Starting phenix.real_space_refine on Fri Aug 7 07:37:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh2_37526/08_2026/8wh2_37526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh2_37526/08_2026/8wh2_37526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wh2_37526/08_2026/8wh2_37526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh2_37526/08_2026/8wh2_37526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wh2_37526/08_2026/8wh2_37526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh2_37526/08_2026/8wh2_37526.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 15 5.49 5 Mg 1 5.21 5 S 85 5.16 5 C 12742 2.51 5 N 3539 2.21 5 O 3814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20196 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3443 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 4, 'PHE:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 169 Chain: "B" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3446 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 6, 'ASP:plan': 9, 'PHE:plan': 7, 'HIS:plan': 3, 'TYR:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 180 Chain: "C" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3041 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 737 Unresolved non-hydrogen angles: 932 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'ASN:plan1': 16, 'GLU:plan': 15, 'ARG:plan': 11, 'ASP:plan': 19, 'TYR:plan': 9, 'PHE:plan': 12, 'GLN:plan1': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 391 Chain: "D" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3411 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 297 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 5, 'PHE:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 190 Chain: "E" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3117 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 661 Unresolved non-hydrogen angles: 834 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 14, 'ARG:plan': 10, 'ASP:plan': 13, 'PHE:plan': 11, 'HIS:plan': 5, 'TYR:plan': 6, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 340 Chain: "F" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3526 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 3, 'PHE:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 133 Chain: "T" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 693 residue: pdb=" N ASP C 335 " occ=0.71 ... (6 atoms not shown) pdb=" OD2 ASP C 335 " occ=0.71 residue: pdb=" N THR C 342 " occ=0.79 ... (5 atoms not shown) pdb=" CG2 THR C 342 " occ=0.79 residue: pdb=" N GLU C 343 " occ=0.87 ... (3 atoms not shown) pdb=" CB GLU C 343 " occ=0.87 residue: pdb=" N ARG C 344 " occ=0.47 ... (3 atoms not shown) pdb=" CB ARG C 344 " occ=0.47 residue: pdb=" N GLY C 345 " occ=0.43 ... (2 atoms not shown) pdb=" O GLY C 345 " occ=0.43 residue: pdb=" N ASN C 352 " occ=0.51 ... (6 atoms not shown) pdb=" ND2 ASN C 352 " occ=0.51 residue: pdb=" N ASN C 353 " occ=0.68 ... (6 atoms not shown) pdb=" ND2 ASN C 353 " occ=0.68 residue: pdb=" N TRP C 355 " occ=0.76 ... (12 atoms not shown) pdb=" CH2 TRP C 355 " occ=0.76 residue: pdb=" N LYS C 356 " occ=0.70 ... (7 atoms not shown) pdb=" NZ LYS C 356 " occ=0.70 residue: pdb=" N PHE C 357 " occ=0.79 ... (9 atoms not shown) pdb=" CZ PHE C 357 " occ=0.79 residue: pdb=" N ASN C 358 " occ=0.49 ... (3 atoms not shown) pdb=" CB ASN C 358 " occ=0.49 residue: pdb=" N SER C 359 " occ=0.66 ... (4 atoms not shown) pdb=" OG SER C 359 " occ=0.66 ... (remaining 681 not shown) Time building chain proxies: 4.43, per 1000 atoms: 0.22 Number of scatterers: 20196 At special positions: 0 Unit cell: (122.64, 131.04, 117.6, 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 85 16.00 P 15 15.00 Mg 1 11.99 O 3814 8.00 N 3539 7.00 C 12742 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 816.7 milliseconds 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 40 sheets defined 46.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.578A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.822A pdb=" N LEU A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.811A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.862A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.629A pdb=" N GLU A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.585A pdb=" N ASN A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 696 through 704 removed outlier: 3.736A pdb=" N THR A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 716 through 724 Processing helix chain 'A' and resid 735 through 747 removed outlier: 3.545A pdb=" N LYS A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 removed outlier: 6.795A pdb=" N HIS A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.749A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.596A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 Processing helix chain 'B' and resid 616 through 619 removed outlier: 3.608A pdb=" N ARG B 619 " --> pdb=" O ALA B 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 619' Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 693 through 695 No H-bonds generated for 'chain 'B' and resid 693 through 695' Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.587A pdb=" N THR B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 716 through 721 Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 736 through 745 Processing helix chain 'B' and resid 748 through 764 removed outlier: 3.616A pdb=" N PHE B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N HIS B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 362 through 372 Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.555A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.512A pdb=" N LEU C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 434 Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.864A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 489 removed outlier: 3.911A pdb=" N CYS C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 579 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.536A pdb=" N ASN C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 4.539A pdb=" N GLY C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 679 Processing helix chain 'C' and resid 695 through 705 removed outlier: 4.332A pdb=" N TYR C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 714 removed outlier: 3.628A pdb=" N HIS C 713 " --> pdb=" O SER C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 724 Processing helix chain 'C' and resid 735 through 747 removed outlier: 4.124A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 763 Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.702A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.691A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.732A pdb=" N LYS D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 435' Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.571A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU D 460 " --> pdb=" O PRO D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 541 through 547 removed outlier: 3.568A pdb=" N ALA D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 577 Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.552A pdb=" N ASN D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 4.589A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 removed outlier: 3.631A pdb=" N PHE D 668 " --> pdb=" O TYR D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 695 removed outlier: 3.792A pdb=" N ILE D 693 " --> pdb=" O PRO D 690 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 696 through 705 removed outlier: 3.717A pdb=" N THR D 704 " --> pdb=" O LEU D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 716 through 721 Processing helix chain 'D' and resid 736 through 745 removed outlier: 3.638A pdb=" N LYS D 745 " --> pdb=" O GLN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 764 removed outlier: 6.865A pdb=" N HIS D 754 " --> pdb=" O ARG D 750 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 784 Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.538A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 383 Processing helix chain 'E' and resid 389 through 400 Processing helix chain 'E' and resid 429 through 434 removed outlier: 3.591A pdb=" N ASP E 432 " --> pdb=" O SER E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.568A pdb=" N LYS E 450 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 475 through 488 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 528 through 532 removed outlier: 3.803A pdb=" N ILE E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 532 " --> pdb=" O GLN E 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 528 through 532' Processing helix chain 'E' and resid 541 through 546 removed outlier: 3.508A pdb=" N ASN E 546 " --> pdb=" O PRO E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 579 Processing helix chain 'E' and resid 614 through 619 Processing helix chain 'E' and resid 635 through 640 Processing helix chain 'E' and resid 653 through 661 removed outlier: 4.477A pdb=" N GLY E 657 " --> pdb=" O GLU E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 679 Processing helix chain 'E' and resid 689 through 695 Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 696 through 703 removed outlier: 4.490A pdb=" N GLY E 703 " --> pdb=" O TYR E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 715 Proline residue: E 715 - end of helix Processing helix chain 'E' and resid 716 through 723 removed outlier: 4.103A pdb=" N LEU E 720 " --> pdb=" O LEU E 716 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 722 " --> pdb=" O THR E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 736 through 744 removed outlier: 3.921A pdb=" N SER E 744 " --> pdb=" O GLN E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 763 Processing helix chain 'E' and resid 779 through 784 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.695A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 382 removed outlier: 3.785A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 430 through 435 removed outlier: 3.918A pdb=" N LYS F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 469 Processing helix chain 'F' and resid 475 through 488 Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 508 through 521 removed outlier: 3.663A pdb=" N THR F 512 " --> pdb=" O GLY F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 541 through 546 Processing helix chain 'F' and resid 571 through 576 removed outlier: 3.924A pdb=" N LYS F 575 " --> pdb=" O SER F 571 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS F 576 " --> pdb=" O ASP F 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 571 through 576' Processing helix chain 'F' and resid 632 through 641 removed outlier: 4.361A pdb=" N GLU F 637 " --> pdb=" O PRO F 633 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA F 638 " --> pdb=" O SER F 634 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN F 641 " --> pdb=" O GLU F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 661 Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 689 through 695 removed outlier: 3.564A pdb=" N GLU F 692 " --> pdb=" O THR F 689 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE F 693 " --> pdb=" O PRO F 690 " (cutoff:3.500A) Proline residue: F 694 - end of helix No H-bonds generated for 'chain 'F' and resid 689 through 695' Processing helix chain 'F' and resid 696 through 705 removed outlier: 3.904A pdb=" N GLY F 703 " --> pdb=" O TYR F 699 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR F 704 " --> pdb=" O LEU F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 715 Proline residue: F 715 - end of helix Processing helix chain 'F' and resid 716 through 724 Processing helix chain 'F' and resid 735 through 744 Processing helix chain 'F' and resid 748 through 763 removed outlier: 6.926A pdb=" N HIS F 754 " --> pdb=" O ARG F 750 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP F 755 " --> pdb=" O LEU F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 779 through 784 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 8.864A pdb=" N VAL A 404 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 341 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.096A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.221A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 706 through 708 Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 727 Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AA9, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AB1, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB2, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.362A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB4, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.451A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 706 through 708 Processing sheet with id=AB6, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.553A pdb=" N LEU B 734 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 774 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB8, first strand: chain 'C' and resid 412 through 415 Processing sheet with id=AB9, first strand: chain 'C' and resid 524 through 527 removed outlier: 5.820A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N CYS C 555 " --> pdb=" O ASP C 603 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.799A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AC3, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC4, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.938A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 524 through 527 removed outlier: 6.263A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC7, first strand: chain 'D' and resid 629 through 630 removed outlier: 6.754A pdb=" N HIS D 629 " --> pdb=" O LYS D 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AC9, first strand: chain 'D' and resid 726 through 728 Processing sheet with id=AD1, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD2, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AD3, first strand: chain 'E' and resid 524 through 526 removed outlier: 6.663A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 628 through 631 removed outlier: 6.053A pdb=" N HIS E 629 " --> pdb=" O LYS E 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 706 through 707 Processing sheet with id=AD6, first strand: chain 'E' and resid 726 through 728 removed outlier: 3.990A pdb=" N ILE E 726 " --> pdb=" O THR E 733 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR E 733 " --> pdb=" O ILE E 726 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AD8, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AD9, first strand: chain 'F' and resid 524 through 526 removed outlier: 6.042A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 581 through 582 Processing sheet with id=AE2, first strand: chain 'F' and resid 629 through 630 removed outlier: 6.593A pdb=" N HIS F 629 " --> pdb=" O LYS F 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 706 through 708 Processing sheet with id=AE4, first strand: chain 'F' and resid 726 through 728 819 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.19: 1 1.19 - 1.35: 6747 1.35 - 1.50: 5403 1.50 - 1.66: 8301 1.66 - 1.82: 120 Bond restraints: 20572 Sorted by residual: bond pdb=" CB PRO E 470 " pdb=" CG PRO E 470 " ideal model delta sigma weight residual 1.492 1.039 0.453 5.00e-02 4.00e+02 8.22e+01 bond pdb=" CG PRO E 470 " pdb=" CD PRO E 470 " ideal model delta sigma weight residual 1.503 1.247 0.256 3.40e-02 8.65e+02 5.68e+01 bond pdb=" N PRO E 470 " pdb=" CA PRO E 470 " ideal model delta sigma weight residual 1.466 1.533 -0.067 1.17e-02 7.31e+03 3.29e+01 bond pdb=" CB PRO C 682 " pdb=" CG PRO C 682 " ideal model delta sigma weight residual 1.492 1.660 -0.168 5.00e-02 4.00e+02 1.12e+01 bond pdb=" C1' DC T 4 " pdb=" N1 DC T 4 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.86e+00 ... (remaining 20567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 28030 14.77 - 29.53: 1 29.53 - 44.30: 2 44.30 - 59.06: 0 59.06 - 73.83: 1 Bond angle restraints: 28034 Sorted by residual: angle pdb=" CB PRO E 470 " pdb=" CG PRO E 470 " pdb=" CD PRO E 470 " ideal model delta sigma weight residual 106.10 179.93 -73.83 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO E 470 " pdb=" CD PRO E 470 " pdb=" CG PRO E 470 " ideal model delta sigma weight residual 103.20 73.09 30.11 1.50e+00 4.44e-01 4.03e+02 angle pdb=" CA PRO E 470 " pdb=" CB PRO E 470 " pdb=" CG PRO E 470 " ideal model delta sigma weight residual 104.50 69.47 35.03 1.90e+00 2.77e-01 3.40e+02 angle pdb=" CA PRO C 410 " pdb=" N PRO C 410 " pdb=" CD PRO C 410 " ideal model delta sigma weight residual 112.00 96.96 15.04 1.40e+00 5.10e-01 1.15e+02 angle pdb=" CA PRO C 682 " pdb=" N PRO C 682 " pdb=" CD PRO C 682 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.23e+01 ... (remaining 28029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.57: 12060 34.57 - 69.14: 342 69.14 - 103.71: 16 103.71 - 138.29: 1 138.29 - 172.86: 4 Dihedral angle restraints: 12423 sinusoidal: 4272 harmonic: 8151 Sorted by residual: dihedral pdb=" N PRO E 470 " pdb=" CG PRO E 470 " pdb=" CD PRO E 470 " pdb=" CB PRO E 470 " ideal model delta sinusoidal sigma weight residual 30.00 177.81 -147.81 1 1.50e+01 4.44e-03 7.88e+01 dihedral pdb=" CA ILE B 681 " pdb=" C ILE B 681 " pdb=" N PRO B 682 " pdb=" CA PRO B 682 " ideal model delta harmonic sigma weight residual -180.00 -143.95 -36.05 0 5.00e+00 4.00e-02 5.20e+01 dihedral pdb=" CA ILE A 681 " pdb=" C ILE A 681 " pdb=" N PRO A 682 " pdb=" CA PRO A 682 " ideal model delta harmonic sigma weight residual -180.00 -146.56 -33.44 0 5.00e+00 4.00e-02 4.47e+01 ... (remaining 12420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2617 0.049 - 0.099: 532 0.099 - 0.148: 132 0.148 - 0.197: 6 0.197 - 0.247: 2 Chirality restraints: 3289 Sorted by residual: chirality pdb=" CA PRO C 410 " pdb=" N PRO C 410 " pdb=" C PRO C 410 " pdb=" CB PRO C 410 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO E 470 " pdb=" N PRO E 470 " pdb=" C PRO E 470 " pdb=" CB PRO E 470 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO C 580 " pdb=" N PRO C 580 " pdb=" C PRO C 580 " pdb=" CB PRO C 580 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 3286 not shown) Planarity restraints: 3625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 681 " -0.093 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO C 682 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO C 682 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 682 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 469 " -0.091 5.00e-02 4.00e+02 1.26e-01 2.56e+01 pdb=" N PRO E 470 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO E 470 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO E 470 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 579 " 0.071 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO C 580 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO C 580 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 580 " 0.055 5.00e-02 4.00e+02 ... (remaining 3622 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 100 2.56 - 3.15: 15236 3.15 - 3.73: 29816 3.73 - 4.32: 41694 4.32 - 4.90: 70201 Nonbonded interactions: 157047 Sorted by model distance: nonbonded pdb=" OG SER B 510 " pdb="MG MG B 802 " model vdw 1.977 2.170 nonbonded pdb=" O3G ATP B 801 " pdb="MG MG B 802 " model vdw 2.122 2.170 nonbonded pdb=" NH2 ARG F 585 " pdb=" OP2 DC T 5 " model vdw 2.172 3.120 nonbonded pdb=" O GLU E 504 " pdb=" OG1 THR E 507 " model vdw 2.206 3.040 nonbonded pdb=" O ASP E 421 " pdb=" N GLY E 425 " model vdw 2.221 3.120 ... (remaining 157042 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 323 or (resid 324 and (name N or name CA or name C or name \ O or name CB )) or resid 325 through 342 or (resid 343 through 344 and (name N \ or name CA or name C or name O or name CB )) or resid 345 or (resid 346 and (nam \ e N or name CA or name C or name O or name CB )) or resid 347 through 348 or (re \ sid 349 and (name N or name CA or name C or name O or name CB )) or resid 350 th \ rough 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) \ or resid 357 or (resid 358 through 361 and (name N or name CA or name C or name \ O or name CB )) or resid 362 through 386 or (resid 387 and (name N or name CA o \ r name C or name O or name CB )) or resid 388 through 390 or (resid 391 and (nam \ e N or name CA or name C or name O or name CB )) or resid 392 through 395 or (re \ sid 396 and (name N or name CA or name C or name O or name CB )) or resid 397 or \ (resid 398 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 9 through 405 or (resid 406 and (name N or name CA or name C or name O or name C \ B )) or resid 407 through 416 or (resid 417 and (name N or name CA or name C or \ name O or name CB )) or resid 418 through 423 or (resid 424 and (name N or name \ CA or name C or name O or name CB )) or resid 425 or (resid 426 and (name N or n \ ame CA or name C or name O or name CB )) or resid 427 or (resid 428 and (name N \ or name CA or name C or name O or name CB )) or resid 429 through 436 or (resid \ 437 and (name N or name CA or name C or name O or name CB )) or resid 438 throug \ h 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) or \ resid 446 or (resid 447 and (name N or name CA or name C or name O or name CB )) \ or resid 448 or (resid 449 through 450 and (name N or name CA or name C or name \ O or name CB )) or resid 451 or (resid 452 through 453 and (name N or name CA o \ r name C or name O or name CB )) or resid 454 through 455 or (resid 456 through \ 457 and (name N or name CA or name C or name O or name CB )) or resid 458 or (re \ sid 459 through 463 and (name N or name CA or name C or name O or name CB )) or \ resid 464 through 467 or (resid 468 and (name N or name CA or name C or name O o \ r name CB )) or resid 469 through 472 or (resid 473 and (name N or name CA or na \ me C or name O or name CB )) or resid 474 or (resid 475 and (name N or name CA o \ r name C or name O or name CB )) or resid 476 through 477 or (resid 478 through \ 480 and (name N or name CA or name C or name O or name CB )) or resid 481 throug \ h 482 or (resid 483 and (name N or name CA or name C or name O or name CB )) or \ resid 484 through 489 or (resid 490 and (name N or name CA or name C or name O o \ r name CB )) or resid 491 through 497 or (resid 498 through 499 and (name N or n \ ame CA or name C or name O or name CB )) or resid 500 through 504 or (resid 505 \ through 507 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 8 or (resid 509 and (name N or name CA or name C or name O or name CB )) or resi \ d 510 through 512 or (resid 513 through 514 and (name N or name CA or name C or \ name O or name CB )) or resid 515 or (resid 516 through 517 and (name N or name \ CA or name C or name O or name CB )) or resid 518 through 519 or (resid 520 and \ (name N or name CA or name C or name O or name CB )) or resid 521 or (resid 522 \ and (name N or name CA or name C or name O or name CB )) or resid 523 or (resid \ 524 through 526 and (name N or name CA or name C or name O or name CB )) or resi \ d 527 through 528 or (resid 529 through 532 and (name N or name CA or name C or \ name O or name CB )) or resid 533 or (resid 534 through 538 and (name N or name \ CA or name C or name O or name CB )) or resid 539 or (resid 540 through 564 and \ (name N or name CA or name C or name O or name CB )) or (resid 565 through 583 a \ nd (name N or name CA or name C or name O or name CB )) or resid 584 or (resid 5 \ 85 through 595 and (name N or name CA or name C or name O or name CB )) or resid \ 596 through 599 or (resid 600 and (name N or name CA or name C or name O or nam \ e CB )) or resid 601 or (resid 602 through 607 and (name N or name CA or name C \ or name O or name CB )) or resid 608 through 610 or (resid 611 and (name N or na \ me CA or name C or name O or name CB )) or resid 612 through 613 or (resid 614 t \ hrough 623 and (name N or name CA or name C or name O or name CB )) or resid 624 \ or (resid 625 and (name N or name CA or name C or name O or name CB )) or resid \ 626 or (resid 627 and (name N or name CA or name C or name O or name CB )) or r \ esid 628 through 635 or (resid 636 through 653 and (name N or name CA or name C \ or name O or name CB )) or resid 654 or (resid 655 and (name N or name CA or nam \ e C or name O or name CB )) or resid 656 through 657 or (resid 658 and (name N o \ r name CA or name C or name O or name CB )) or resid 659 or (resid 660 through 6 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 662 or (res \ id 663 and (name N or name CA or name C or name O or name CB )) or resid 664 thr \ ough 665 or (resid 666 through 669 and (name N or name CA or name C or name O or \ name CB )) or resid 670 or (resid 671 and (name N or name CA or name C or name \ O or name CB )) or resid 672 through 673 or (resid 674 and (name N or name CA or \ name C or name O or name CB )) or resid 675 through 676 or (resid 677 through 6 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 679 or (res \ id 680 through 682 and (name N or name CA or name C or name O or name CB )) or r \ esid 683 through 688 or (resid 689 through 702 and (name N or name CA or name C \ or name O or name CB )) or resid 703 or (resid 704 through 723 and (name N or na \ me CA or name C or name O or name CB )) or resid 724 through 785)) selection = (chain 'B' and (resid 323 or (resid 324 and (name N or name CA or name C or name \ O or name CB )) or resid 325 through 342 or (resid 343 through 344 and (name N \ or name CA or name C or name O or name CB )) or resid 345 or (resid 346 and (nam \ e N or name CA or name C or name O or name CB )) or resid 347 through 348 or (re \ sid 349 and (name N or name CA or name C or name O or name CB )) or resid 350 th \ rough 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) \ or resid 357 through 358 or (resid 359 through 361 and (name N or name CA or na \ me C or name O or name CB )) or resid 362 through 376 or (resid 377 and (name N \ or name CA or name C or name O or name CB )) or resid 378 through 386 or (resid \ 387 and (name N or name CA or name C or name O or name CB )) or resid 388 throug \ h 390 or (resid 391 and (name N or name CA or name C or name O or name CB )) or \ resid 392 through 395 or (resid 396 and (name N or name CA or name C or name O o \ r name CB )) or resid 397 or (resid 398 and (name N or name CA or name C or name \ O or name CB )) or resid 399 through 404 or (resid 405 through 406 and (name N \ or name CA or name C or name O or name CB )) or resid 407 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throug \ h 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or \ resid 425 or (resid 426 and (name N or name CA or name C or name O or name CB )) \ or resid 427 or (resid 428 and (name N or name CA or name C or name O or name C \ B )) or resid 429 through 436 or (resid 437 and (name N or name CA or name C or \ name O or name CB )) or resid 438 through 444 or (resid 445 and (name N or name \ CA or name C or name O or name CB )) or resid 446 or (resid 447 and (name N or n \ ame CA or name C or name O or name CB )) or resid 448 or (resid 449 through 450 \ and (name N or name CA or name C or name O or name CB )) or resid 451 or (resid \ 452 through 453 and (name N or name CA or name C or name O or name CB )) or resi \ d 454 or (resid 455 through 457 and (name N or name CA or name C or name O or na \ me CB )) or resid 458 through 459 or (resid 460 through 463 and (name N or name \ CA or name C or name O or name CB )) or resid 464 through 467 or (resid 468 and \ (name N or name CA or name C or name O or name CB )) or resid 469 through 472 or \ (resid 473 and (name N or name CA or name C or name O or name CB )) or resid 47 \ 4 or (resid 475 and (name N or name CA or name C or name O or name CB )) or resi \ d 476 through 477 or (resid 478 through 480 and (name N or name CA or name C or \ name O or name CB )) or resid 481 through 482 or (resid 483 and (name N or name \ CA or name C or name O or name CB )) or resid 484 through 489 or (resid 490 and \ (name N or name CA or name C or name O or name CB )) or resid 491 through 497 or \ (resid 498 through 499 and (name N or name CA or name C or name O or name CB )) \ or resid 500 through 503 or (resid 504 through 507 and (name N or name CA or na \ me C or name O or name CB )) or resid 508 or (resid 509 and (name N or name CA o \ r name C or name O or name CB )) or resid 510 through 512 or (resid 513 through \ 514 and (name N or name CA or name C or name O or name CB )) or resid 515 or (re \ sid 516 through 517 and (name N or name CA or name C or name O or name CB )) or \ resid 518 through 519 or (resid 520 and (name N or name CA or name C or name O o \ r name CB )) or resid 521 or (resid 522 and (name N or name CA or name C or name \ O or name CB )) or resid 523 or (resid 524 through 526 and (name N or name CA o \ r name C or name O or name CB )) or resid 527 through 528 or (resid 529 through \ 532 and (name N or name CA or name C or name O or name CB )) or resid 533 or (re \ sid 534 through 538 and (name N or name CA or name C or name O or name CB )) or \ resid 539 or (resid 540 through 564 and (name N or name CA or name C or name O o \ r name CB )) or (resid 565 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 584 or (resid 585 through 595 and (name N or name CA or \ name C or name O or name CB )) or resid 596 through 599 or (resid 600 and (name \ N or name CA or name C or name O or name CB )) or resid 601 or (resid 602 throu \ gh 607 and (name N or name CA or name C or name O or name CB )) or resid 608 or \ (resid 609 and (name N or name CA or name C or name O or name CB )) or resid 610 \ or (resid 611 and (name N or name CA or name C or name O or name CB )) or resid \ 612 through 613 or (resid 614 through 623 and (name N or name CA or name C or n \ ame O or name CB )) or resid 624 or (resid 625 and (name N or name CA or name C \ or name O or name CB )) or resid 626 or (resid 627 and (name N or name CA or nam \ e C or name O or name CB )) or resid 628 through 630 or (resid 631 and (name N o \ r name CA or name C or name O or name CB )) or resid 632 through 635 or (resid 6 \ 36 through 653 and (name N or name CA or name C or name O or name CB )) or resid \ 654 or (resid 655 and (name N or name CA or name C or name O or name CB )) or r \ esid 656 through 657 or (resid 658 and (name N or name CA or name C or name O or \ name CB )) or resid 659 or (resid 660 through 661 and (name N or name CA or nam \ e C or name O or name CB )) or resid 662 or (resid 663 and (name N or name CA or \ name C or name O or name CB )) or resid 664 through 665 or (resid 666 through 6 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 670 or (res \ id 671 and (name N or name CA or name C or name O or name CB )) or resid 672 thr \ ough 673 or (resid 674 and (name N or name CA or name C or name O or name CB )) \ or resid 675 through 676 or (resid 677 through 678 and (name N or name CA or nam \ e C or name O or name CB )) or resid 679 or (resid 680 through 682 and (name N o \ r name CA or name C or name O or name CB )) or resid 683 through 684 or (resid 6 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 686 through \ 688 or (resid 689 through 702 and (name N or name CA or name C or name O or nam \ e CB )) or resid 703 or (resid 704 through 723 and (name N or name CA or name C \ or name O or name CB )) or resid 724 through 785)) selection = (chain 'C' and (resid 323 through 348 or (resid 349 and (name N or name CA or na \ me C or name O or name CB )) or resid 350 through 355 or (resid 356 and (name N \ or name CA or name C or name O or name CB )) or resid 357 through 358 or (resid \ 359 through 361 and (name N or name CA or name C or name O or name CB )) or resi \ d 362 through 376 or (resid 377 and (name N or name CA or name C or name O or na \ me CB )) or resid 378 through 386 or (resid 387 and (name N or name CA or name C \ or name O or name CB )) or resid 388 through 404 or (resid 405 through 406 and \ (name N or name CA or name C or name O or name CB )) or resid 407 through 416 or \ (resid 417 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 8 through 448 or (resid 449 through 450 and (name N or name CA or name C or name \ O or name CB )) or resid 451 through 454 or (resid 455 through 457 and (name N \ or name CA or name C or name O or name CB )) or resid 458 or (resid 459 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 467 or (resid 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 498 or (resid 499 and (name N or name CA or name C or name O o \ r name CB )) or resid 500 through 515 or (resid 516 through 517 and (name N or n \ ame CA or name C or name O or name CB )) or resid 518 through 519 or (resid 520 \ and (name N or name CA or name C or name O or name CB )) or resid 521 through 52 \ 8 or (resid 529 through 532 and (name N or name CA or name C or name O or name C \ B )) or resid 533 through 539 or (resid 540 through 564 and (name N or name CA o \ r name C or name O or name CB )) or (resid 565 through 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 or (resid 585 through 595 and ( \ name N or name CA or name C or name O or name CB )) or resid 596 through 602 or \ (resid 603 through 607 and (name N or name CA or name C or name O or name CB )) \ or resid 608 through 610 or (resid 611 and (name N or name CA or name C or name \ O or name CB )) or resid 612 through 613 or (resid 614 through 623 and (name N o \ r name CA or name C or name O or name CB )) or resid 624 through 630 or (resid 6 \ 31 and (name N or name CA or name C or name O or name CB )) or resid 632 through \ 635 or (resid 636 through 653 and (name N or name CA or name C or name O or nam \ e CB )) or resid 654 through 680 or (resid 681 through 682 and (name N or name C \ A or name C or name O or name CB )) or resid 683 through 785)) selection = (chain 'D' and (resid 323 or (resid 324 and (name N or name CA or name C or name \ O or name CB )) or resid 325 through 342 or (resid 343 through 344 and (name N \ or name CA or name C or name O or name CB )) or resid 345 or (resid 346 and (nam \ e N or name CA or name C or name O or name CB )) or resid 347 through 348 or (re \ sid 349 and (name N or name CA or name C or name O or name CB )) or resid 350 th \ rough 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) \ or resid 357 or (resid 358 through 361 and (name N or name CA or name C or name \ O or name CB )) or resid 362 through 376 or (resid 377 and (name N or name CA o \ r name C or name O or name CB )) or resid 378 through 386 or (resid 387 and (nam \ e N or name CA or name C or name O or name CB )) or resid 388 through 390 or (re \ sid 391 and (name N or name CA or name C or name O or name CB )) or resid 392 th \ rough 395 or (resid 396 and (name N or name CA or name C or name O or name CB )) \ or resid 397 or (resid 398 and (name N or name CA or name C or name O or name C \ B )) or resid 399 through 404 or (resid 405 through 406 and (name N or name CA o \ r name C or name O or name CB )) or resid 407 through 416 or (resid 417 and (nam \ e N or name CA or name C or name O or name CB )) or resid 418 through 423 or (re \ sid 424 and (name N or name CA or name C or name O or name CB )) or resid 425 or \ (resid 426 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 7 or (resid 428 and (name N or name CA or name C or name O or name CB )) or resi \ d 429 through 444 or (resid 445 and (name N or name CA or name C or name O or na \ me CB )) or resid 446 or (resid 447 and (name N or name CA or name C or name O o \ r name CB )) or resid 448 or (resid 449 through 450 and (name N or name CA or na \ me C or name O or name CB )) or resid 451 or (resid 452 through 453 and (name N \ or name CA or name C or name O or name CB )) or resid 454 or (resid 455 through \ 457 and (name N or name CA or name C or name O or name CB )) or resid 458 or (re \ sid 459 through 463 and (name N or name CA or name C or name O or name CB )) or \ resid 464 through 467 or (resid 468 and (name N or name CA or name C or name O o \ r name CB )) or resid 469 through 472 or (resid 473 and (name N or name CA or na \ me C or name O or name CB )) or resid 474 or (resid 475 and (name N or name CA o \ r name C or name O or name CB )) or resid 476 through 477 or (resid 478 through \ 480 and (name N or name CA or name C or name O or name CB )) or resid 481 throug \ h 482 or (resid 483 and (name N or name CA or name C or name O or name CB )) or \ resid 484 through 489 or (resid 490 and (name N or name CA or name C or name O o \ r name CB )) or resid 491 through 497 or (resid 498 through 499 and (name N or n \ ame CA or name C or name O or name CB )) or resid 500 through 504 or (resid 505 \ through 507 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 8 or (resid 509 and (name N or name CA or name C or name O or name CB )) or resi \ d 510 through 512 or (resid 513 through 514 and (name N or name CA or name C or \ name O or name CB )) or resid 515 or (resid 516 through 517 and (name N or name \ CA or name C or name O or name CB )) or resid 518 through 519 or (resid 520 and \ (name N or name CA or name C or name O or name CB )) or resid 521 or (resid 522 \ and (name N or name CA or name C or name O or name CB )) or resid 523 or (resid \ 524 through 526 and (name N or name CA or name C or name O or name CB )) or resi \ d 527 through 529 or (resid 530 through 532 and (name N or name CA or name C or \ name O or name CB )) or resid 533 or (resid 534 through 538 and (name N or name \ CA or name C or name O or name CB )) or resid 539 or (resid 540 through 564 and \ (name N or name CA or name C or name O or name CB )) or (resid 565 through 583 a \ nd (name N or name CA or name C or name O or name CB )) or resid 584 or (resid 5 \ 85 through 595 and (name N or name CA or name C or name O or name CB )) or resid \ 596 through 599 or (resid 600 and (name N or name CA or name C or name O or nam \ e CB )) or resid 601 or (resid 602 through 607 and (name N or name CA or name C \ or name O or name CB )) or resid 608 or (resid 609 and (name N or name CA or nam \ e C or name O or name CB )) or resid 610 through 613 or (resid 614 through 623 a \ nd (name N or name CA or name C or name O or name CB )) or resid 624 or (resid 6 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 626 or (res \ id 627 and (name N or name CA or name C or name O or name CB )) or resid 628 thr \ ough 630 or (resid 631 and (name N or name CA or name C or name O or name CB )) \ or resid 632 through 635 or (resid 636 through 653 and (name N or name CA or nam \ e C or name O or name CB )) or resid 654 or (resid 655 and (name N or name CA or \ name C or name O or name CB )) or resid 656 through 659 or (resid 660 through 6 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 662 or (res \ id 663 and (name N or name CA or name C or name O or name CB )) or resid 664 thr \ ough 665 or (resid 666 through 669 and (name N or name CA or name C or name O or \ name CB )) or resid 670 or (resid 671 and (name N or name CA or name C or name \ O or name CB )) or resid 672 through 673 or (resid 674 and (name N or name CA or \ name C or name O or name CB )) or resid 675 through 676 or (resid 677 through 6 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 679 or (res \ id 680 through 682 and (name N or name CA or name C or name O or name CB )) or r \ esid 683 through 684 or (resid 685 and (name N or name CA or name C or name O or \ name CB )) or resid 686 through 688 or (resid 689 through 702 and (name N or na \ me CA or name C or name O or name CB )) or resid 703 or (resid 704 through 723 a \ nd (name N or name CA or name C or name O or name CB )) or resid 724 through 785 \ )) selection = (chain 'E' and (resid 323 or (resid 324 and (name N or name CA or name C or name \ O or name CB )) or resid 325 through 343 or (resid 344 and (name N or name CA o \ r name C or name O or name CB )) or resid 345 or (resid 346 and (name N or name \ CA or name C or name O or name CB )) or resid 347 through 376 or (resid 377 and \ (name N or name CA or name C or name O or name CB )) or resid 378 through 390 or \ (resid 391 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 2 through 395 or (resid 396 and (name N or name CA or name C or name O or name C \ B )) or resid 397 through 423 or (resid 424 and (name N or name CA or name C or \ name O or name CB )) or resid 425 or (resid 426 and (name N or name CA or name C \ or name O or name CB )) or resid 427 or (resid 428 and (name N or name CA or na \ me C or name O or name CB )) or resid 429 through 436 or (resid 437 and (name N \ or name CA or name C or name O or name CB )) or resid 438 through 451 or (resid \ 452 through 453 and (name N or name CA or name C or name O or name CB )) or resi \ d 454 or (resid 455 through 457 and (name N or name CA or name C or name O or na \ me CB )) or resid 458 through 459 or (resid 460 through 463 and (name N or name \ CA or name C or name O or name CB )) or resid 464 through 472 or (resid 473 and \ (name N or name CA or name C or name O or name CB )) or resid 474 or (resid 475 \ and (name N or name CA or name C or name O or name CB )) or resid 476 through 47 \ 7 or (resid 478 through 480 and (name N or name CA or name C or name O or name C \ B )) or resid 481 through 489 or (resid 490 and (name N or name CA or name C or \ name O or name CB )) or resid 491 through 506 or (resid 507 and (name N or name \ CA or name C or name O or name CB )) or resid 508 or (resid 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 512 or (resid 513 \ through 514 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 5 through 516 or (resid 517 and (name N or name CA or name C or name O or name C \ B )) or resid 518 through 523 or (resid 524 through 526 and (name N or name CA o \ r name C or name O or name CB )) or resid 527 through 528 or (resid 529 through \ 532 and (name N or name CA or name C or name O or name CB )) or resid 533 throug \ h 599 or (resid 600 and (name N or name CA or name C or name O or name CB )) or \ resid 601 or (resid 602 through 607 and (name N or name CA or name C or name O o \ r name CB )) or resid 608 or (resid 609 and (name N or name CA or name C or name \ O or name CB )) or resid 610 or (resid 611 and (name N or name CA or name C or \ name O or name CB )) or resid 612 through 614 or (resid 615 through 623 and (nam \ e N or name CA or name C or name O or name CB )) or resid 624 or (resid 625 and \ (name N or name CA or name C or name O or name CB )) or resid 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 63 \ 0 or (resid 631 and (name N or name CA or name C or name O or name CB )) or resi \ d 632 through 640 or (resid 641 through 653 and (name N or name CA or name C or \ name O or name CB )) or resid 654 or (resid 655 and (name N or name CA or name C \ or name O or name CB )) or resid 656 through 657 or (resid 658 and (name N or n \ ame CA or name C or name O or name CB )) or resid 659 or (resid 660 through 661 \ and (name N or name CA or name C or name O or name CB )) or resid 662 or (resid \ 663 and (name N or name CA or name C or name O or name CB )) or resid 664 throug \ h 665 or (resid 666 through 669 and (name N or name CA or name C or name O or na \ me CB )) or resid 670 or (resid 671 and (name N or name CA or name C or name O o \ r name CB )) or resid 672 through 673 or (resid 674 and (name N or name CA or na \ me C or name O or name CB )) or resid 675 through 676 or (resid 677 through 678 \ and (name N or name CA or name C or name O or name CB )) or resid 679 through 68 \ 0 or (resid 681 through 682 and (name N or name CA or name C or name O or name C \ B )) or resid 683 through 684 or (resid 685 and (name N or name CA or name C or \ name O or name CB )) or resid 686 through 688 or (resid 689 through 702 and (nam \ e N or name CA or name C or name O or name CB )) or resid 703 through 785)) selection = (chain 'F' and (resid 323 or (resid 324 and (name N or name CA or name C or name \ O or name CB )) or resid 325 through 342 or (resid 343 through 344 and (name N \ or name CA or name C or name O or name CB )) or resid 345 or (resid 346 and (nam \ e N or name CA or name C or name O or name CB )) or resid 347 through 348 or (re \ sid 349 and (name N or name CA or name C or name O or name CB )) or resid 350 th \ rough 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) \ or resid 357 or (resid 358 through 361 and (name N or name CA or name C or name \ O or name CB )) or resid 362 through 376 or (resid 377 and (name N or name CA o \ r name C or name O or name CB )) or resid 378 through 386 or (resid 387 and (nam \ e N or name CA or name C or name O or name CB )) or resid 388 through 390 or (re \ sid 391 and (name N or name CA or name C or name O or name CB )) or resid 392 th \ rough 395 or (resid 396 and (name N or name CA or name C or name O or name CB )) \ or resid 397 or (resid 398 and (name N or name CA or name C or name O or name C \ B )) or resid 399 through 404 or (resid 405 through 406 and (name N or name CA o \ r name C or name O or name CB )) or resid 407 through 416 or (resid 417 and (nam \ e N or name CA or name C or name O or name CB )) or resid 418 through 423 or (re \ sid 424 and (name N or name CA or name C or name O or name CB )) or resid 425 or \ (resid 426 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 7 or (resid 428 and (name N or name CA or name C or name O or name CB )) or resi \ d 429 through 436 or (resid 437 and (name N or name CA or name C or name O or na \ me CB )) or resid 438 through 444 or (resid 445 and (name N or name CA or name C \ or name O or name CB )) or resid 446 or (resid 447 and (name N or name CA or na \ me C or name O or name CB )) or resid 448 or (resid 449 through 450 and (name N \ or name CA or name C or name O or name CB )) or resid 451 or (resid 452 through \ 453 and (name N or name CA or name C or name O or name CB )) or resid 454 or (re \ sid 455 through 457 and (name N or name CA or name C or name O or name CB )) or \ resid 458 or (resid 459 through 463 and (name N or name CA or name C or name O o \ r name CB )) or resid 464 through 467 or (resid 468 and (name N or name CA or na \ me C or name O or name CB )) or resid 469 through 472 or (resid 473 and (name N \ or name CA or name C or name O or name CB )) or resid 474 or (resid 475 and (nam \ e N or name CA or name C or name O or name CB )) or resid 476 through 477 or (re \ sid 478 through 480 and (name N or name CA or name C or name O or name CB )) or \ resid 481 through 482 or (resid 483 and (name N or name CA or name C or name O o \ r name CB )) or resid 484 through 489 or (resid 490 and (name N or name CA or na \ me C or name O or name CB )) or resid 491 through 497 or (resid 498 through 499 \ and (name N or name CA or name C or name O or name CB )) or resid 500 through 50 \ 4 or (resid 505 through 507 and (name N or name CA or name C or name O or name C \ B )) or resid 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 512 or (resid 513 through 514 and (name N or name \ CA or name C or name O or name CB )) or resid 515 or (resid 516 through 517 and \ (name N or name CA or name C or name O or name CB )) or resid 518 through 519 or \ (resid 520 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 1 or (resid 522 and (name N or name CA or name C or name O or name CB )) or resi \ d 523 or (resid 524 through 526 and (name N or name CA or name C or name O or na \ me CB )) or resid 527 through 528 or (resid 529 through 532 and (name N or name \ CA or name C or name O or name CB )) or resid 533 or (resid 534 through 538 and \ (name N or name CA or name C or name O or name CB )) or resid 539 or (resid 540 \ through 564 and (name N or name CA or name C or name O or name CB )) or (resid 5 \ 65 through 583 and (name N or name CA or name C or name O or name CB )) or resid \ 584 or (resid 585 through 595 and (name N or name CA or name C or name O or nam \ e CB )) or resid 596 through 599 or (resid 600 and (name N or name CA or name C \ or name O or name CB )) or resid 601 or (resid 602 through 607 and (name N or na \ me CA or name C or name O or name CB )) or resid 608 or (resid 609 and (name N o \ r name CA or name C or name O or name CB )) or resid 610 or (resid 611 and (name \ N or name CA or name C or name O or name CB )) or resid 612 through 613 or (res \ id 614 through 623 and (name N or name CA or name C or name O or name CB )) or r \ esid 624 or (resid 625 and (name N or name CA or name C or name O or name CB )) \ or resid 626 or (resid 627 and (name N or name CA or name C or name O or name CB \ )) or resid 628 through 630 or (resid 631 and (name N or name CA or name C or n \ ame O or name CB )) or resid 632 through 635 or (resid 636 through 653 and (name \ N or name CA or name C or name O or name CB )) or resid 654 or (resid 655 and ( \ name N or name CA or name C or name O or name CB )) or resid 656 through 657 or \ (resid 658 and (name N or name CA or name C or name O or name CB )) or resid 659 \ or (resid 660 through 661 and (name N or name CA or name C or name O or name CB \ )) or resid 662 or (resid 663 and (name N or name CA or name C or name O or nam \ e CB )) or resid 664 through 665 or (resid 666 through 669 and (name N or name C \ A or name C or name O or name CB )) or resid 670 or (resid 671 and (name N or na \ me CA or name C or name O or name CB )) or resid 672 through 673 or (resid 674 a \ nd (name N or name CA or name C or name O or name CB )) or resid 675 through 676 \ or (resid 677 through 678 and (name N or name CA or name C or name O or name CB \ )) or resid 679 or (resid 680 through 682 and (name N or name CA or name C or n \ ame O or name CB )) or resid 683 through 684 or (resid 685 and (name N or name C \ A or name C or name O or name CB )) or resid 686 through 688 or (resid 689 throu \ gh 702 and (name N or name CA or name C or name O or name CB )) or resid 703 or \ (resid 704 through 723 and (name N or name CA or name C or name O or name CB )) \ or (resid 724 through 752 and (name N or name CA or name C or name O or name CB \ )) or (resid 753 through 785 and (name N or name CA or name C or name O or name \ CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.87 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.190 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.005 0.453 20574 Z= 0.170 Angle : 0.789 73.828 28034 Z= 0.399 Chirality : 0.043 0.247 3289 Planarity : 0.006 0.131 3625 Dihedral : 16.224 172.858 7119 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.05 % Allowed : 15.98 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78925 / 0.40 (28034) hydrogen bonds : bond 0.07785 / 5.15 ( 819) hydrogen bonds : angle 4.59346 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.548 Fit side-chains REVERT: C 684 MET cc_start: 0.6076 (mtp) cc_final: 0.5686 (mtt) REVERT: F 462 MET cc_start: 0.8393 (mmm) cc_final: 0.8180 (mmm) outliers start: 19 outliers final: 13 residues processed: 240 average time/residue: 0.5332 time to fit residues: 146.8193 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0570 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 40.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.180457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123804 restraints weight = 21093.793| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.97 r_work: 0.3241 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 663 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.899 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.77 % Allowed : 16.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59286 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.800 Fit side-chains REVERT: C 684 MET cc_start: 0.5728 (mtp) cc_final: 0.5426 (mtt) REVERT: E 324 ASN cc_start: 0.8116 (t0) cc_final: 0.7910 (m-40) REVERT: F 462 MET cc_start: 0.8525 (mmm) cc_final: 0.8287 (mmm) outliers start: 14 outliers final: 13 residues processed: 238 average time/residue: 0.5964 time to fit residues: 161.9121 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 237 optimal weight: 0.5980 chunk 188 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 261 optimal weight: 0.4980 chunk 86 optimal weight: 40.0000 chunk 193 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.181389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131579 restraints weight = 21181.982| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.07 r_work: 0.3276 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.900 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.77 % Allowed : 16.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59285 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.821 Fit side-chains REVERT: C 684 MET cc_start: 0.5663 (mtp) cc_final: 0.5367 (mtt) REVERT: E 324 ASN cc_start: 0.8082 (t0) cc_final: 0.7872 (m-40) REVERT: F 462 MET cc_start: 0.8475 (mmm) cc_final: 0.8245 (mmm) outliers start: 14 outliers final: 13 residues processed: 238 average time/residue: 0.5932 time to fit residues: 161.1032 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 252 optimal weight: 3.9990 chunk 130 optimal weight: 40.0000 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.182332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130026 restraints weight = 21350.933| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.42 r_work: 0.3267 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.900 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.77 % Allowed : 16.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59285 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.788 Fit side-chains REVERT: C 684 MET cc_start: 0.5595 (mtp) cc_final: 0.5305 (mtt) REVERT: E 324 ASN cc_start: 0.8084 (t0) cc_final: 0.7873 (m-40) REVERT: F 462 MET cc_start: 0.8467 (mmm) cc_final: 0.8233 (mmm) outliers start: 14 outliers final: 13 residues processed: 238 average time/residue: 0.5422 time to fit residues: 147.2882 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 156 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 190 optimal weight: 0.0020 chunk 93 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 130 optimal weight: 40.0000 chunk 159 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.185853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137162 restraints weight = 21255.928| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.04 r_work: 0.3290 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.900 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.77 % Allowed : 16.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59285 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.732 Fit side-chains REVERT: C 684 MET cc_start: 0.5436 (mtp) cc_final: 0.5158 (mtt) REVERT: E 324 ASN cc_start: 0.8006 (t0) cc_final: 0.7803 (m-40) REVERT: F 462 MET cc_start: 0.8357 (mmm) cc_final: 0.8098 (mmm) outliers start: 14 outliers final: 13 residues processed: 238 average time/residue: 0.5769 time to fit residues: 156.8298 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 40.0000 chunk 28 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 190 optimal weight: 0.1980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.187319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142295 restraints weight = 21234.774| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.15 r_work: 0.3236 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.900 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.77 % Allowed : 16.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59285 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.641 Fit side-chains REVERT: C 684 MET cc_start: 0.5279 (mtp) cc_final: 0.5022 (mtt) REVERT: F 462 MET cc_start: 0.8424 (mmm) cc_final: 0.8157 (mmm) outliers start: 14 outliers final: 13 residues processed: 238 average time/residue: 0.5561 time to fit residues: 150.8573 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 262 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 198 optimal weight: 50.0000 chunk 62 optimal weight: 0.5980 chunk 199 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 324 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.188226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143859 restraints weight = 21240.168| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.93 r_work: 0.3246 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.900 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.83 % Allowed : 16.47 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59285 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.820 Fit side-chains REVERT: C 684 MET cc_start: 0.5273 (mtp) cc_final: 0.5024 (mtt) REVERT: F 462 MET cc_start: 0.8465 (mmm) cc_final: 0.8214 (mmm) outliers start: 15 outliers final: 13 residues processed: 238 average time/residue: 0.5325 time to fit residues: 144.1909 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 108 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 198 optimal weight: 30.0000 chunk 148 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 137 optimal weight: 40.0000 chunk 112 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.189311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141743 restraints weight = 21341.395| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.55 r_work: 0.3223 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.900 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.77 % Allowed : 16.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59285 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.755 Fit side-chains REVERT: C 684 MET cc_start: 0.5154 (mtp) cc_final: 0.4917 (mtt) REVERT: F 462 MET cc_start: 0.8470 (mmm) cc_final: 0.8212 (mmm) outliers start: 14 outliers final: 13 residues processed: 238 average time/residue: 0.5631 time to fit residues: 153.1392 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 238 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 0.0270 chunk 157 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 240 optimal weight: 0.5980 chunk 182 optimal weight: 40.0000 chunk 68 optimal weight: 1.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 324 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.189931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136795 restraints weight = 21306.544| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.59 r_work: 0.3262 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.900 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.83 % Allowed : 16.47 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59285 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.792 Fit side-chains REVERT: C 684 MET cc_start: 0.5128 (mtp) cc_final: 0.4888 (mtt) REVERT: F 462 MET cc_start: 0.8424 (mmm) cc_final: 0.8175 (mmm) outliers start: 15 outliers final: 13 residues processed: 238 average time/residue: 0.5573 time to fit residues: 151.8474 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 171 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 72 optimal weight: 0.3980 chunk 254 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 266 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.185618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128406 restraints weight = 21456.223| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.27 r_work: 0.3238 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.900 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.77 % Allowed : 16.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59285 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.875 Fit side-chains REVERT: C 684 MET cc_start: 0.5161 (mtp) cc_final: 0.4926 (mtt) REVERT: E 324 ASN cc_start: 0.8106 (t0) cc_final: 0.7901 (m-40) REVERT: F 462 MET cc_start: 0.8519 (mmm) cc_final: 0.8283 (mmm) outliers start: 14 outliers final: 13 residues processed: 238 average time/residue: 0.5718 time to fit residues: 155.7438 Evaluate side-chains 238 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 693 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 121 optimal weight: 6.9990 chunk 54 optimal weight: 0.0970 chunk 129 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 189 optimal weight: 0.0570 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 661 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.190273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130593 restraints weight = 21379.328| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.31 r_work: 0.3250 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 606 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 20574 Z= 0.168 Angle : 0.789 73.900 28034 Z= 0.398 Chirality : 0.043 0.241 3289 Planarity : 0.006 0.130 3625 Dihedral : 10.977 172.828 3111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.77 % Allowed : 16.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2766 helix: 1.05 (0.16), residues: 1094 sheet: 0.31 (0.29), residues: 361 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 612 TYR 0.028 0.001 TYR C 676 PHE 0.038 0.001 PHE C 357 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.17 (20572) covalent geometry : angle 0.78876 / 0.40 (28034) hydrogen bonds : bond 0.07775 / 5.14 ( 819) hydrogen bonds : angle 4.59285 / 3.21 ( 2352) Misc. bond : bond 0.00056 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7179.41 seconds wall clock time: 122 minutes 44.58 seconds (7364.58 seconds total)