Starting phenix.real_space_refine on Sun Sep 29 18:46:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/09_2024/7lqz_23492_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/09_2024/7lqz_23492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/09_2024/7lqz_23492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/09_2024/7lqz_23492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/09_2024/7lqz_23492_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/09_2024/7lqz_23492_trim.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22765 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "B" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "C" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "D" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "A" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 442 Unusual residues: {' NA': 1, '6EU': 1, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "B" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 441 Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 441 Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 441 Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Time building chain proxies: 12.95, per 1000 atoms: 0.57 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: 5.13 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.05 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: 5.84 Time building geometry restraints manager: 6.04 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 779 or resid 901 or (resid 904 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e 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 O3 \ 2 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 or resid 907 through 908 or (resid 909 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 na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or nam \ e 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 na \ me C217 or name 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 45.160 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.193 23220 Z= 0.799 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.004 TRP C 751 HIS 0.010 0.003 HIS C 366 PHE 0.040 0.003 PHE C 431 TYR 0.025 0.003 TYR A 465 ARG 0.010 0.001 ARG C 703 *********************** 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 fitting. rotamer outliers: 8 poor density : 349 time to evaluate : 2.469 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: 0.8461 (mt) cc_final: 0.7987 (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: 0.7872 (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: 0.7866 (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: 0.8387 (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: 0.6470 (mp0) outliers start: 8 outliers final: 4 residues processed: 357 average time/residue: 0.3572 time to fit residues: 193.0167 Evaluate side-chains 207 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 203 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 219 optimal weight: 0.9990 chunk 197 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 0.0270 chunk 236 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 215 ASN A 230 GLN A 261 ASN A 291 HIS A 312 ASN A 366 HIS A 421 ASN A 630 ASN A 750 ASN A 755 ASN A 762 ASN A 767 ASN B 166 ASN B 215 ASN B 225 ASN B 230 GLN B 261 ASN B 291 HIS B 312 ASN B 366 HIS B 421 ASN B 630 ASN B 750 ASN B 755 ASN B 762 ASN B 767 ASN C 166 ASN C 169 ASN C 215 ASN C 225 ASN C 230 GLN C 261 ASN C 291 HIS C 312 ASN C 366 HIS C 421 ASN C 630 ASN C 729 GLN C 750 ASN C 755 ASN C 767 ASN D 166 ASN D 184 GLN 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: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23220 Z= 0.160 Angle : 0.602 7.712 31176 Z= 0.319 Chirality : 0.038 0.164 3340 Planarity : 0.005 0.039 3756 Dihedral : 21.501 159.708 4524 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.99 % Allowed : 8.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.14), residues: 2588 helix: -2.30 (0.10), residues: 1512 sheet: -3.89 (0.39), residues: 84 loop : -1.95 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 551 HIS 0.002 0.001 HIS D 208 PHE 0.020 0.002 PHE D 191 TYR 0.015 0.001 TYR A 673 ARG 0.005 0.000 ARG D 411 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 2.576 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: 0.6087 (tptm) cc_final: 0.5779 (tttp) REVERT: A 166 ASN cc_start: 0.8032 (m110) cc_final: 0.7716 (m-40) REVERT: A 169 ASN cc_start: 0.7618 (t0) cc_final: 0.7371 (t0) REVERT: A 222 LEU cc_start: 0.8467 (mt) cc_final: 0.8215 (tp) REVERT: B 162 LYS cc_start: 0.6117 (tptm) cc_final: 0.5823 (tttp) REVERT: B 169 ASN cc_start: 0.7473 (t0) cc_final: 0.7239 (t0) REVERT: B 673 TYR cc_start: 0.8746 (t80) cc_final: 0.8512 (t80) REVERT: C 115 ASP cc_start: 0.8013 (p0) cc_final: 0.7691 (p0) REVERT: C 166 ASN cc_start: 0.8021 (m110) cc_final: 0.7540 (m-40) REVERT: C 168 HIS cc_start: 0.7008 (m170) cc_final: 0.6770 (m170) REVERT: C 193 ASN cc_start: 0.7731 (m-40) cc_final: 0.6729 (t0) REVERT: C 207 LEU cc_start: 0.7610 (tp) cc_final: 0.7351 (tp) REVERT: D 162 LYS cc_start: 0.6118 (tptm) cc_final: 0.5877 (tttp) REVERT: D 166 ASN cc_start: 0.7832 (m110) cc_final: 0.7547 (m-40) outliers start: 46 outliers final: 22 residues processed: 274 average time/residue: 0.3354 time to fit residues: 144.7238 Evaluate side-chains 207 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 65 optimal weight: 40.0000 chunk 236 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 210 optimal weight: 0.5980 chunk 234 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN C 169 ASN C 380 HIS 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23220 Z= 0.306 Angle : 0.634 6.789 31176 Z= 0.331 Chirality : 0.042 0.153 3340 Planarity : 0.004 0.046 3756 Dihedral : 20.260 153.176 4524 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.38 % Allowed : 11.27 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2588 helix: -1.09 (0.13), residues: 1512 sheet: -3.36 (0.52), residues: 76 loop : -1.84 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 742 HIS 0.010 0.002 HIS D 380 PHE 0.026 0.002 PHE B 450 TYR 0.013 0.002 TYR D 353 ARG 0.006 0.001 ARG B 723 *********************** 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 259 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 204 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.6053 (tptm) cc_final: 0.5757 (tttp) REVERT: A 166 ASN cc_start: 0.7945 (m110) cc_final: 0.7685 (m-40) REVERT: A 168 HIS cc_start: 0.6829 (m170) cc_final: 0.6471 (m170) REVERT: A 169 ASN cc_start: 0.7844 (t0) cc_final: 0.7420 (t0) REVERT: A 171 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7565 (pp30) REVERT: A 193 ASN cc_start: 0.7874 (m-40) cc_final: 0.7529 (m110) REVERT: A 431 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7987 (p90) REVERT: A 714 PHE cc_start: 0.7146 (m-80) cc_final: 0.6915 (m-80) REVERT: B 160 LEU cc_start: 0.7971 (tp) cc_final: 0.7738 (mt) REVERT: B 162 LYS cc_start: 0.6166 (tptm) cc_final: 0.5914 (tttp) REVERT: B 169 ASN cc_start: 0.7725 (t0) cc_final: 0.7444 (t0) REVERT: B 193 ASN cc_start: 0.7919 (m-40) cc_final: 0.7583 (m110) REVERT: B 422 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7968 (tpt-90) REVERT: B 431 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8055 (p90) REVERT: B 714 PHE cc_start: 0.7001 (m-80) cc_final: 0.6783 (m-80) REVERT: C 162 LYS cc_start: 0.5833 (tptt) cc_final: 0.5080 (tttp) REVERT: C 168 HIS cc_start: 0.7130 (m170) cc_final: 0.6854 (m170) REVERT: C 184 GLN cc_start: 0.8944 (tp40) cc_final: 0.8741 (tp40) REVERT: C 193 ASN cc_start: 0.7767 (m-40) cc_final: 0.7374 (m-40) REVERT: C 431 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7953 (p90) REVERT: D 166 ASN cc_start: 0.7865 (m110) cc_final: 0.7569 (m-40) REVERT: D 184 GLN cc_start: 0.8503 (mm110) cc_final: 0.8275 (tp40) REVERT: D 262 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6777 (mp-120) REVERT: D 431 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7960 (p90) outliers start: 55 outliers final: 35 residues processed: 248 average time/residue: 0.3132 time to fit residues: 125.5931 Evaluate side-chains 225 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 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 380 HIS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 505 MET 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 262 GLN Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 224 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 ASN A 767 ASN B 166 ASN C 166 ASN C 169 ASN C 380 HIS C 767 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23220 Z= 0.143 Angle : 0.527 6.556 31176 Z= 0.279 Chirality : 0.038 0.152 3340 Planarity : 0.003 0.039 3756 Dihedral : 19.029 145.267 4524 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.99 % Allowed : 11.66 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2588 helix: -0.19 (0.14), residues: 1492 sheet: -3.00 (0.53), residues: 64 loop : -1.72 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 374 HIS 0.002 0.000 HIS B 380 PHE 0.025 0.001 PHE A 191 TYR 0.009 0.001 TYR A 353 ARG 0.004 0.000 ARG D 214 *********************** 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 266 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 197 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.6033 (tptm) cc_final: 0.5758 (tttp) REVERT: A 166 ASN cc_start: 0.8030 (m110) cc_final: 0.7766 (m-40) REVERT: A 169 ASN cc_start: 0.7842 (t0) cc_final: 0.7501 (t0) REVERT: A 193 ASN cc_start: 0.7796 (m-40) cc_final: 0.7447 (m110) REVERT: A 431 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7882 (p90) REVERT: B 162 LYS cc_start: 0.6071 (tptm) cc_final: 0.5851 (tttp) REVERT: B 169 ASN cc_start: 0.7781 (t0) cc_final: 0.7540 (t0) REVERT: B 193 ASN cc_start: 0.7849 (m-40) cc_final: 0.7500 (m110) REVERT: B 422 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7958 (tpt-90) REVERT: B 431 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7958 (p90) REVERT: C 168 HIS cc_start: 0.6932 (m170) cc_final: 0.6701 (m170) REVERT: C 193 ASN cc_start: 0.7715 (m-40) cc_final: 0.7330 (m110) REVERT: C 431 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7913 (p90) REVERT: D 160 LEU cc_start: 0.7850 (tp) cc_final: 0.7648 (mt) REVERT: D 166 ASN cc_start: 0.7920 (m110) cc_final: 0.7629 (m-40) REVERT: D 169 ASN cc_start: 0.7526 (t0) cc_final: 0.7283 (t0) REVERT: D 171 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7230 (pp30) REVERT: D 184 GLN cc_start: 0.8503 (mm110) cc_final: 0.8285 (tp40) REVERT: D 193 ASN cc_start: 0.7748 (m-40) cc_final: 0.6799 (t0) REVERT: D 262 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6159 (mp10) REVERT: D 431 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7872 (p90) outliers start: 69 outliers final: 30 residues processed: 259 average time/residue: 0.3064 time to fit residues: 129.4168 Evaluate side-chains 226 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 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 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 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 363 GLU Chi-restraints excluded: chain C residue 380 HIS 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 171 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 3 optimal weight: 0.0570 chunk 187 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 128 optimal weight: 0.2980 chunk 225 optimal weight: 0.2980 chunk 63 optimal weight: 9.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 757 ASN B 767 ASN C 166 ASN C 169 ASN C 380 HIS C 729 GLN D 757 ASN D 767 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23220 Z= 0.139 Angle : 0.524 7.974 31176 Z= 0.274 Chirality : 0.038 0.170 3340 Planarity : 0.003 0.036 3756 Dihedral : 18.242 138.936 4524 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.82 % Allowed : 12.48 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2588 helix: 0.28 (0.14), residues: 1468 sheet: -2.96 (0.54), residues: 64 loop : -1.52 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 374 HIS 0.004 0.001 HIS A 168 PHE 0.023 0.001 PHE B 191 TYR 0.009 0.001 TYR A 353 ARG 0.004 0.000 ARG D 723 *********************** 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 274 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 209 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.7717 (mt) cc_final: 0.7416 (mt) REVERT: A 162 LYS cc_start: 0.6020 (tptm) cc_final: 0.5702 (tttp) REVERT: A 166 ASN cc_start: 0.8051 (m110) cc_final: 0.7789 (m-40) REVERT: A 169 ASN cc_start: 0.7923 (t0) cc_final: 0.7572 (t0) REVERT: A 171 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7647 (pp30) REVERT: A 184 GLN cc_start: 0.8980 (tp40) cc_final: 0.8727 (tp40) REVERT: A 193 ASN cc_start: 0.7704 (m-40) cc_final: 0.7367 (m110) REVERT: A 431 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7897 (p90) REVERT: B 162 LYS cc_start: 0.6117 (tptm) cc_final: 0.5853 (tttp) REVERT: B 169 ASN cc_start: 0.7792 (t0) cc_final: 0.7498 (t0) REVERT: B 171 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7568 (pp30) REVERT: B 193 ASN cc_start: 0.7772 (m-40) cc_final: 0.7406 (m110) REVERT: B 422 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7983 (tpt-90) REVERT: B 431 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7900 (p90) REVERT: C 168 HIS cc_start: 0.7091 (m170) cc_final: 0.6827 (m170) REVERT: C 193 ASN cc_start: 0.7629 (m-40) cc_final: 0.7267 (m-40) REVERT: C 431 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7882 (p90) REVERT: D 166 ASN cc_start: 0.7943 (m110) cc_final: 0.7671 (m-40) REVERT: D 169 ASN cc_start: 0.7387 (t0) cc_final: 0.7166 (t0) REVERT: D 171 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7271 (pp30) REVERT: D 184 GLN cc_start: 0.8520 (mm110) cc_final: 0.8308 (tp40) REVERT: D 193 ASN cc_start: 0.7695 (m-40) cc_final: 0.6689 (t0) REVERT: D 431 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7871 (p90) outliers start: 65 outliers final: 30 residues processed: 261 average time/residue: 0.2989 time to fit residues: 128.1083 Evaluate side-chains 223 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 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 B residue 767 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 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 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 177 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 Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 251 optimal weight: 3.9990 chunk 208 optimal weight: 0.0470 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS B 767 ASN C 169 ASN D 767 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23220 Z= 0.138 Angle : 0.513 6.521 31176 Z= 0.268 Chirality : 0.038 0.208 3340 Planarity : 0.003 0.037 3756 Dihedral : 17.632 133.245 4524 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.82 % Allowed : 13.08 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2588 helix: 0.61 (0.14), residues: 1488 sheet: -2.93 (0.52), residues: 64 loop : -1.43 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 754 HIS 0.004 0.001 HIS A 168 PHE 0.026 0.001 PHE D 191 TYR 0.008 0.001 TYR D 353 ARG 0.005 0.000 ARG D 411 *********************** 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 266 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 201 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.7680 (mt) cc_final: 0.7385 (mt) REVERT: A 162 LYS cc_start: 0.5943 (tptm) cc_final: 0.5655 (tttp) REVERT: A 166 ASN cc_start: 0.8007 (m110) cc_final: 0.7736 (m-40) REVERT: A 169 ASN cc_start: 0.7874 (t0) cc_final: 0.7532 (t0) REVERT: A 171 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7675 (pp30) REVERT: A 184 GLN cc_start: 0.9008 (tp40) cc_final: 0.8793 (tp40) REVERT: A 193 ASN cc_start: 0.7662 (m-40) cc_final: 0.7351 (m110) REVERT: A 431 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7907 (p90) REVERT: B 169 ASN cc_start: 0.7746 (t0) cc_final: 0.7458 (t0) REVERT: B 171 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7592 (pp30) REVERT: B 193 ASN cc_start: 0.7669 (m-40) cc_final: 0.7301 (m110) REVERT: B 422 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7960 (tpt-90) REVERT: B 431 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7933 (p90) REVERT: B 447 MET cc_start: 0.8428 (mmt) cc_final: 0.7959 (mmt) REVERT: C 168 HIS cc_start: 0.7159 (m170) cc_final: 0.6882 (m170) REVERT: C 193 ASN cc_start: 0.7571 (m-40) cc_final: 0.7186 (m110) REVERT: C 431 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.7872 (p90) REVERT: D 166 ASN cc_start: 0.8017 (m110) cc_final: 0.7430 (m110) REVERT: D 171 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7281 (pp30) REVERT: D 193 ASN cc_start: 0.7706 (m-40) cc_final: 0.6676 (t0) REVERT: D 431 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7868 (p90) outliers start: 65 outliers final: 32 residues processed: 255 average time/residue: 0.3021 time to fit residues: 126.4203 Evaluate side-chains 220 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain 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 175 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 531 LEU 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 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 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 Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 0.0060 chunk 183 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 767 ASN B 767 ASN C 169 ASN D 262 GLN D 767 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23220 Z= 0.129 Angle : 0.507 8.198 31176 Z= 0.263 Chirality : 0.037 0.143 3340 Planarity : 0.003 0.038 3756 Dihedral : 17.069 127.804 4524 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.69 % Allowed : 13.69 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2588 helix: 0.86 (0.14), residues: 1516 sheet: -2.97 (0.51), residues: 64 loop : -1.52 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 754 HIS 0.004 0.000 HIS A 168 PHE 0.021 0.001 PHE C 431 TYR 0.008 0.001 TYR A 353 ARG 0.003 0.000 ARG A 422 *********************** 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 258 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 196 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.7622 (mt) cc_final: 0.7300 (mt) REVERT: A 162 LYS cc_start: 0.5940 (tptm) cc_final: 0.5649 (tttp) REVERT: A 166 ASN cc_start: 0.8037 (m110) cc_final: 0.7762 (m-40) REVERT: A 169 ASN cc_start: 0.7876 (t0) cc_final: 0.7542 (t0) REVERT: A 171 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7660 (pp30) REVERT: A 431 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7882 (p90) REVERT: A 718 MET cc_start: 0.6446 (pmm) cc_final: 0.6233 (pmm) REVERT: B 162 LYS cc_start: 0.5989 (tptt) cc_final: 0.5328 (tttp) REVERT: B 169 ASN cc_start: 0.7758 (t0) cc_final: 0.7478 (t0) REVERT: B 171 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7641 (pp30) REVERT: B 193 ASN cc_start: 0.7677 (m-40) cc_final: 0.7341 (m110) REVERT: B 431 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7917 (p90) REVERT: B 714 PHE cc_start: 0.6774 (m-80) cc_final: 0.6447 (m-10) REVERT: C 168 HIS cc_start: 0.7165 (m170) cc_final: 0.6948 (m170) REVERT: C 193 ASN cc_start: 0.7525 (m-40) cc_final: 0.7158 (m-40) REVERT: C 431 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.7822 (p90) REVERT: D 162 LYS cc_start: 0.6366 (tptt) cc_final: 0.5742 (tttp) REVERT: D 166 ASN cc_start: 0.8087 (m110) cc_final: 0.7866 (m-40) REVERT: D 171 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7270 (pp30) REVERT: D 193 ASN cc_start: 0.7770 (m-40) cc_final: 0.6695 (t0) REVERT: D 418 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7026 (tp30) REVERT: D 431 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.7841 (p90) outliers start: 62 outliers final: 38 residues processed: 250 average time/residue: 0.3113 time to fit residues: 125.4259 Evaluate side-chains 232 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 187 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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 262 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain 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 431 PHE Chi-restraints excluded: chain B residue 531 LEU 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 254 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 431 PHE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain 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 431 PHE Chi-restraints excluded: chain D residue 543 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.0570 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 767 ASN B 767 ASN D 169 ASN D 767 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4163 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= 0.168 Angle : 0.532 7.441 31176 Z= 0.275 Chirality : 0.038 0.141 3340 Planarity : 0.003 0.039 3756 Dihedral : 16.876 125.529 4524 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.51 % Allowed : 14.43 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2588 helix: 0.89 (0.14), residues: 1512 sheet: -2.97 (0.51), residues: 64 loop : -1.49 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 754 HIS 0.004 0.001 HIS A 168 PHE 0.022 0.001 PHE C 431 TYR 0.016 0.001 TYR A 732 ARG 0.006 0.000 ARG B 723 *********************** 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 245 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 187 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5946 (tptm) cc_final: 0.5619 (tttp) REVERT: A 166 ASN cc_start: 0.7988 (m110) cc_final: 0.7715 (m-40) REVERT: A 169 ASN cc_start: 0.7862 (t0) cc_final: 0.7534 (t0) REVERT: A 171 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7648 (pp30) REVERT: A 431 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.7898 (p90) REVERT: A 718 MET cc_start: 0.6341 (pmm) cc_final: 0.6138 (pmm) REVERT: B 162 LYS cc_start: 0.5977 (tptt) cc_final: 0.5310 (tttp) REVERT: B 169 ASN cc_start: 0.7793 (t0) cc_final: 0.7505 (t0) REVERT: B 171 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7659 (pp30) REVERT: B 431 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7962 (p90) REVERT: C 168 HIS cc_start: 0.7144 (m170) cc_final: 0.6885 (m170) REVERT: C 193 ASN cc_start: 0.7505 (m-40) cc_final: 0.7103 (m110) REVERT: C 431 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7896 (p90) REVERT: D 162 LYS cc_start: 0.6210 (tptt) cc_final: 0.5738 (tttp) REVERT: D 166 ASN cc_start: 0.8047 (m110) cc_final: 0.7756 (m110) REVERT: D 171 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7423 (pp30) REVERT: D 262 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7202 (mp-120) REVERT: D 418 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7029 (tp30) REVERT: D 431 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7877 (p90) outliers start: 58 outliers final: 41 residues processed: 236 average time/residue: 0.3077 time to fit residues: 119.4563 Evaluate side-chains 227 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 178 time to evaluate : 2.472 ------------------------------------------------------------------------------- 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 262 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 558 THR 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 431 PHE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 445 LEU 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 C residue 767 ASN Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 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 558 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.7980 chunk 240 optimal weight: 8.9990 chunk 219 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 232 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 767 ASN B 767 ASN C 169 ASN D 169 ASN D 767 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4276 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= 0.143 Angle : 0.523 10.207 31176 Z= 0.272 Chirality : 0.038 0.141 3340 Planarity : 0.003 0.039 3756 Dihedral : 16.592 122.136 4524 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.38 % Allowed : 14.95 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2588 helix: 1.02 (0.14), residues: 1520 sheet: -2.87 (0.52), residues: 64 loop : -1.47 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 754 HIS 0.004 0.000 HIS A 168 PHE 0.022 0.001 PHE C 431 TYR 0.013 0.001 TYR A 732 ARG 0.003 0.000 ARG D 411 *********************** 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 246 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 191 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5946 (tptm) cc_final: 0.5613 (tttp) REVERT: A 166 ASN cc_start: 0.7979 (m110) cc_final: 0.7712 (m-40) REVERT: A 169 ASN cc_start: 0.7885 (t0) cc_final: 0.7619 (t0) REVERT: A 216 MET cc_start: 0.7722 (tpp) cc_final: 0.7394 (tpp) REVERT: A 431 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7903 (p90) REVERT: A 718 MET cc_start: 0.6236 (pmm) cc_final: 0.6016 (pmm) REVERT: B 162 LYS cc_start: 0.5933 (tptt) cc_final: 0.5275 (tttp) REVERT: B 169 ASN cc_start: 0.7766 (t0) cc_final: 0.7472 (t0) REVERT: B 171 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7712 (pp30) REVERT: B 321 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7870 (mm) REVERT: B 431 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7953 (p90) REVERT: B 748 GLU cc_start: 0.5955 (tm-30) cc_final: 0.5670 (tm-30) REVERT: C 168 HIS cc_start: 0.7240 (m170) cc_final: 0.7020 (m170) REVERT: C 193 ASN cc_start: 0.7487 (m-40) cc_final: 0.7109 (m-40) REVERT: C 431 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7862 (p90) REVERT: D 162 LYS cc_start: 0.6261 (tptt) cc_final: 0.5631 (tttp) REVERT: D 166 ASN cc_start: 0.8071 (m110) cc_final: 0.7777 (m-40) REVERT: D 262 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7048 (mp-120) REVERT: D 431 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7880 (p90) outliers start: 55 outliers final: 41 residues processed: 236 average time/residue: 0.3267 time to fit residues: 124.6305 Evaluate side-chains 225 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 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 558 THR 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 321 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 177 LEU 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 380 HIS 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 131 LEU Chi-restraints excluded: chain D residue 169 ASN 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 363 GLU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 117 optimal weight: 0.4980 chunk 171 optimal weight: 0.7980 chunk 259 optimal weight: 7.9990 chunk 238 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 159 optimal weight: 0.2980 chunk 126 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 767 ASN B 767 ASN D 168 HIS D 169 ASN D 767 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4389 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= 0.142 Angle : 0.537 11.193 31176 Z= 0.281 Chirality : 0.038 0.141 3340 Planarity : 0.003 0.039 3756 Dihedral : 16.257 119.078 4524 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.17 % Allowed : 15.25 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2588 helix: 1.14 (0.14), residues: 1520 sheet: -2.79 (0.52), residues: 64 loop : -1.47 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 754 HIS 0.004 0.001 HIS D 168 PHE 0.022 0.001 PHE C 431 TYR 0.012 0.001 TYR A 732 ARG 0.003 0.000 ARG D 411 ********************** 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 238 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 188 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5909 (tptm) cc_final: 0.5578 (tttp) REVERT: A 166 ASN cc_start: 0.7973 (m110) cc_final: 0.7715 (m-40) REVERT: A 169 ASN cc_start: 0.7901 (t0) cc_final: 0.7646 (t0) REVERT: A 216 MET cc_start: 0.7728 (tpp) cc_final: 0.7399 (tpp) REVERT: A 431 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7860 (p90) REVERT: A 718 MET cc_start: 0.6189 (pmm) cc_final: 0.5969 (pmm) REVERT: B 169 ASN cc_start: 0.7810 (t0) cc_final: 0.7526 (t0) REVERT: B 171 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7701 (pp30) REVERT: B 321 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7868 (mm) REVERT: B 431 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7900 (p90) REVERT: C 168 HIS cc_start: 0.7237 (m170) cc_final: 0.7014 (m170) REVERT: C 193 ASN cc_start: 0.7482 (m-40) cc_final: 0.7080 (m110) REVERT: C 431 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7847 (p90) REVERT: D 166 ASN cc_start: 0.8045 (m110) cc_final: 0.7427 (m-40) REVERT: D 168 HIS cc_start: 0.5583 (OUTLIER) cc_final: 0.5116 (p90) REVERT: D 431 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7864 (p90) outliers start: 50 outliers final: 36 residues processed: 229 average time/residue: 0.2988 time to fit residues: 112.3930 Evaluate side-chains 222 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 179 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 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 558 THR 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 321 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 PHE 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 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 380 HIS 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 169 ASN 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 431 PHE Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 190 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 212 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 ASN B 767 ASN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS D 169 ASN D 767 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.152564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107019 restraints weight = 37153.548| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.76 r_work: 0.3389 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4490 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= 0.139 Angle : 0.535 10.799 31176 Z= 0.279 Chirality : 0.037 0.141 3340 Planarity : 0.003 0.038 3756 Dihedral : 15.855 117.147 4524 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.91 % Allowed : 15.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2588 helix: 1.24 (0.14), residues: 1520 sheet: -2.81 (0.48), residues: 84 loop : -1.43 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 754 HIS 0.005 0.000 HIS D 168 PHE 0.022 0.001 PHE C 431 TYR 0.011 0.001 TYR A 732 ARG 0.003 0.000 ARG C 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4364.87 seconds wall clock time: 79 minutes 16.73 seconds (4756.73 seconds total)