Starting phenix.real_space_refine on Sat Jul 4 20:09:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqz_23492/07_2026/7lqz_23492_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqz_23492/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lqz_23492/07_2026/7lqz_23492_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqz_23492/07_2026/7lqz_23492_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lqz_23492/07_2026/7lqz_23492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqz_23492/07_2026/7lqz_23492.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 441 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 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: 4.16, per 1000 atoms: 0.18 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: 1.73 Conformation dependent library (CDL) restraints added in 915.0 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: 0.56 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: 3.05 Time building geometry restraints manager: 2.35 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: 1.710 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.850 Find NCS groups from input model: 0.610 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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/Z covalent geometry : bond 0.01347 / 0.63 (23220) covalent geometry : angle 1.55426 / 0.73 (31176) hydrogen bonds : bond 0.32613 / 21.24 ( 829) hydrogen bonds : angle 9.78381 / 6.75 ( 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 : 0.805 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: 0.1699 time to fit residues: 92.8955 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 : 0.832 ------------------------------------------------------------------------------- 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... 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 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: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.151423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108583 restraints weight = 38159.941| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.03 r_work: 0.3335 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23220 Z= 0.123 Angle : 0.605 7.886 31176 Z= 0.321 Chirality : 0.039 0.164 3340 Planarity : 0.005 0.041 3756 Dihedral : 21.505 159.386 4524 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.91 % Allowed : 9.06 % 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: -3.54 (0.13), residues: 2588 helix: -2.33 (0.10), residues: 1512 sheet: -3.87 (0.39), residues: 84 loop : -1.96 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 411 TYR 0.014 0.001 TYR A 673 PHE 0.019 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/Z covalent geometry : bond 0.00256 / 0.12 (23220) covalent geometry : angle 0.60495 / 0.32 (31176) hydrogen bonds : bond 0.05095 / 3.28 ( 829) hydrogen bonds : angle 4.21778 / 2.89 ( 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 280 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.804 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: A 162 LYS cc_start: 0.6080 (tptm) cc_final: 0.5762 (tttp) REVERT: A 166 ASN cc_start: 0.8036 (m110) cc_final: 0.7662 (m-40) REVERT: A 169 ASN cc_start: 0.7665 (t0) cc_final: 0.7409 (t0) REVERT: A 426 ASP cc_start: 0.8044 (m-30) cc_final: 0.7843 (t0) REVERT: A 718 MET cc_start: 0.6544 (mtp) cc_final: 0.6272 (mtm) REVERT: B 162 LYS cc_start: 0.6125 (tptm) cc_final: 0.5809 (tttp) REVERT: B 169 ASN cc_start: 0.7517 (t0) cc_final: 0.7264 (t0) REVERT: B 426 ASP cc_start: 0.8029 (m-30) cc_final: 0.7808 (t0) REVERT: B 673 TYR cc_start: 0.9003 (t80) cc_final: 0.8771 (t80) REVERT: C 166 ASN cc_start: 0.8024 (m110) cc_final: 0.7463 (m-40) REVERT: C 168 HIS cc_start: 0.6760 (m170) cc_final: 0.6490 (m170) REVERT: C 169 ASN cc_start: 0.8261 (t0) cc_final: 0.7991 (t0) REVERT: C 193 ASN cc_start: 0.7769 (m-40) cc_final: 0.6839 (t0) REVERT: C 207 LEU cc_start: 0.7474 (tp) cc_final: 0.7232 (tp) REVERT: C 222 LEU cc_start: 0.8431 (mt) cc_final: 0.8185 (tp) REVERT: C 380 HIS cc_start: 0.6776 (t-90) cc_final: 0.6389 (t70) REVERT: C 505 MET cc_start: 0.6754 (tpt) cc_final: 0.6446 (ttt) REVERT: D 162 LYS cc_start: 0.6160 (tptm) cc_final: 0.5906 (tttp) REVERT: D 166 ASN cc_start: 0.7836 (m110) cc_final: 0.7465 (m-40) REVERT: D 169 ASN cc_start: 0.7530 (t0) cc_final: 0.7302 (t0) REVERT: D 673 TYR cc_start: 0.8998 (t80) cc_final: 0.8787 (t80) REVERT: D 686 GLU cc_start: 0.8459 (tt0) cc_final: 0.8002 (tm-30) outliers start: 44 outliers final: 21 residues processed: 273 average time/residue: 0.1587 time to fit residues: 68.5304 Evaluate side-chains 209 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 187 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 ASN B 262 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.144910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100427 restraints weight = 37538.099| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.69 r_work: 0.3285 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23220 Z= 0.216 Angle : 0.651 7.167 31176 Z= 0.338 Chirality : 0.042 0.153 3340 Planarity : 0.004 0.044 3756 Dihedral : 20.321 153.670 4524 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.69 % Allowed : 11.01 % Favored : 86.31 % 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: -2.31 (0.15), residues: 2588 helix: -1.09 (0.13), residues: 1504 sheet: -3.34 (0.40), residues: 108 loop : -1.83 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 723 TYR 0.013 0.002 TYR D 353 PHE 0.027 0.002 PHE B 450 TRP 0.011 0.002 TRP B 742 HIS 0.004 0.001 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (23220) covalent geometry : angle 0.65074 / 0.34 (31176) hydrogen bonds : bond 0.05025 / 3.24 ( 829) hydrogen bonds : angle 4.12771 / 2.81 ( 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 262 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 162 LYS cc_start: 0.6158 (tptm) cc_final: 0.5865 (tttp) REVERT: A 166 ASN cc_start: 0.7986 (m110) cc_final: 0.7696 (m-40) REVERT: A 168 HIS cc_start: 0.6845 (m170) cc_final: 0.6483 (m170) REVERT: A 169 ASN cc_start: 0.7901 (t0) cc_final: 0.7472 (t0) REVERT: A 171 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7642 (pp30) REVERT: A 193 ASN cc_start: 0.7910 (m-40) cc_final: 0.7532 (m110) REVERT: A 422 ARG cc_start: 0.8661 (mtt-85) cc_final: 0.7989 (tpt-90) REVERT: A 426 ASP cc_start: 0.8071 (m-30) cc_final: 0.7709 (t0) REVERT: A 431 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8240 (p90) REVERT: A 505 MET cc_start: 0.6951 (tpt) cc_final: 0.6644 (ttt) REVERT: B 160 LEU cc_start: 0.7924 (tp) cc_final: 0.7708 (mt) REVERT: B 162 LYS cc_start: 0.6204 (tptm) cc_final: 0.5958 (tttp) REVERT: B 169 ASN cc_start: 0.7828 (t0) cc_final: 0.7536 (t0) REVERT: B 193 ASN cc_start: 0.7963 (m-40) cc_final: 0.7602 (m110) REVERT: B 422 ARG cc_start: 0.8646 (mtt-85) cc_final: 0.7995 (tpt-90) REVERT: B 426 ASP cc_start: 0.8086 (m-30) cc_final: 0.7658 (t0) REVERT: B 431 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8304 (p90) REVERT: B 505 MET cc_start: 0.6943 (tpt) cc_final: 0.6682 (ttt) REVERT: C 166 ASN cc_start: 0.8031 (m110) cc_final: 0.7626 (m-40) REVERT: C 168 HIS cc_start: 0.7089 (m170) cc_final: 0.6846 (m170) REVERT: C 193 ASN cc_start: 0.7745 (m-40) cc_final: 0.7333 (m-40) REVERT: C 207 LEU cc_start: 0.7742 (tp) cc_final: 0.7524 (tp) REVERT: C 222 LEU cc_start: 0.8389 (mt) cc_final: 0.8137 (tp) REVERT: C 380 HIS cc_start: 0.6833 (t-90) cc_final: 0.6568 (t-90) REVERT: C 431 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8199 (p90) REVERT: C 505 MET cc_start: 0.6982 (tpt) cc_final: 0.6677 (ttt) REVERT: D 166 ASN cc_start: 0.7921 (m110) cc_final: 0.7571 (m110) REVERT: D 169 ASN cc_start: 0.7849 (t0) cc_final: 0.7599 (t0) REVERT: D 422 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.8056 (tpt-90) REVERT: D 431 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8184 (p90) REVERT: D 505 MET cc_start: 0.6791 (tpt) cc_final: 0.6571 (ttt) outliers start: 62 outliers final: 35 residues processed: 251 average time/residue: 0.1475 time to fit residues: 60.6282 Evaluate side-chains 221 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 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 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 171 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 177 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 757 ASN A 767 ASN B 166 ASN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN C 767 ASN ** D 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.148482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.104131 restraints weight = 37419.153| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.72 r_work: 0.3345 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23220 Z= 0.110 Angle : 0.528 6.691 31176 Z= 0.278 Chirality : 0.038 0.151 3340 Planarity : 0.003 0.034 3756 Dihedral : 19.139 145.867 4524 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.77 % Allowed : 11.96 % Favored : 85.27 % 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: -1.39 (0.16), residues: 2588 helix: -0.24 (0.14), residues: 1484 sheet: -2.91 (0.57), residues: 76 loop : -1.68 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 282 TYR 0.009 0.001 TYR A 353 PHE 0.029 0.001 PHE D 306 TRP 0.009 0.001 TRP B 374 HIS 0.002 0.000 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (23220) covalent geometry : angle 0.52754 / 0.28 (31176) hydrogen bonds : bond 0.03680 / 2.36 ( 829) hydrogen bonds : angle 3.67969 / 2.50 ( 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 265 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 0.852 Fit side-chains REVERT: A 162 LYS cc_start: 0.6093 (tptm) cc_final: 0.5826 (tttp) REVERT: A 166 ASN cc_start: 0.8054 (m110) cc_final: 0.7765 (m-40) REVERT: A 169 ASN cc_start: 0.7941 (t0) cc_final: 0.7577 (t0) REVERT: A 193 ASN cc_start: 0.7790 (m-40) cc_final: 0.7395 (m110) REVERT: A 422 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.8033 (tpt-90) REVERT: A 426 ASP cc_start: 0.8037 (m-30) cc_final: 0.7602 (t0) REVERT: A 431 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8116 (p90) REVERT: A 505 MET cc_start: 0.6878 (tpt) cc_final: 0.6599 (ttt) REVERT: B 160 LEU cc_start: 0.7905 (tp) cc_final: 0.7688 (mt) REVERT: B 162 LYS cc_start: 0.6165 (tptm) cc_final: 0.5893 (tttp) REVERT: B 169 ASN cc_start: 0.7929 (t0) cc_final: 0.7653 (t0) REVERT: B 193 ASN cc_start: 0.7911 (m-40) cc_final: 0.7532 (m110) REVERT: B 422 ARG cc_start: 0.8665 (mtt-85) cc_final: 0.7965 (tpt-90) REVERT: B 426 ASP cc_start: 0.8033 (m-30) cc_final: 0.7610 (t0) REVERT: B 431 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8121 (p90) REVERT: B 505 MET cc_start: 0.6824 (tpt) cc_final: 0.6565 (ttt) REVERT: C 166 ASN cc_start: 0.8035 (m110) cc_final: 0.7708 (m-40) REVERT: C 168 HIS cc_start: 0.6901 (m170) cc_final: 0.6690 (m170) REVERT: C 169 ASN cc_start: 0.8121 (t0) cc_final: 0.7811 (t0) REVERT: C 193 ASN cc_start: 0.7672 (m-40) cc_final: 0.7218 (m110) REVERT: C 222 LEU cc_start: 0.8260 (mt) cc_final: 0.7998 (tp) REVERT: C 380 HIS cc_start: 0.6830 (t-90) cc_final: 0.6429 (t-90) REVERT: C 431 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8094 (p90) REVERT: C 505 MET cc_start: 0.6902 (tpt) cc_final: 0.6625 (ttt) REVERT: D 160 LEU cc_start: 0.7754 (tp) cc_final: 0.7540 (mt) REVERT: D 166 ASN cc_start: 0.7955 (m110) cc_final: 0.7600 (m-40) REVERT: D 169 ASN cc_start: 0.7890 (t0) cc_final: 0.7684 (t0) REVERT: D 193 ASN cc_start: 0.7797 (m-40) cc_final: 0.6844 (t0) REVERT: D 422 ARG cc_start: 0.8728 (mtt-85) cc_final: 0.8052 (tpt-90) REVERT: D 431 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8118 (p90) REVERT: D 505 MET cc_start: 0.6783 (tpt) cc_final: 0.6542 (ttt) outliers start: 64 outliers final: 28 residues processed: 258 average time/residue: 0.1407 time to fit residues: 59.9702 Evaluate side-chains 218 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 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 727 LEU Chi-restraints excluded: chain B residue 749 VAL 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 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 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 Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 198 optimal weight: 0.0070 chunk 224 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 78 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS A 262 GLN B 262 GLN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN C 729 GLN 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 = 0.4094 r_free = 0.4094 target = 0.149813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106829 restraints weight = 37030.448| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.03 r_work: 0.3326 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 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 = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23220 Z= 0.103 Angle : 0.517 7.769 31176 Z= 0.270 Chirality : 0.038 0.164 3340 Planarity : 0.003 0.036 3756 Dihedral : 18.245 138.483 4524 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.60 % Allowed : 12.78 % Favored : 84.62 % 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: -0.92 (0.17), residues: 2588 helix: 0.22 (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 0.003 0.000 ARG D 723 TYR 0.009 0.001 TYR A 353 PHE 0.024 0.001 PHE D 306 TRP 0.008 0.001 TRP B 374 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (23220) covalent geometry : angle 0.51717 / 0.27 (31176) hydrogen bonds : bond 0.03381 / 2.16 ( 829) hydrogen bonds : angle 3.49649 / 2.38 ( 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 265 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 160 LEU cc_start: 0.7568 (mt) cc_final: 0.7265 (mt) REVERT: A 162 LYS cc_start: 0.6009 (tptm) cc_final: 0.5689 (tttp) REVERT: A 166 ASN cc_start: 0.7891 (m110) cc_final: 0.7598 (m-40) REVERT: A 169 ASN cc_start: 0.8046 (t0) cc_final: 0.7647 (t0) REVERT: A 171 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7628 (pp30) REVERT: A 184 GLN cc_start: 0.8951 (tp40) cc_final: 0.8716 (tp40) REVERT: A 193 ASN cc_start: 0.7749 (m-40) cc_final: 0.7373 (m110) REVERT: A 422 ARG cc_start: 0.8632 (mtt-85) cc_final: 0.7969 (tpt-90) REVERT: A 426 ASP cc_start: 0.7976 (m-30) cc_final: 0.7559 (t0) REVERT: A 431 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8051 (p90) REVERT: A 505 MET cc_start: 0.6745 (tpt) cc_final: 0.6425 (ttt) REVERT: B 160 LEU cc_start: 0.7861 (tp) cc_final: 0.7628 (mt) REVERT: B 169 ASN cc_start: 0.7960 (t0) cc_final: 0.7599 (t0) REVERT: B 171 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7511 (pp30) REVERT: B 193 ASN cc_start: 0.7854 (m-40) cc_final: 0.7468 (m110) REVERT: B 422 ARG cc_start: 0.8696 (mtt-85) cc_final: 0.7943 (tpt-90) REVERT: B 426 ASP cc_start: 0.7921 (m-30) cc_final: 0.7304 (t0) REVERT: B 431 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8098 (p90) REVERT: B 505 MET cc_start: 0.6710 (tpt) cc_final: 0.6416 (ttt) REVERT: C 166 ASN cc_start: 0.7953 (m110) cc_final: 0.7506 (m-40) REVERT: C 168 HIS cc_start: 0.6680 (m170) cc_final: 0.6416 (m170) REVERT: C 169 ASN cc_start: 0.8091 (t0) cc_final: 0.7706 (t0) REVERT: C 193 ASN cc_start: 0.7653 (m-40) cc_final: 0.7205 (m110) REVERT: C 207 LEU cc_start: 0.7314 (tp) cc_final: 0.6936 (tp) REVERT: C 380 HIS cc_start: 0.6755 (t-90) cc_final: 0.6379 (t-90) REVERT: C 431 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8031 (p90) REVERT: C 505 MET cc_start: 0.6793 (tpt) cc_final: 0.6452 (ttt) REVERT: D 166 ASN cc_start: 0.7862 (m110) cc_final: 0.7497 (m-40) REVERT: D 169 ASN cc_start: 0.7879 (t0) cc_final: 0.7528 (t0) REVERT: D 171 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7265 (pp30) REVERT: D 193 ASN cc_start: 0.7812 (m-40) cc_final: 0.6937 (t0) REVERT: D 321 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7885 (mm) REVERT: D 410 ASN cc_start: 0.7050 (m110) cc_final: 0.6236 (t0) REVERT: D 422 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.8006 (tpt-90) REVERT: D 431 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8055 (p90) REVERT: D 505 MET cc_start: 0.6688 (tpt) cc_final: 0.6427 (ttt) outliers start: 60 outliers final: 27 residues processed: 253 average time/residue: 0.1406 time to fit residues: 58.7624 Evaluate side-chains 221 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 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 727 LEU Chi-restraints excluded: chain B residue 749 VAL 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 171 GLN Chi-restraints excluded: chain D residue 175 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 128 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.145814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100305 restraints weight = 38070.647| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.76 r_work: 0.3259 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23220 Z= 0.220 Angle : 0.613 7.535 31176 Z= 0.314 Chirality : 0.042 0.156 3340 Planarity : 0.004 0.038 3756 Dihedral : 18.614 137.739 4524 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.29 % Allowed : 13.39 % Favored : 83.32 % 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: -1.16 (0.16), residues: 2588 helix: 0.06 (0.14), residues: 1480 sheet: -3.22 (0.42), residues: 108 loop : -1.67 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 723 TYR 0.013 0.002 TYR C 513 PHE 0.024 0.002 PHE D 191 TRP 0.007 0.001 TRP D 742 HIS 0.004 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (23220) covalent geometry : angle 0.61321 / 0.31 (31176) hydrogen bonds : bond 0.04407 / 2.83 ( 829) hydrogen bonds : angle 3.89481 / 2.67 ( 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 260 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 184 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5955 (tptm) cc_final: 0.5654 (tttp) REVERT: A 166 ASN cc_start: 0.7932 (m110) cc_final: 0.7657 (m-40) REVERT: A 169 ASN cc_start: 0.8119 (t0) cc_final: 0.7706 (t0) REVERT: A 171 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7692 (pp30) REVERT: A 422 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8020 (tpt-90) REVERT: A 431 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8245 (p90) REVERT: A 505 MET cc_start: 0.6973 (tpt) cc_final: 0.6666 (ttt) REVERT: B 160 LEU cc_start: 0.7884 (tp) cc_final: 0.7637 (mt) REVERT: B 162 LYS cc_start: 0.5902 (tptt) cc_final: 0.5201 (tttp) REVERT: B 168 HIS cc_start: 0.6295 (m170) cc_final: 0.5983 (m170) REVERT: B 169 ASN cc_start: 0.8085 (t0) cc_final: 0.7673 (t0) REVERT: B 171 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7655 (pp30) REVERT: B 422 ARG cc_start: 0.8685 (mtt-85) cc_final: 0.7963 (tpt-90) REVERT: B 431 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8234 (p90) REVERT: B 505 MET cc_start: 0.6979 (tpt) cc_final: 0.6656 (ttt) REVERT: C 162 LYS cc_start: 0.5953 (tptt) cc_final: 0.5069 (tttp) REVERT: C 168 HIS cc_start: 0.6890 (m170) cc_final: 0.6648 (m170) REVERT: C 169 ASN cc_start: 0.8230 (t0) cc_final: 0.7843 (t0) REVERT: C 431 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8221 (p90) REVERT: D 166 ASN cc_start: 0.7929 (m110) cc_final: 0.7561 (m110) REVERT: D 168 HIS cc_start: 0.6268 (m170) cc_final: 0.5959 (m170) REVERT: D 169 ASN cc_start: 0.7972 (t0) cc_final: 0.7607 (t0) REVERT: D 171 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7374 (pp30) REVERT: D 321 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7926 (mm) REVERT: D 422 ARG cc_start: 0.8739 (mtt-85) cc_final: 0.8104 (tpt-90) REVERT: D 431 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8203 (p90) REVERT: D 505 MET cc_start: 0.6945 (tpt) cc_final: 0.6619 (ttt) REVERT: D 547 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8391 (tt) outliers start: 76 outliers final: 40 residues processed: 254 average time/residue: 0.1388 time to fit residues: 58.6219 Evaluate side-chains 221 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 363 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 544 VAL 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 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 558 THR 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 177 LEU 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 544 VAL Chi-restraints excluded: chain C residue 558 THR 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 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 544 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 18 optimal weight: 0.4980 chunk 204 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.0570 chunk 96 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS A 767 ASN B 757 ASN B 767 ASN C 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.148230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105467 restraints weight = 37541.053| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.12 r_work: 0.3290 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23220 Z= 0.112 Angle : 0.528 8.201 31176 Z= 0.273 Chirality : 0.038 0.193 3340 Planarity : 0.003 0.036 3756 Dihedral : 17.852 129.957 4524 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.56 % Allowed : 14.17 % Favored : 83.28 % 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: -0.65 (0.17), residues: 2588 helix: 0.40 (0.14), residues: 1516 sheet: -2.95 (0.52), residues: 64 loop : -1.49 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 411 TYR 0.009 0.001 TYR C 732 PHE 0.023 0.001 PHE D 306 TRP 0.009 0.001 TRP D 374 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (23220) covalent geometry : angle 0.52820 / 0.27 (31176) hydrogen bonds : bond 0.03432 / 2.19 ( 829) hydrogen bonds : angle 3.50616 / 2.40 ( 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 246 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5939 (tptm) cc_final: 0.5649 (tttp) REVERT: A 166 ASN cc_start: 0.7911 (m110) cc_final: 0.7635 (m-40) REVERT: A 169 ASN cc_start: 0.8115 (t0) cc_final: 0.7679 (t0) REVERT: A 171 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7744 (pp30) REVERT: A 422 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8016 (tpt-90) REVERT: A 426 ASP cc_start: 0.7995 (m-30) cc_final: 0.7423 (t0) REVERT: A 431 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8085 (p90) REVERT: A 505 MET cc_start: 0.6883 (tpt) cc_final: 0.6533 (ttt) REVERT: B 160 LEU cc_start: 0.7830 (tp) cc_final: 0.7596 (mt) REVERT: B 168 HIS cc_start: 0.6210 (m170) cc_final: 0.5861 (m170) REVERT: B 169 ASN cc_start: 0.8118 (t0) cc_final: 0.7679 (t0) REVERT: B 171 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7650 (pp30) REVERT: B 422 ARG cc_start: 0.8712 (mtt-85) cc_final: 0.7997 (tpt-90) REVERT: B 426 ASP cc_start: 0.7995 (m-30) cc_final: 0.7433 (t0) REVERT: B 431 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8158 (p90) REVERT: B 505 MET cc_start: 0.6879 (tpt) cc_final: 0.6561 (ttt) REVERT: C 168 HIS cc_start: 0.6993 (m170) cc_final: 0.6723 (m170) REVERT: C 169 ASN cc_start: 0.8235 (t0) cc_final: 0.7829 (t0) REVERT: C 380 HIS cc_start: 0.6912 (t-90) cc_final: 0.6656 (t-90) REVERT: C 431 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8095 (p90) REVERT: C 505 MET cc_start: 0.6937 (tpt) cc_final: 0.6640 (ttt) REVERT: D 166 ASN cc_start: 0.7949 (m110) cc_final: 0.7552 (m110) REVERT: D 168 HIS cc_start: 0.6155 (m170) cc_final: 0.5861 (m170) REVERT: D 169 ASN cc_start: 0.7977 (t0) cc_final: 0.7613 (t0) REVERT: D 171 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7442 (pp30) REVERT: D 321 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7892 (mm) REVERT: D 410 ASN cc_start: 0.7062 (m110) cc_final: 0.6399 (t0) REVERT: D 422 ARG cc_start: 0.8730 (mtt-85) cc_final: 0.8072 (tpt-90) REVERT: D 431 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8116 (p90) REVERT: D 505 MET cc_start: 0.6883 (tpt) cc_final: 0.6528 (ttt) outliers start: 59 outliers final: 36 residues processed: 237 average time/residue: 0.1470 time to fit residues: 57.4120 Evaluate side-chains 218 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 205 THR 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 543 MET 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 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE 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 166 ASN 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 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 262 GLN 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 543 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 54 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 194 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN A 168 HIS A 767 ASN B 767 ASN C 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.147767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.105743 restraints weight = 37210.670| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.99 r_work: 0.3295 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 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 = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23220 Z= 0.122 Angle : 0.539 7.463 31176 Z= 0.279 Chirality : 0.039 0.147 3340 Planarity : 0.003 0.037 3756 Dihedral : 17.628 126.240 4524 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.60 % Allowed : 14.69 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2588 helix: 0.46 (0.14), residues: 1520 sheet: -2.85 (0.56), residues: 76 loop : -1.34 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 411 TYR 0.018 0.001 TYR B 732 PHE 0.024 0.001 PHE B 191 TRP 0.007 0.001 TRP B 374 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (23220) covalent geometry : angle 0.53894 / 0.28 (31176) hydrogen bonds : bond 0.03549 / 2.27 ( 829) hydrogen bonds : angle 3.51087 / 2.41 ( 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 235 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5940 (tptm) cc_final: 0.5641 (tttp) REVERT: A 166 ASN cc_start: 0.7916 (m110) cc_final: 0.7628 (m-40) REVERT: A 169 ASN cc_start: 0.8130 (t0) cc_final: 0.7679 (t0) REVERT: A 171 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7727 (pp30) REVERT: A 422 ARG cc_start: 0.8691 (mtt-85) cc_final: 0.7997 (tpt-90) REVERT: A 426 ASP cc_start: 0.7962 (m-30) cc_final: 0.7395 (t0) REVERT: A 431 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8068 (p90) REVERT: A 505 MET cc_start: 0.6878 (tpt) cc_final: 0.6521 (ttt) REVERT: B 160 LEU cc_start: 0.7820 (tp) cc_final: 0.7578 (mt) REVERT: B 162 LYS cc_start: 0.5763 (tptt) cc_final: 0.5079 (tttm) REVERT: B 168 HIS cc_start: 0.6290 (m170) cc_final: 0.5939 (m170) REVERT: B 169 ASN cc_start: 0.8116 (t0) cc_final: 0.7668 (t0) REVERT: B 171 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7706 (pp30) REVERT: B 306 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6951 (p90) REVERT: B 422 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.7971 (tpt-90) REVERT: B 426 ASP cc_start: 0.7966 (m-30) cc_final: 0.7392 (t0) REVERT: B 431 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8110 (p90) REVERT: B 505 MET cc_start: 0.6869 (tpt) cc_final: 0.6548 (ttt) REVERT: C 168 HIS cc_start: 0.6922 (m170) cc_final: 0.6653 (m170) REVERT: C 169 ASN cc_start: 0.8218 (t0) cc_final: 0.7785 (t0) REVERT: C 306 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7326 (p90) REVERT: C 380 HIS cc_start: 0.6876 (t-90) cc_final: 0.6633 (t-90) REVERT: C 431 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8094 (p90) REVERT: C 505 MET cc_start: 0.6901 (tpt) cc_final: 0.6603 (ttt) REVERT: D 166 ASN cc_start: 0.7963 (m110) cc_final: 0.7280 (m110) REVERT: D 169 ASN cc_start: 0.8007 (t0) cc_final: 0.7745 (t0) REVERT: D 321 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7866 (mm) REVERT: D 410 ASN cc_start: 0.7103 (m110) cc_final: 0.6419 (t0) REVERT: D 422 ARG cc_start: 0.8732 (mtt-85) cc_final: 0.8063 (tpt-90) REVERT: D 431 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8134 (p90) REVERT: D 505 MET cc_start: 0.6842 (tpt) cc_final: 0.6490 (ttt) outliers start: 60 outliers final: 36 residues processed: 230 average time/residue: 0.1487 time to fit residues: 55.7917 Evaluate side-chains 220 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 205 THR 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 543 MET 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 306 PHE 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 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 166 ASN Chi-restraints excluded: chain C residue 171 GLN 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 306 PHE 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 262 GLN 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 558 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL 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: 0.5980 chunk 101 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS A 767 ASN B 767 ASN C 166 ASN D 168 HIS D 767 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.149134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.106564 restraints weight = 37402.713| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.18 r_work: 0.3306 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23220 Z= 0.104 Angle : 0.523 10.201 31176 Z= 0.270 Chirality : 0.038 0.169 3340 Planarity : 0.003 0.036 3756 Dihedral : 17.219 120.591 4524 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.30 % Allowed : 15.08 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2588 helix: 0.74 (0.14), residues: 1516 sheet: -2.93 (0.52), residues: 64 loop : -1.36 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 411 TYR 0.014 0.001 TYR A 732 PHE 0.022 0.001 PHE D 306 TRP 0.008 0.001 TRP B 374 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (23220) covalent geometry : angle 0.52300 / 0.27 (31176) hydrogen bonds : bond 0.03259 / 2.08 ( 829) hydrogen bonds : angle 3.39275 / 2.33 ( 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 242 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5948 (tptm) cc_final: 0.5642 (tttp) REVERT: A 166 ASN cc_start: 0.7957 (m110) cc_final: 0.7688 (m-40) REVERT: A 169 ASN cc_start: 0.8111 (t0) cc_final: 0.7730 (t0) REVERT: A 306 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.6654 (p90) REVERT: A 422 ARG cc_start: 0.8681 (mtt-85) cc_final: 0.8043 (tpt-90) REVERT: A 426 ASP cc_start: 0.7916 (m-30) cc_final: 0.7367 (t0) REVERT: A 431 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8032 (p90) REVERT: A 505 MET cc_start: 0.6892 (tpt) cc_final: 0.6556 (ttt) REVERT: B 160 LEU cc_start: 0.7838 (tp) cc_final: 0.7611 (mt) REVERT: B 162 LYS cc_start: 0.5829 (tptt) cc_final: 0.5041 (tttp) REVERT: B 168 HIS cc_start: 0.6369 (m170) cc_final: 0.6017 (m170) REVERT: B 169 ASN cc_start: 0.8134 (t0) cc_final: 0.7693 (t0) REVERT: B 171 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7824 (pp30) REVERT: B 306 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6883 (p90) REVERT: B 321 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7889 (mm) REVERT: B 422 ARG cc_start: 0.8740 (mtt-85) cc_final: 0.8025 (tpt-90) REVERT: B 426 ASP cc_start: 0.7908 (m-30) cc_final: 0.7326 (t0) REVERT: B 431 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8084 (p90) REVERT: B 505 MET cc_start: 0.6879 (tpt) cc_final: 0.6563 (ttt) REVERT: C 168 HIS cc_start: 0.6900 (m170) cc_final: 0.6682 (m170) REVERT: C 169 ASN cc_start: 0.8216 (t0) cc_final: 0.7775 (t0) REVERT: C 306 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7361 (p90) REVERT: C 380 HIS cc_start: 0.6902 (t-90) cc_final: 0.6676 (t-90) REVERT: C 431 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8056 (p90) REVERT: C 447 MET cc_start: 0.8707 (tpp) cc_final: 0.8439 (tpt) REVERT: C 505 MET cc_start: 0.6887 (tpt) cc_final: 0.6614 (ttt) REVERT: D 166 ASN cc_start: 0.7982 (m110) cc_final: 0.7400 (m-40) REVERT: D 168 HIS cc_start: 0.5493 (OUTLIER) cc_final: 0.4964 (p90) REVERT: D 169 ASN cc_start: 0.8029 (t0) cc_final: 0.7670 (t0) REVERT: D 321 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7898 (mm) REVERT: D 410 ASN cc_start: 0.7015 (m110) cc_final: 0.6627 (t0) REVERT: D 418 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7703 (mm-30) REVERT: D 422 ARG cc_start: 0.8762 (mtt-85) cc_final: 0.8085 (tpt-90) REVERT: D 431 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8055 (p90) REVERT: D 505 MET cc_start: 0.6871 (tpt) cc_final: 0.6532 (ttt) outliers start: 53 outliers final: 36 residues processed: 237 average time/residue: 0.1514 time to fit residues: 57.7691 Evaluate side-chains 224 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 296 VAL Chi-restraints excluded: chain A residue 306 PHE 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 531 LEU Chi-restraints excluded: chain A residue 543 MET 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 306 PHE Chi-restraints excluded: chain B residue 321 LEU 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 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain C residue 131 LEU 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 205 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 306 PHE 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 168 HIS Chi-restraints excluded: chain D residue 175 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 212 optimal weight: 0.1980 chunk 128 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS A 767 ASN B 767 ASN C 166 ASN D 168 HIS D 767 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.149659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.106987 restraints weight = 37368.386| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.13 r_work: 0.3320 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23220 Z= 0.104 Angle : 0.535 11.184 31176 Z= 0.277 Chirality : 0.038 0.144 3340 Planarity : 0.003 0.036 3756 Dihedral : 16.918 117.471 4524 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.30 % Allowed : 15.25 % Favored : 82.45 % 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: -0.10 (0.17), residues: 2588 helix: 0.91 (0.14), residues: 1520 sheet: -2.87 (0.51), residues: 64 loop : -1.36 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 723 TYR 0.013 0.001 TYR A 732 PHE 0.022 0.001 PHE C 431 TRP 0.008 0.001 TRP B 374 HIS 0.003 0.000 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (23220) covalent geometry : angle 0.53454 / 0.28 (31176) hydrogen bonds : bond 0.03185 / 2.03 ( 829) hydrogen bonds : angle 3.36134 / 2.30 ( 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 240 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5936 (tptm) cc_final: 0.5628 (tttp) REVERT: A 166 ASN cc_start: 0.7951 (m110) cc_final: 0.7687 (m-40) REVERT: A 169 ASN cc_start: 0.8122 (t0) cc_final: 0.7728 (t0) REVERT: A 306 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6538 (p90) REVERT: A 422 ARG cc_start: 0.8681 (mtt-85) cc_final: 0.7963 (tpt-90) REVERT: A 431 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7976 (p90) REVERT: A 505 MET cc_start: 0.6869 (tpt) cc_final: 0.6599 (ttt) REVERT: B 160 LEU cc_start: 0.7832 (tp) cc_final: 0.7588 (mt) REVERT: B 162 LYS cc_start: 0.5826 (tptt) cc_final: 0.5031 (tttp) REVERT: B 169 ASN cc_start: 0.8131 (t0) cc_final: 0.7773 (t0) REVERT: B 306 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6810 (p90) REVERT: B 321 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7869 (mm) REVERT: B 422 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.8040 (tpt-90) REVERT: B 426 ASP cc_start: 0.7845 (m-30) cc_final: 0.7242 (t0) REVERT: B 431 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8024 (p90) REVERT: B 505 MET cc_start: 0.6876 (tpt) cc_final: 0.6557 (ttt) REVERT: C 168 HIS cc_start: 0.6943 (m170) cc_final: 0.6654 (m170) REVERT: C 169 ASN cc_start: 0.8189 (t0) cc_final: 0.7712 (t0) REVERT: C 306 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7240 (p90) REVERT: C 380 HIS cc_start: 0.6898 (t-90) cc_final: 0.6672 (t-90) REVERT: C 431 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.7981 (p90) REVERT: C 447 MET cc_start: 0.8674 (tpp) cc_final: 0.8431 (tpt) REVERT: C 505 MET cc_start: 0.6877 (tpt) cc_final: 0.6551 (ttt) REVERT: D 166 ASN cc_start: 0.7960 (m110) cc_final: 0.7271 (m-40) REVERT: D 168 HIS cc_start: 0.5752 (OUTLIER) cc_final: 0.5435 (p-80) REVERT: D 169 ASN cc_start: 0.8066 (t0) cc_final: 0.7670 (t0) REVERT: D 171 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.6918 (pp30) REVERT: D 321 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7885 (mm) REVERT: D 422 ARG cc_start: 0.8712 (mtt-85) cc_final: 0.8080 (tpt-90) REVERT: D 431 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8019 (p90) REVERT: D 505 MET cc_start: 0.6813 (tpt) cc_final: 0.6582 (ttt) outliers start: 53 outliers final: 40 residues processed: 234 average time/residue: 0.1512 time to fit residues: 57.3495 Evaluate side-chains 226 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 254 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 MET 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 306 PHE Chi-restraints excluded: chain B residue 321 LEU 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 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 166 ASN Chi-restraints excluded: chain C residue 171 GLN 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 306 PHE 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 168 HIS 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 321 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 646 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 115 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 241 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 228 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 767 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.149559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.106766 restraints weight = 37230.929| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.99 r_work: 0.3334 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 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 = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 23220 Z= 0.192 Angle : 0.839 59.200 31176 Z= 0.500 Chirality : 0.041 0.538 3340 Planarity : 0.006 0.203 3756 Dihedral : 16.939 117.455 4524 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.30 % Allowed : 15.47 % Favored : 82.24 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.91 (0.14), residues: 1520 sheet: -2.85 (0.52), residues: 64 loop : -1.36 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 117 TYR 0.013 0.001 TYR A 732 PHE 0.022 0.001 PHE C 431 TRP 0.008 0.001 TRP B 374 HIS 0.326 0.006 HIS D 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (23220) covalent geometry : angle 0.83877 / 0.50 (31176) hydrogen bonds : bond 0.03265 / 2.06 ( 829) hydrogen bonds : angle 3.36192 / 2.31 ( 2391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5304.11 seconds wall clock time: 92 minutes 0.67 seconds (5520.67 seconds total)