removed outlier: 3.971A pdb=" N PHE C 584 " --> pdb=" O CYS C 580 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 585 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 598 " --> pdb=" O SER C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 639 removed outlier: 3.609A pdb=" N THR C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 645 removed outlier: 3.524A pdb=" N ILE C 644 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 673 Processing helix chain 'C' and resid 675 through 713 removed outlier: 3.754A pdb=" N ILE C 681 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 682 " --> pdb=" O ASN C 678 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN C 693 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU C 694 " --> pdb=" O LYS C 690 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS C 696 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN C 697 " --> pdb=" O GLN C 693 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 700 " --> pdb=" O LYS C 696 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 701 " --> pdb=" O ASN C 697 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR C 706 " --> pdb=" O GLN C 702 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 707 " --> pdb=" O ARG C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 719 removed outlier: 3.510A pdb=" N ARG C 719 " --> pdb=" O LEU C 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 Processing helix chain 'D' and resid 133 through 141 Processing helix chain 'D' and resid 158 through 166 removed outlier: 3.512A pdb=" N LEU D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 185 removed outlier: 3.622A pdb=" N GLN D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.693A pdb=" N ASN D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 4.211A pdb=" N LYS D 202 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 215 through 224 removed outlier: 3.504A pdb=" N VAL D 219 " --> pdb=" O ASN D 215 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU D 224 " --> pdb=" O THR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 262 through 269 removed outlier: 3.666A pdb=" N LYS D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.868A pdb=" N VAL D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 322 removed outlier: 3.598A pdb=" N LYS D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 308 " --> pdb=" O THR D 304 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 314 " --> pdb=" O MET D 310 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 316 " --> pdb=" O ASN D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.671A pdb=" N GLU D 329 " --> pdb=" O LYS D 326 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 330 " --> pdb=" O LEU D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 330' Processing helix chain 'D' and resid 337 through 345 removed outlier: 3.563A pdb=" N ALA D 342 " --> pdb=" O PRO D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 356 Processing helix chain 'D' and resid 396 through 403 removed outlier: 3.772A pdb=" N ALA D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 416 removed outlier: 3.806A pdb=" N LEU D 415 " --> pdb=" O HIS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 removed outlier: 3.608A pdb=" N ARG D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 429 removed outlier: 3.549A pdb=" N ASP D 429 " --> pdb=" O GLN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 456 removed outlier: 3.501A pdb=" N ILE D 448 " --> pdb=" O CYS D 444 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 499 removed outlier: 3.619A pdb=" N PHE D 475 " --> pdb=" O VAL D 471 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 499 " --> pdb=" O ILE D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 Processing helix chain 'D' and resid 512 through 533 removed outlier: 3.963A pdb=" N PHE D 518 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 522 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 529 " --> pdb=" O MET D 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 533 " --> pdb=" O VAL D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 541 removed outlier: 3.752A pdb=" N TYR D 539 " --> pdb=" O ARG D 536 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 540 " --> pdb=" O LYS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 553 removed outlier: 3.812A pdb=" N THR D 552 " --> pdb=" O ALA D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 557 Processing helix chain 'D' and resid 561 through 574 removed outlier: 4.118A pdb=" N TYR D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 568 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET D 570 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 571 " --> pdb=" O TYR D 567 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 601 removed outlier: 3.971A pdb=" N PHE D 584 " --> pdb=" O CYS D 580 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 585 " --> pdb=" O ARG D 581 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL D 598 " --> pdb=" O SER D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 639 removed outlier: 3.609A pdb=" N THR D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 645 removed outlier: 3.524A pdb=" N ILE D 644 " --> pdb=" O PHE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 673 Processing helix chain 'D' and resid 675 through 713 removed outlier: 3.754A pdb=" N ILE D 681 " --> pdb=" O LEU D 677 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 682 " --> pdb=" O ASN D 678 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN D 689 " --> pdb=" O GLY D 685 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN D 693 " --> pdb=" O ASN D 689 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU D 694 " --> pdb=" O LYS D 690 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN D 697 " --> pdb=" O GLN D 693 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 701 " --> pdb=" O ASN D 697 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR D 706 " --> pdb=" O GLN D 702 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 707 " --> pdb=" O ARG D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 719 removed outlier: 3.510A pdb=" N ARG D 719 " --> pdb=" O LEU D 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 376 removed outlier: 7.211A pdb=" N SER A 381 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 375 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 382 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 371 through 376 removed outlier: 7.211A pdb=" N SER B 381 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 375 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 382 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 371 through 376 removed outlier: 7.212A pdb=" N SER C 381 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA C 375 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 382 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 371 through 376 removed outlier: 7.211A pdb=" N SER D 381 " --> pdb=" O GLU D 373 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA D 375 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 382 " --> pdb=" O VAL D 746 " (cutoff:3.500A) 829 hydrogen bonds defined for protein. 2391 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: 3.26 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3428 1.31 - 1.44: 6289 1.44 - 1.56: 13215 1.56 - 1.69: 88 1.69 - 1.82: 200 Bond restraints: 23220 Sorted by residual: bond pdb=" CAV 6EU A 902 " pdb=" CBB 6EU A 902 " ideal model delta sigma weight residual 1.330 1.523 -0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" CAV 6EU B 903 " pdb=" CBB 6EU B 903 " ideal model delta sigma weight residual 1.330 1.523 -0.193 2.00e-02 2.50e+03 9.34e+01 bond pdb=" CAV 6EU C 903 " pdb=" CBB 6EU C 903 " ideal model delta sigma weight residual 1.330 1.523 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" CAV 6EU D 906 " pdb=" CBB 6EU D 906 " ideal model delta sigma weight residual 1.330 1.522 -0.192 2.00e-02 2.50e+03 9.25e+01 bond pdb=" CAR 6EU C 903 " pdb=" CAZ 6EU C 903 " ideal model delta sigma weight residual 1.538 1.372 0.166 2.00e-02 2.50e+03 6.91e+01 ... (remaining 23215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 29552 2.88 - 5.76: 1190 5.76 - 8.65: 248 8.65 - 11.53: 130 11.53 - 14.41: 56 Bond angle restraints: 31176 Sorted by residual: angle pdb=" N ILE D 575 " pdb=" CA ILE D 575 " pdb=" C ILE D 575 " ideal model delta sigma weight residual 113.20 104.22 8.98 9.60e-01 1.09e+00 8.76e+01 angle pdb=" N ILE C 575 " pdb=" CA ILE C 575 " pdb=" C ILE C 575 " ideal model delta sigma weight residual 113.20 104.22 8.98 9.60e-01 1.09e+00 8.74e+01 angle pdb=" N ILE B 575 " pdb=" CA ILE B 575 " pdb=" C ILE B 575 " ideal model delta sigma weight residual 113.20 104.23 8.97 9.60e-01 1.09e+00 8.73e+01 angle pdb=" N ILE A 575 " pdb=" CA ILE A 575 " pdb=" C ILE A 575 " ideal model delta sigma weight residual 113.20 104.24 8.96 9.60e-01 1.09e+00 8.71e+01 angle pdb=" C ARG D 430 " pdb=" N PHE D 431 " pdb=" CA PHE D 431 " ideal model delta sigma weight residual 121.54 133.92 -12.38 1.91e+00 2.74e-01 4.20e+01 ... (remaining 31171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 13611 33.32 - 66.65: 678 66.65 - 99.97: 106 99.97 - 133.30: 24 133.30 - 166.62: 25 Dihedral angle restraints: 14444 sinusoidal: 6788 harmonic: 7656 Sorted by residual: dihedral pdb=" CA LEU D 462 " pdb=" C LEU D 462 " pdb=" N PRO D 463 " pdb=" CA PRO D 463 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LEU B 462 " pdb=" C LEU B 462 " pdb=" N PRO B 463 " pdb=" CA PRO B 463 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LEU C 462 " pdb=" C LEU C 462 " pdb=" N PRO C 463 " pdb=" CA PRO C 463 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 14441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2906 0.079 - 0.158: 356 0.158 - 0.237: 46 0.237 - 0.316: 24 0.316 - 0.395: 8 Chirality restraints: 3340 Sorted by residual: chirality pdb=" CAR 6EU B 903 " pdb=" CAO 6EU B 903 " pdb=" CAU 6EU B 903 " pdb=" CAZ 6EU B 903 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CAR 6EU D 906 " pdb=" CAO 6EU D 906 " pdb=" CAU 6EU D 906 " pdb=" CAZ 6EU D 906 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CAR 6EU C 903 " pdb=" CAO 6EU C 903 " pdb=" CAU 6EU C 903 " pdb=" CAZ 6EU C 903 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 3337 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 431 " 0.012 2.00e-02 2.50e+03 1.74e-02 5.33e+00 pdb=" CG PHE C 431 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 431 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 431 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 431 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 431 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 431 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 431 " 0.012 2.00e-02 2.50e+03 1.74e-02 5.27e+00 pdb=" CG PHE B 431 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 431 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 431 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 431 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 431 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 431 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 431 " -0.013 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE A 431 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 431 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 431 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 431 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 431 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 431 " 0.001 2.00e-02 2.50e+03 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3671 2.75 - 3.29: 20329 3.29 - 3.82: 34221 3.82 - 4.36: 43259 4.36 - 4.90: 73751 Nonbonded interactions: 175231 Sorted by model distance: nonbonded pdb=" O PRO B 765 " pdb=" OH TYR C 201 " model vdw 2.211 3.040 nonbonded pdb=" O PRO C 765 " pdb=" OH TYR D 201 " model vdw 2.256 3.040 nonbonded pdb=" O VAL D 400 " pdb=" OG SER D 404 " model vdw 2.276 3.040 nonbonded pdb=" O VAL A 400 " pdb=" OG SER A 404 " model vdw 2.276 3.040 nonbonded pdb=" O VAL B 400 " pdb=" OG SER B 404 " model vdw 2.276 3.040 ... (remaining 175226 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 111 through 901 or (resid 904 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P o \ r name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216 or name C217 or name C218 or name C310 or name C311)) or resid 905 or \ resid 907 through 908 or (resid 909 and (name N or name C1 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or nam \ e C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or \ name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 or \ name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or na \ me C218)))) selection = (chain 'B' and (resid 111 through 779 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 904 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 o \ r name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 o \ r name C216 or name C217 or name C218)) or resid 907 through 908 or (resid 909 a \ nd (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P or name C210 or name C211 or name C212 or name C213 or name C214 o \ r name C215 or name C216 or name C217 or name C218)))) selection = (chain 'C' and (resid 111 through 779 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 904 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 o \ r name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 o \ r name C216 or name C217 or name C218)) or resid 907 through 908 or (resid 909 a \ nd (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P or name C210 or name C211 or name C212 or name C213 or name C214 o \ r name C215 or name C216 or name C217 or name C218)))) selection = (chain 'D' and (resid 111 through 779 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or resid 904 through 905 or resid 907 through 909)) } 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=0.45 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: 1.700 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.950 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 : 0.013 0.193 23220 Z= 0.627 Angle : 1.554 14.412 31176 Z= 0.726 Chirality : 0.062 0.395 3340 Planarity : 0.007 0.053 3756 Dihedral : 20.374 166.620 9516 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.35 % Allowed : 6.98 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.71 (0.11), residues: 2588 helix: -4.44 (0.05), residues: 1472 sheet: -3.92 (0.40), residues: 84 loop : -2.42 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 703 TYR 0.025 0.003 TYR A 465 PHE 0.040 0.003 PHE C 431 TRP 0.026 0.004 TRP C 751 HIS 0.010 0.003 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.01347 (23220) covalent geometry : angle 1.55426 (31176) hydrogen bonds : bond 0.32613 ( 829) hydrogen bonds : angle 9.78381 ( 2391) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 349 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.8232 (m-40) cc_final: 0.8031 (m-40) REVERT: A 184 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8341 (tp40) REVERT: A 207 LEU cc_start: 0.7924 (tp) cc_final: 0.7721 (tp) REVERT: A 222 LEU cc_start: 0.8462 (mt) cc_final: 0.7988 (tp) REVERT: A 380 HIS cc_start: 0.6734 (t-90) cc_final: 0.6373 (t-90) REVERT: A 483 SER cc_start: 0.8344 (m) cc_final: 0.7979 (p) REVERT: A 655 TYR cc_start: 0.8722 (p90) cc_final: 0.7977 (p90) REVERT: B 162 LYS cc_start: 0.5915 (tptm) cc_final: 0.5604 (tttp) REVERT: B 222 LEU cc_start: 0.8479 (mt) cc_final: 0.8047 (tp) REVERT: B 380 HIS cc_start: 0.6810 (t-90) cc_final: 0.6343 (t-90) REVERT: B 418 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7061 (tp30) REVERT: B 483 SER cc_start: 0.8383 (m) cc_final: 0.8023 (p) REVERT: C 115 ASP cc_start: 0.8096 (p0) cc_final: 0.7873 (p0) REVERT: C 166 ASN cc_start: 0.8169 (m-40) cc_final: 0.7935 (m-40) REVERT: C 168 HIS cc_start: 0.7109 (m170) cc_final: 0.6721 (m170) REVERT: C 169 ASN cc_start: 0.8097 (t160) cc_final: 0.7867 (t0) REVERT: C 207 LEU cc_start: 0.7804 (tp) cc_final: 0.7594 (tp) REVERT: C 222 LEU cc_start: 0.8436 (mt) cc_final: 0.7939 (tp) REVERT: C 380 HIS cc_start: 0.6666 (t-90) cc_final: 0.6275 (t-90) REVERT: C 483 SER cc_start: 0.8388 (m) cc_final: 0.7929 (p) REVERT: D 162 LYS cc_start: 0.5916 (tptm) cc_final: 0.5655 (tttp) REVERT: D 166 ASN cc_start: 0.7992 (m-40) cc_final: 0.7764 (p0) REVERT: D 380 HIS cc_start: 0.6548 (t-90) cc_final: 0.6105 (t-90) REVERT: D 483 SER cc_start: 0.8189 (m) cc_final: 0.7956 (p) REVERT: D 748 GLU cc_start: 0.6862 (mp0) cc_final: 0.6469 (mp0) outliers start: 8 outliers final: 4 residues processed: 357 average time/residue: 0.1720 time to fit residues: 93.1954 Evaluate side-chains 207 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 258 optimal weight: 20.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 215 ASN A 230 GLN A 261 ASN A 291 HIS A 312 ASN A 366 HIS A 421 ASN A 630 ASN A 750 ASN A 755 ASN A 762 ASN A 767 ASN B 166 ASN B 215 ASN B 225 ASN B 230 GLN B 261 ASN B 291 HIS B 312 ASN B 366 HIS B 421 ASN B 630 ASN B 750 ASN B 755 ASN B 762 ASN B 767 ASN C 166 ASN C 169 ASN C 215 ASN C 225 ASN C 230 GLN C 261 ASN C 291 HIS C 312 ASN C 366 HIS C 421 ASN C 630 ASN C 729 GLN C 750 ASN C 755 ASN C 767 ASN D 166 ASN D 215 ASN D 225 ASN D 230 GLN D 261 ASN D 291 HIS D 312 ASN D 366 HIS D 421 ASN D 630 ASN D 750 ASN D 755 ASN D 762 ASN D 767 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.151724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.108932 restraints weight = 38098.716| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.03 r_work: 0.3343 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23220 Z= 0.121 Angle : 0.599 7.874 31176 Z= 0.318 Chirality : 0.039 0.165 3340 Planarity : 0.005 0.041 3756 Dihedral : 21.420 159.498 4524 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.95 % Allowed : 9.01 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.14), residues: 2588 helix: -2.29 (0.10), residues: 1512 sheet: -3.88 (0.39), residues: 84 loop : -1.95 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 411 TYR 0.015 0.001 TYR A 673 PHE 0.020 0.002 PHE D 191 TRP 0.010 0.001 TRP C 551 HIS 0.002 0.001 HIS D 208 Details of bonding type rmsd covalent geometry : bond 0.00252 (23220) covalent geometry : angle 0.59927 (31176) hydrogen bonds : bond 0.04731 ( 829) hydrogen bonds : angle 4.16422 ( 2391) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.6088 (tptm) cc_final: 0.5794 (tttp) REVERT: A 166 ASN cc_start: 0.7995 (m110) cc_final: 0.7624 (m-40) REVERT: A 169 ASN cc_start: 0.7681 (t0) cc_final: 0.7419 (t0) REVERT: A 718 MET cc_start: 0.6579 (mtp) cc_final: 0.6319 (mtm) REVERT: B 162 LYS cc_start: 0.6126 (tptm) cc_final: 0.5809 (tttp) REVERT: B 169 ASN cc_start: 0.7549 (t0) cc_final: 0.7295 (t0) REVERT: B 426 ASP cc_start: 0.8031 (m-30) cc_final: 0.7818 (t0) REVERT: B 673 TYR cc_start: 0.8985 (t80) cc_final: 0.8750 (t80) REVERT: C 166 ASN cc_start: 0.8008 (m110) cc_final: 0.7444 (m-40) REVERT: C 168 HIS cc_start: 0.6760 (m170) cc_final: 0.6492 (m170) REVERT: C 169 ASN cc_start: 0.8256 (t0) cc_final: 0.7984 (t0) REVERT: C 193 ASN cc_start: 0.7762 (m-40) cc_final: 0.7414 (m-40) REVERT: C 207 LEU cc_start: 0.7471 (tp) cc_final: 0.7227 (tp) REVERT: C 380 HIS cc_start: 0.6767 (t-90) cc_final: 0.6372 (t70) REVERT: C 505 MET cc_start: 0.6756 (tpt) cc_final: 0.6448 (ttt) REVERT: D 162 LYS cc_start: 0.6166 (tptm) cc_final: 0.5913 (tttp) REVERT: D 166 ASN cc_start: 0.7801 (m110) cc_final: 0.7435 (m-40) REVERT: D 169 ASN cc_start: 0.7571 (t0) cc_final: 0.7352 (t0) REVERT: D 184 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8141 (tp40) REVERT: D 673 TYR cc_start: 0.8990 (t80) cc_final: 0.8774 (t80) REVERT: D 686 GLU cc_start: 0.8465 (tt0) cc_final: 0.8001 (tm-30) outliers start: 45 outliers final: 22 residues processed: 275 average time/residue: 0.1572 time to fit residues: 68.2430 Evaluate side-chains 210 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 112 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN B 166 ASN B 262 GLN ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN C 767 ASN D 262 GLN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.147767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.101751 restraints weight = 38179.681| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.83 r_work: 0.3317 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23220 Z= 0.153 Angle : 0.581 6.643 31176 Z= 0.304 Chirality : 0.040 0.154 3340 Planarity : 0.004 0.038 3756 Dihedral : 19.957 151.783 4524 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.43 % Allowed : 10.66 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.16), residues: 2588 helix: -0.83 (0.13), residues: 1492 sheet: -3.28 (0.53), residues: 76 loop : -1.82 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 723 TYR 0.012 0.001 TYR D 353 PHE 0.021 0.002 PHE C 431 TRP 0.010 0.001 TRP D 551 HIS 0.004 0.001 HIS D 208 Details of bonding type rmsd covalent geometry : bond 0.00358 (23220) covalent geometry : angle 0.58066 (31176) hydrogen bonds : bond 0.04506 ( 829) hydrogen bonds : angle 3.89851 ( 2391) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.7924 (tp) cc_final: 0.7713 (mt) REVERT: A 162 LYS cc_start: 0.6103 (tptm) cc_final: 0.5815 (tttp) REVERT: A 166 ASN cc_start: 0.8003 (m110) cc_final: 0.7712 (m-40) REVERT: A 169 ASN cc_start: 0.7830 (t0) cc_final: 0.7407 (t0) REVERT: A 171 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7601 (pp30) REVERT: A 193 ASN cc_start: 0.7764 (m-40) cc_final: 0.6757 (t0) REVERT: A 422 ARG cc_start: 0.8736 (mtt-85) cc_final: 0.8025 (tpt-90) REVERT: A 431 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8106 (p90) REVERT: A 505 MET cc_start: 0.6831 (tpt) cc_final: 0.6574 (ttt) REVERT: B 160 LEU cc_start: 0.7786 (tp) cc_final: 0.7560 (mt) REVERT: B 162 LYS cc_start: 0.6225 (tptm) cc_final: 0.5982 (tttp) REVERT: B 169 ASN cc_start: 0.7786 (t0) cc_final: 0.7492 (t0) REVERT: B 193 ASN cc_start: 0.7785 (m-40) cc_final: 0.6805 (t0) REVERT: B 422 ARG cc_start: 0.8678 (mtt-85) cc_final: 0.7961 (tpt-90) REVERT: B 426 ASP cc_start: 0.8030 (m-30) cc_final: 0.7572 (t0) REVERT: B 431 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8190 (p90) REVERT: B 505 MET cc_start: 0.6842 (tpt) cc_final: 0.6582 (ttt) REVERT: C 162 LYS cc_start: 0.5871 (tptt) cc_final: 0.5077 (tttp) REVERT: C 168 HIS cc_start: 0.6965 (m170) cc_final: 0.6686 (m170) REVERT: C 169 ASN cc_start: 0.8293 (t0) cc_final: 0.8055 (t0) REVERT: C 184 GLN cc_start: 0.8922 (tp40) cc_final: 0.8719 (tp40) REVERT: C 193 ASN cc_start: 0.7746 (m-40) cc_final: 0.7404 (m-40) REVERT: C 380 HIS cc_start: 0.6800 (t-90) cc_final: 0.6422 (t-90) REVERT: C 431 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8041 (p90) REVERT: C 505 MET cc_start: 0.6938 (tpt) cc_final: 0.6664 (ttt) REVERT: D 166 ASN cc_start: 0.7938 (m110) cc_final: 0.7599 (m110) REVERT: D 169 ASN cc_start: 0.7826 (t0) cc_final: 0.7554 (t0) REVERT: D 184 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8214 (tp40) REVERT: D 262 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6428 (mp-120) REVERT: D 422 ARG cc_start: 0.8714 (mtt-85) cc_final: 0.8071 (tpt-90) REVERT: D 431 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8158 (p90) REVERT: D 686 GLU cc_start: 0.8441 (tt0) cc_final: 0.8214 (tm-30) outliers start: 56 outliers final: 28 residues processed: 250 average time/residue: 0.1545 time to fit residues: 62.7148 Evaluate side-chains 222 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 212 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 ASN A 767 ASN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN C 166 ASN C 767 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 757 ASN D 767 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.148166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103674 restraints weight = 37493.458| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.73 r_work: 0.3337 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23220 Z= 0.126 Angle : 0.529 6.574 31176 Z= 0.279 Chirality : 0.038 0.150 3340 Planarity : 0.003 0.036 3756 Dihedral : 18.993 146.044 4524 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.82 % Allowed : 11.53 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.16), residues: 2588 helix: -0.15 (0.14), residues: 1496 sheet: -2.88 (0.56), residues: 76 loop : -1.63 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 214 TYR 0.010 0.001 TYR D 353 PHE 0.030 0.001 PHE D 306 TRP 0.007 0.001 TRP D 551 HIS 0.002 0.001 HIS D 208 Details of bonding type rmsd covalent geometry : bond 0.00291 (23220) covalent geometry : angle 0.52903 (31176) hydrogen bonds : bond 0.03787 ( 829) hydrogen bonds : angle 3.70959 ( 2391) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 204 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.7925 (tp) cc_final: 0.7715 (mt) REVERT: A 162 LYS cc_start: 0.6089 (tptm) cc_final: 0.5810 (tttp) REVERT: A 166 ASN cc_start: 0.8012 (m110) cc_final: 0.7721 (m-40) REVERT: A 168 HIS cc_start: 0.6668 (m170) cc_final: 0.6330 (m170) REVERT: A 169 ASN cc_start: 0.7980 (t0) cc_final: 0.7595 (t0) REVERT: A 171 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7639 (pp30) REVERT: A 184 GLN cc_start: 0.8953 (tp40) cc_final: 0.8693 (tp40) REVERT: A 193 ASN cc_start: 0.7854 (m-40) cc_final: 0.7477 (m110) REVERT: A 422 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8090 (tpt-90) REVERT: A 431 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8106 (p90) REVERT: A 505 MET cc_start: 0.6823 (tpt) cc_final: 0.6589 (ttt) REVERT: B 160 LEU cc_start: 0.7812 (tp) cc_final: 0.7568 (mt) REVERT: B 162 LYS cc_start: 0.6114 (tptm) cc_final: 0.5857 (tttp) REVERT: B 169 ASN cc_start: 0.7863 (t0) cc_final: 0.7564 (t0) REVERT: B 171 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7575 (pp30) REVERT: B 193 ASN cc_start: 0.7875 (m-40) cc_final: 0.6809 (t0) REVERT: B 422 ARG cc_start: 0.8666 (mtt-85) cc_final: 0.7987 (tpt-90) REVERT: B 426 ASP cc_start: 0.8016 (m-30) cc_final: 0.7560 (t0) REVERT: B 431 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8183 (p90) REVERT: B 505 MET cc_start: 0.6809 (tpt) cc_final: 0.6576 (ttt) REVERT: C 168 HIS cc_start: 0.7042 (m170) cc_final: 0.6777 (m170) REVERT: C 169 ASN cc_start: 0.8293 (t0) cc_final: 0.8037 (t0) REVERT: C 193 ASN cc_start: 0.7746 (m-40) cc_final: 0.7312 (m110) REVERT: C 380 HIS cc_start: 0.6771 (t-90) cc_final: 0.6451 (t-90) REVERT: C 431 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8078 (p90) REVERT: C 505 MET cc_start: 0.6885 (tpt) cc_final: 0.6628 (ttt) REVERT: D 160 LEU cc_start: 0.7808 (tp) cc_final: 0.7592 (mt) REVERT: D 166 ASN cc_start: 0.7949 (m110) cc_final: 0.7572 (m-40) REVERT: D 169 ASN cc_start: 0.7822 (t0) cc_final: 0.7605 (t0) REVERT: D 184 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8257 (tp40) REVERT: D 193 ASN cc_start: 0.7854 (m-40) cc_final: 0.6935 (t0) REVERT: D 262 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.5942 (mp10) REVERT: D 422 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8035 (tpt-90) REVERT: D 431 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8173 (p90) outliers start: 65 outliers final: 32 residues processed: 262 average time/residue: 0.1503 time to fit residues: 63.8875 Evaluate side-chains 233 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 198 optimal weight: 40.0000 chunk 224 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 114 optimal weight: 0.0470 chunk 120 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN B 757 ASN B 767 ASN C 166 ASN D 767 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.150812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.108299 restraints weight = 37107.147| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.03 r_work: 0.3349 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23220 Z= 0.096 Angle : 0.511 7.940 31176 Z= 0.267 Chirality : 0.038 0.168 3340 Planarity : 0.003 0.037 3756 Dihedral : 17.969 138.122 4524 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.73 % Allowed : 12.52 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2588 helix: 0.33 (0.14), residues: 1496 sheet: -2.90 (0.52), residues: 64 loop : -1.58 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 411 TYR 0.009 0.001 TYR C 353 PHE 0.024 0.001 PHE D 306 TRP 0.009 0.001 TRP B 374 HIS 0.003 0.000 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00205 (23220) covalent geometry : angle 0.51054 (31176) hydrogen bonds : bond 0.03193 ( 829) hydrogen bonds : angle 3.43219 ( 2391) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.7884 (tp) cc_final: 0.7659 (mt) REVERT: A 166 ASN cc_start: 0.7905 (m110) cc_final: 0.7227 (m-40) REVERT: A 169 ASN cc_start: 0.7999 (t0) cc_final: 0.7673 (t0) REVERT: A 184 GLN cc_start: 0.8992 (tp40) cc_final: 0.8783 (tp40) REVERT: A 193 ASN cc_start: 0.7778 (m-40) cc_final: 0.7397 (m110) REVERT: A 422 ARG cc_start: 0.8732 (mtt-85) cc_final: 0.8051 (tpt-90) REVERT: A 431 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8077 (p90) REVERT: A 505 MET cc_start: 0.6712 (tpt) cc_final: 0.6473 (ttt) REVERT: B 160 LEU cc_start: 0.7740 (tp) cc_final: 0.7530 (mt) REVERT: B 162 LYS cc_start: 0.6122 (tptm) cc_final: 0.5842 (tttp) REVERT: B 169 ASN cc_start: 0.7897 (t0) cc_final: 0.7600 (t0) REVERT: B 193 ASN cc_start: 0.7883 (m-40) cc_final: 0.6849 (t0) REVERT: B 422 ARG cc_start: 0.8686 (mtt-85) cc_final: 0.7940 (tpt-90) REVERT: B 426 ASP cc_start: 0.7883 (m-30) cc_final: 0.7223 (t0) REVERT: B 431 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8026 (p90) REVERT: B 505 MET cc_start: 0.6672 (tpt) cc_final: 0.6380 (ttt) REVERT: C 168 HIS cc_start: 0.7002 (m170) cc_final: 0.6711 (m170) REVERT: C 169 ASN cc_start: 0.8257 (t0) cc_final: 0.7993 (t0) REVERT: C 193 ASN cc_start: 0.7689 (m-40) cc_final: 0.7302 (m-40) REVERT: C 380 HIS cc_start: 0.6678 (t-90) cc_final: 0.6353 (t-90) REVERT: C 431 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8007 (p90) REVERT: C 505 MET cc_start: 0.6773 (tpt) cc_final: 0.6504 (ttt) REVERT: D 160 LEU cc_start: 0.7742 (tp) cc_final: 0.7502 (mt) REVERT: D 166 ASN cc_start: 0.7886 (m110) cc_final: 0.7517 (m-40) REVERT: D 169 ASN cc_start: 0.7860 (t0) cc_final: 0.7552 (t0) REVERT: D 171 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7212 (pp30) REVERT: D 193 ASN cc_start: 0.7859 (m-40) cc_final: 0.7000 (t0) REVERT: D 321 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7833 (mm) REVERT: D 410 ASN cc_start: 0.6990 (m110) cc_final: 0.6183 (t0) REVERT: D 422 ARG cc_start: 0.8733 (mtt-85) cc_final: 0.8076 (tpt-90) REVERT: D 431 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8025 (p90) outliers start: 63 outliers final: 30 residues processed: 258 average time/residue: 0.1432 time to fit residues: 60.6448 Evaluate side-chains 221 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 128 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 0.0570 chunk 95 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN B 767 ASN D 262 GLN D 767 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.147747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.102428 restraints weight = 37549.052| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.73 r_work: 0.3313 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23220 Z= 0.142 Angle : 0.546 6.505 31176 Z= 0.282 Chirality : 0.039 0.143 3340 Planarity : 0.003 0.039 3756 Dihedral : 17.909 134.983 4524 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.99 % Allowed : 13.04 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2588 helix: 0.43 (0.14), residues: 1496 sheet: -2.87 (0.56), residues: 76 loop : -1.52 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 411 TYR 0.010 0.001 TYR B 513 PHE 0.023 0.002 PHE D 306 TRP 0.006 0.001 TRP D 754 HIS 0.002 0.001 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00337 (23220) covalent geometry : angle 0.54644 (31176) hydrogen bonds : bond 0.03770 ( 829) hydrogen bonds : angle 3.56774 ( 2391) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.7904 (tp) cc_final: 0.7680 (mt) REVERT: A 166 ASN cc_start: 0.8002 (m110) cc_final: 0.7566 (m-40) REVERT: A 168 HIS cc_start: 0.6511 (m170) cc_final: 0.6165 (m170) REVERT: A 169 ASN cc_start: 0.8032 (t0) cc_final: 0.7629 (t0) REVERT: A 171 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7671 (pp30) REVERT: A 216 MET cc_start: 0.8015 (tpp) cc_final: 0.7716 (tpp) REVERT: A 422 ARG cc_start: 0.8740 (mtt-85) cc_final: 0.8141 (tpt-90) REVERT: A 431 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8180 (p90) REVERT: A 447 MET cc_start: 0.8633 (mmt) cc_final: 0.8119 (mmt) REVERT: A 505 MET cc_start: 0.6906 (tpt) cc_final: 0.6621 (ttt) REVERT: B 160 LEU cc_start: 0.7900 (tp) cc_final: 0.7693 (mt) REVERT: B 169 ASN cc_start: 0.7901 (t0) cc_final: 0.7542 (t0) REVERT: B 171 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7524 (pp30) REVERT: B 193 ASN cc_start: 0.7843 (m-40) cc_final: 0.7479 (m110) REVERT: B 262 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6541 (mp-120) REVERT: B 422 ARG cc_start: 0.8671 (mtt-85) cc_final: 0.7907 (tpt-90) REVERT: B 431 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8101 (p90) REVERT: B 447 MET cc_start: 0.8727 (mmt) cc_final: 0.8526 (mmm) REVERT: B 505 MET cc_start: 0.6824 (tpt) cc_final: 0.6534 (ttt) REVERT: B 718 MET cc_start: 0.5216 (mtm) cc_final: 0.4848 (mtm) REVERT: C 168 HIS cc_start: 0.6942 (m170) cc_final: 0.6682 (m170) REVERT: C 169 ASN cc_start: 0.8291 (t0) cc_final: 0.8019 (t0) REVERT: C 380 HIS cc_start: 0.6788 (t-90) cc_final: 0.6465 (t-90) REVERT: C 431 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8123 (p90) REVERT: C 505 MET cc_start: 0.6953 (tpt) cc_final: 0.6625 (ttt) REVERT: D 166 ASN cc_start: 0.8017 (m110) cc_final: 0.7621 (m110) REVERT: D 169 ASN cc_start: 0.7901 (t0) cc_final: 0.7573 (t0) REVERT: D 171 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7277 (pp30) REVERT: D 193 ASN cc_start: 0.7916 (m-40) cc_final: 0.6946 (t0) REVERT: D 262 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6443 (mp-120) REVERT: D 321 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7891 (mm) REVERT: D 410 ASN cc_start: 0.7119 (m110) cc_final: 0.6406 (t0) REVERT: D 422 ARG cc_start: 0.8719 (mtt-85) cc_final: 0.8081 (tpt-90) REVERT: D 431 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8192 (p90) outliers start: 69 outliers final: 35 residues processed: 257 average time/residue: 0.1467 time to fit residues: 61.9987 Evaluate side-chains 226 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 18 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 96 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 ASN B 262 GLN B 767 ASN C 729 GLN D 767 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.149733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.107515 restraints weight = 37352.422| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.16 r_work: 0.3301 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23220 Z= 0.098 Angle : 0.512 7.559 31176 Z= 0.264 Chirality : 0.037 0.142 3340 Planarity : 0.003 0.038 3756 Dihedral : 17.477 131.745 4524 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.34 % Allowed : 13.73 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.17), residues: 2588 helix: 0.69 (0.14), residues: 1500 sheet: -2.90 (0.51), residues: 64 loop : -1.47 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 411 TYR 0.009 0.001 TYR C 732 PHE 0.025 0.001 PHE D 191 TRP 0.008 0.001 TRP C 754 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00217 (23220) covalent geometry : angle 0.51173 (31176) hydrogen bonds : bond 0.03221 ( 829) hydrogen bonds : angle 3.41129 ( 2391) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5893 (tptt) cc_final: 0.5106 (tttp) REVERT: A 166 ASN cc_start: 0.7929 (m110) cc_final: 0.7699 (m-40) REVERT: A 168 HIS cc_start: 0.6326 (m170) cc_final: 0.5968 (m170) REVERT: A 169 ASN cc_start: 0.8005 (t0) cc_final: 0.7572 (t0) REVERT: A 171 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7622 (pp30) REVERT: A 216 MET cc_start: 0.7993 (tpp) cc_final: 0.7691 (tpp) REVERT: A 422 ARG cc_start: 0.8772 (mtt-85) cc_final: 0.8049 (tpt-90) REVERT: A 431 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8100 (p90) REVERT: A 505 MET cc_start: 0.6835 (tpt) cc_final: 0.6517 (ttt) REVERT: B 160 LEU cc_start: 0.7857 (tp) cc_final: 0.7645 (mt) REVERT: B 169 ASN cc_start: 0.7962 (t0) cc_final: 0.7585 (t0) REVERT: B 171 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7528 (pp30) REVERT: B 193 ASN cc_start: 0.7801 (m-40) cc_final: 0.7419 (m110) REVERT: B 422 ARG cc_start: 0.8703 (mtt-85) cc_final: 0.7940 (tpt-90) REVERT: B 426 ASP cc_start: 0.7902 (m-30) cc_final: 0.7259 (t0) REVERT: B 431 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8088 (p90) REVERT: B 505 MET cc_start: 0.6708 (tpt) cc_final: 0.6403 (ttt) REVERT: B 718 MET cc_start: 0.5352 (OUTLIER) cc_final: 0.4761 (mtm) REVERT: C 168 HIS cc_start: 0.6908 (m170) cc_final: 0.6625 (m170) REVERT: C 169 ASN cc_start: 0.8296 (t0) cc_final: 0.8005 (t0) REVERT: C 193 ASN cc_start: 0.7595 (m-40) cc_final: 0.7188 (m-40) REVERT: C 380 HIS cc_start: 0.6756 (t-90) cc_final: 0.6401 (t-90) REVERT: C 431 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8065 (p90) REVERT: C 505 MET cc_start: 0.6876 (tpt) cc_final: 0.6514 (ttt) REVERT: D 166 ASN cc_start: 0.7951 (m110) cc_final: 0.7557 (m110) REVERT: D 169 ASN cc_start: 0.7945 (t0) cc_final: 0.7620 (t0) REVERT: D 171 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7227 (pp30) REVERT: D 193 ASN cc_start: 0.7837 (m-40) cc_final: 0.6893 (t0) REVERT: D 321 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7872 (mm) REVERT: D 410 ASN cc_start: 0.7069 (m110) cc_final: 0.6399 (t0) REVERT: D 422 ARG cc_start: 0.8716 (mtt-85) cc_final: 0.8001 (tpt-90) REVERT: D 431 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8104 (p90) outliers start: 54 outliers final: 30 residues processed: 244 average time/residue: 0.1471 time to fit residues: 58.9975 Evaluate side-chains 230 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 54 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 133 optimal weight: 40.0000 chunk 7 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 ASN B 262 GLN B 767 ASN D 262 GLN D 757 ASN D 767 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.148080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.105590 restraints weight = 37207.006| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.10 r_work: 0.3276 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23220 Z= 0.128 Angle : 0.536 7.987 31176 Z= 0.275 Chirality : 0.039 0.140 3340 Planarity : 0.003 0.039 3756 Dihedral : 17.350 129.692 4524 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.56 % Allowed : 14.43 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2588 helix: 0.75 (0.14), residues: 1500 sheet: -2.85 (0.56), residues: 76 loop : -1.41 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 411 TYR 0.017 0.001 TYR D 732 PHE 0.022 0.001 PHE D 306 TRP 0.008 0.001 TRP C 754 HIS 0.002 0.000 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00304 (23220) covalent geometry : angle 0.53592 (31176) hydrogen bonds : bond 0.03535 ( 829) hydrogen bonds : angle 3.49538 ( 2391) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.7938 (m110) cc_final: 0.7375 (m-40) REVERT: A 168 HIS cc_start: 0.6349 (m170) cc_final: 0.5968 (m170) REVERT: A 169 ASN cc_start: 0.7995 (t0) cc_final: 0.7562 (t0) REVERT: A 171 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7678 (pp30) REVERT: A 216 MET cc_start: 0.8028 (tpp) cc_final: 0.7734 (tpp) REVERT: A 422 ARG cc_start: 0.8784 (mtt-85) cc_final: 0.8083 (tpt-90) REVERT: A 431 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8152 (p90) REVERT: A 505 MET cc_start: 0.6929 (tpt) cc_final: 0.6557 (ttt) REVERT: B 160 LEU cc_start: 0.7896 (tp) cc_final: 0.7690 (mt) REVERT: B 162 LYS cc_start: 0.5920 (tptt) cc_final: 0.5208 (tttp) REVERT: B 169 ASN cc_start: 0.7963 (t0) cc_final: 0.7578 (t0) REVERT: B 171 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7531 (pp30) REVERT: B 262 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6299 (mp-120) REVERT: B 422 ARG cc_start: 0.8771 (mtt-85) cc_final: 0.7957 (tpt-90) REVERT: B 431 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8108 (p90) REVERT: B 505 MET cc_start: 0.6789 (tpt) cc_final: 0.6478 (ttt) REVERT: B 718 MET cc_start: 0.5365 (OUTLIER) cc_final: 0.4799 (mtm) REVERT: C 168 HIS cc_start: 0.6993 (m170) cc_final: 0.6705 (m170) REVERT: C 169 ASN cc_start: 0.8310 (t0) cc_final: 0.8031 (t0) REVERT: C 193 ASN cc_start: 0.7577 (m-40) cc_final: 0.7096 (m110) REVERT: C 380 HIS cc_start: 0.6768 (t-90) cc_final: 0.6415 (t-90) REVERT: C 431 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8082 (p90) REVERT: C 447 MET cc_start: 0.8665 (tpp) cc_final: 0.8407 (tpt) REVERT: C 505 MET cc_start: 0.6933 (tpt) cc_final: 0.6553 (ttt) REVERT: D 166 ASN cc_start: 0.7973 (m110) cc_final: 0.7574 (m110) REVERT: D 169 ASN cc_start: 0.7953 (t0) cc_final: 0.7653 (t0) REVERT: D 171 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7304 (pp30) REVERT: D 321 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7875 (mm) REVERT: D 410 ASN cc_start: 0.7143 (m110) cc_final: 0.6539 (t0) REVERT: D 422 ARG cc_start: 0.8762 (mtt-85) cc_final: 0.8071 (tpt-90) REVERT: D 431 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8152 (p90) outliers start: 59 outliers final: 42 residues processed: 241 average time/residue: 0.1431 time to fit residues: 56.6969 Evaluate side-chains 234 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 156 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 93 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 ASN B 262 GLN B 757 ASN B 767 ASN D 767 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.149672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107307 restraints weight = 37211.889| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.12 r_work: 0.3301 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23220 Z= 0.102 Angle : 0.514 7.029 31176 Z= 0.267 Chirality : 0.038 0.141 3340 Planarity : 0.003 0.038 3756 Dihedral : 16.946 125.106 4524 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.12 % Allowed : 15.12 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2588 helix: 0.87 (0.14), residues: 1520 sheet: -2.80 (0.55), residues: 76 loop : -1.33 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 723 TYR 0.013 0.001 TYR D 732 PHE 0.022 0.001 PHE C 431 TRP 0.010 0.001 TRP C 754 HIS 0.002 0.000 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00229 (23220) covalent geometry : angle 0.51450 (31176) hydrogen bonds : bond 0.03187 ( 829) hydrogen bonds : angle 3.38311 ( 2391) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5865 (tptt) cc_final: 0.5028 (tttp) REVERT: A 168 HIS cc_start: 0.6367 (m170) cc_final: 0.5976 (m170) REVERT: A 169 ASN cc_start: 0.8015 (t0) cc_final: 0.7565 (t0) REVERT: A 171 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7677 (pp30) REVERT: A 216 MET cc_start: 0.8036 (tpp) cc_final: 0.7731 (tpp) REVERT: A 422 ARG cc_start: 0.8778 (mtt-85) cc_final: 0.8078 (tpt-90) REVERT: A 431 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8079 (p90) REVERT: A 505 MET cc_start: 0.6928 (tpt) cc_final: 0.6555 (ttt) REVERT: B 162 LYS cc_start: 0.5916 (tptt) cc_final: 0.5195 (tttp) REVERT: B 169 ASN cc_start: 0.8013 (t0) cc_final: 0.7624 (t0) REVERT: B 171 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7555 (pp30) REVERT: B 422 ARG cc_start: 0.8783 (mtt-85) cc_final: 0.7955 (tpt-90) REVERT: B 431 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8080 (p90) REVERT: B 505 MET cc_start: 0.6776 (tpt) cc_final: 0.6511 (ttt) REVERT: B 718 MET cc_start: 0.5294 (OUTLIER) cc_final: 0.4730 (mtm) REVERT: C 168 HIS cc_start: 0.6921 (m170) cc_final: 0.6635 (m170) REVERT: C 169 ASN cc_start: 0.8309 (t0) cc_final: 0.8025 (t0) REVERT: C 193 ASN cc_start: 0.7614 (m-40) cc_final: 0.7149 (m110) REVERT: C 380 HIS cc_start: 0.6721 (t-90) cc_final: 0.6377 (t-90) REVERT: C 431 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8035 (p90) REVERT: C 505 MET cc_start: 0.6890 (tpt) cc_final: 0.6512 (ttt) REVERT: D 166 ASN cc_start: 0.7979 (m110) cc_final: 0.7619 (m-40) REVERT: D 321 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7845 (mm) REVERT: D 410 ASN cc_start: 0.7066 (m110) cc_final: 0.6705 (t0) REVERT: D 422 ARG cc_start: 0.8696 (mtt-85) cc_final: 0.8011 (tpt-90) REVERT: D 431 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8064 (p90) outliers start: 49 outliers final: 38 residues processed: 238 average time/residue: 0.1537 time to fit residues: 58.9459 Evaluate side-chains 226 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 212 optimal weight: 0.0170 chunk 128 optimal weight: 7.9990 chunk 67 optimal weight: 0.4980 chunk 225 optimal weight: 3.9990 chunk 223 optimal weight: 0.0020 chunk 87 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 767 ASN B 262 GLN B 767 ASN D 767 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.151029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.109247 restraints weight = 37184.448| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.02 r_work: 0.3334 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23220 Z= 0.100 Angle : 0.536 10.802 31176 Z= 0.279 Chirality : 0.037 0.142 3340 Planarity : 0.003 0.037 3756 Dihedral : 16.504 119.540 4524 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.91 % Allowed : 15.60 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2588 helix: 1.07 (0.14), residues: 1520 sheet: -2.78 (0.55), residues: 76 loop : -1.28 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 411 TYR 0.012 0.001 TYR D 732 PHE 0.027 0.001 PHE B 191 TRP 0.011 0.001 TRP C 754 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00216 (23220) covalent geometry : angle 0.53592 (31176) hydrogen bonds : bond 0.02951 ( 829) hydrogen bonds : angle 3.31340 ( 2391) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5798 (tptt) cc_final: 0.5011 (tttp) REVERT: A 168 HIS cc_start: 0.6522 (m170) cc_final: 0.6246 (m170) REVERT: A 169 ASN cc_start: 0.7984 (t0) cc_final: 0.7617 (t0) REVERT: A 216 MET cc_start: 0.8015 (tpp) cc_final: 0.7704 (tpp) REVERT: A 422 ARG cc_start: 0.8719 (mtt-85) cc_final: 0.8053 (tpt-90) REVERT: A 431 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.7966 (p90) REVERT: A 505 MET cc_start: 0.6859 (tpt) cc_final: 0.6497 (ttt) REVERT: B 162 LYS cc_start: 0.5932 (tptt) cc_final: 0.5192 (tttp) REVERT: B 169 ASN cc_start: 0.8000 (t0) cc_final: 0.7685 (t0) REVERT: B 422 ARG cc_start: 0.8771 (mtt-85) cc_final: 0.7941 (tpt-90) REVERT: B 431 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.7970 (p90) REVERT: B 505 MET cc_start: 0.6790 (tpt) cc_final: 0.6484 (ttt) REVERT: B 718 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4719 (mtm) REVERT: C 168 HIS cc_start: 0.6790 (m170) cc_final: 0.6467 (m170) REVERT: C 169 ASN cc_start: 0.8266 (t0) cc_final: 0.7994 (t0) REVERT: C 193 ASN cc_start: 0.7551 (m-40) cc_final: 0.7140 (m-40) REVERT: C 380 HIS cc_start: 0.6740 (t-90) cc_final: 0.6409 (t70) REVERT: C 431 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.7975 (p90) REVERT: C 505 MET cc_start: 0.6875 (tpt) cc_final: 0.6505 (ttt) REVERT: D 166 ASN cc_start: 0.8013 (m110) cc_final: 0.7623 (m-40) REVERT: D 321 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7825 (mm) REVERT: D 410 ASN cc_start: 0.7036 (m110) cc_final: 0.6329 (t0) REVERT: D 422 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.7962 (tpt-90) REVERT: D 431 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7957 (p90) REVERT: D 748 GLU cc_start: 0.5863 (tm-30) cc_final: 0.5528 (tm-30) outliers start: 44 outliers final: 36 residues processed: 232 average time/residue: 0.1510 time to fit residues: 56.9015 Evaluate side-chains 223 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 115 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 ASN B 767 ASN D 767 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.150524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.107830 restraints weight = 37220.206| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.12 r_work: 0.3314 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 23220 Z= 0.165 Angle : 0.763 59.196 31176 Z= 0.432 Chirality : 0.040 0.388 3340 Planarity : 0.005 0.133 3756 Dihedral : 16.506 119.540 4524 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.08 % Allowed : 15.55 % Favored : 82.37 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2588 helix: 1.04 (0.14), residues: 1520 sheet: -2.77 (0.55), residues: 76 loop : -1.29 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.000 ARG D 723 TYR 0.008 0.001 TYR A 353 PHE 0.022 0.001 PHE C 431 TRP 0.009 0.001 TRP C 754 HIS 0.005 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00359 (23220) covalent geometry : angle 0.76279 (31176) hydrogen bonds : bond 0.03068 ( 829) hydrogen bonds : angle 3.33263 ( 2391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5355.18 seconds wall clock time: 92 minutes 43.34 seconds (5563.34 seconds total)