Starting phenix.real_space_refine on Fri Aug 7 08:23:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh0_37524/08_2026/8wh0_37524_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh0_37524/08_2026/8wh0_37524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wh0_37524/08_2026/8wh0_37524_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh0_37524/08_2026/8wh0_37524_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wh0_37524/08_2026/8wh0_37524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh0_37524/08_2026/8wh0_37524.map" } resolution = 2.51 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= 0.001 sd= 0.040 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 20 5.49 5 Mg 4 5.21 5 S 83 5.16 5 C 13011 2.51 5 N 3566 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 20548 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3576 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3593 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 20, 'TRANS': 435} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 3409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3409 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 398 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 7, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 162 Chain: "D" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3320 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 10, 'GLU:plan': 9, 'ASP:plan': 14, 'PHE:plan': 6, 'HIS:plan': 3, 'TYR:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 229 Chain: "E" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 2826 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 238} Link IDs: {'PTRANS': 19, 'TRANS': 432} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 888 Unresolved non-hydrogen angles: 1121 Unresolved non-hydrogen dihedrals: 749 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 12, 'PHE:plan': 19, 'ASP:plan': 19, 'ASN:plan1': 10, 'GLN:plan1': 5, 'TYR:plan': 12, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 471 Chain: "F" Number of atoms: 3570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3570 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 85 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.37, per 1000 atoms: 0.21 Number of scatterers: 20548 At special positions: 0 Unit cell: (120.96, 130.2, 116.76, 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 83 16.00 P 20 15.00 Mg 4 11.99 O 3864 8.00 N 3566 7.00 C 13011 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: 1.44 Conformation dependent library (CDL) restraints added in 782.0 milliseconds 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5214 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 42 sheets defined 46.9% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.611A pdb=" N ASN A 337 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.642A 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: 3.639A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' 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 578 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 640 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 710 through 715 Proline residue: A 715 - end of helix Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 752 through 763 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.565A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) 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: 3.845A 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 430 through 435 removed outlier: 3.687A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'B' and resid 508 through 521 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 614 through 619 Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' 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 689 through 695 Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.615A pdb=" N LEU B 700 " --> pdb=" O PHE B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 715 Proline residue: B 715 - end of helix Processing helix chain 'B' and resid 716 through 724 removed outlier: 4.907A pdb=" N LYS B 722 " --> pdb=" O THR B 718 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 723 " --> pdb=" O ASP B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 745 removed outlier: 3.961A pdb=" N LYS B 745 " --> pdb=" O GLN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 764 removed outlier: 6.010A pdb=" N HIS B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 782 No H-bonds generated for 'chain 'B' and resid 780 through 782' Processing helix chain 'C' and resid 324 through 337 removed outlier: 3.638A pdb=" N ASN C 337 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.782A 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 Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.608A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.559A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 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 577 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 635 through 640 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 696 through 705 removed outlier: 3.709A pdb=" N GLY C 703 " --> pdb=" O TYR C 699 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR C 704 " --> pdb=" O LEU C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 724 removed outlier: 4.576A pdb=" N LYS C 722 " --> pdb=" O THR C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 747 removed outlier: 3.629A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 6.649A pdb=" N HIS C 754 " --> pdb=" O ARG C 750 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 Processing helix chain 'D' and resid 362 through 372 removed outlier: 4.073A pdb=" N LYS D 366 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 4.036A 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 429 through 433 Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.511A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.740A 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 546 removed outlier: 3.525A pdb=" N ALA D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 578 Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 653 through 661 removed outlier: 4.520A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 695 through 705 removed outlier: 4.655A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR D 704 " --> pdb=" O LEU D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 715 Proline residue: D 715 - end of helix Processing helix chain 'D' and resid 716 through 724 removed outlier: 4.950A pdb=" N LYS D 722 " --> pdb=" O THR D 718 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 723 " --> pdb=" O ASP D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 747 removed outlier: 3.842A pdb=" N LYS D 745 " --> pdb=" O GLN D 741 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR D 746 " --> pdb=" O LYS D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 764 removed outlier: 5.674A pdb=" N HIS D 754 " --> pdb=" O ARG D 750 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.617A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 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 385 through 400 Processing helix chain 'E' and resid 431 through 435 removed outlier: 3.514A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 removed outlier: 3.642A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 488 removed outlier: 4.501A pdb=" N LYS E 477 " --> pdb=" O ASP E 473 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASN E 478 " --> pdb=" O GLU E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 522 through 524 No H-bonds generated for 'chain 'E' and resid 522 through 524' Processing helix chain 'E' and resid 530 through 534 Processing helix chain 'E' and resid 541 through 546 removed outlier: 3.992A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 578 removed outlier: 3.974A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 620 Processing helix chain 'E' and resid 635 through 641 removed outlier: 3.740A pdb=" N ASN E 641 " --> pdb=" O GLU E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 661 removed outlier: 4.568A pdb=" N GLY E 657 " --> pdb=" O GLU E 653 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 661 " --> pdb=" O GLY E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'E' and resid 693 through 695 No H-bonds generated for 'chain 'E' and resid 693 through 695' Processing helix chain 'E' and resid 696 through 704 removed outlier: 4.218A pdb=" N LEU E 700 " --> pdb=" O PHE E 696 " (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 724 removed outlier: 5.352A pdb=" N LYS E 722 " --> pdb=" O THR E 718 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS E 723 " --> pdb=" O ASP E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 747 removed outlier: 3.802A pdb=" N TYR E 746 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 764 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.639A 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 383 removed outlier: 3.895A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU F 383 " --> pdb=" O TYR F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 430 through 435 removed outlier: 3.668A pdb=" N LYS F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 462 Processing helix chain 'F' and resid 463 through 469 Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.558A pdb=" N SER F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 541 through 546 Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.639A pdb=" N ILE F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS F 575 " --> pdb=" O SER F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 633 through 637 removed outlier: 3.724A pdb=" N ARG F 636 " --> pdb=" O PRO F 633 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 633 through 637' 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: 3.571A pdb=" N GLU F 692 " --> pdb=" O THR F 689 " (cutoff:3.500A) Proline residue: F 694 - end of helix Processing helix chain 'F' and resid 696 through 704 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 removed outlier: 5.036A pdb=" N LYS F 722 " --> pdb=" O THR F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 747 removed outlier: 3.776A pdb=" N LYS F 745 " --> pdb=" O GLN F 741 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR F 746 " --> pdb=" O LYS F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 764 removed outlier: 5.831A pdb=" N HIS F 754 " --> pdb=" O ARG F 750 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP F 755 " --> pdb=" O LEU F 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 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: 6.831A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER A 556 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (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: 6.364A 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 728 removed outlier: 3.544A pdb=" N THR A 733 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB1, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.824A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB3, first strand: chain 'B' and resid 628 through 631 Processing sheet with id=AB4, first strand: chain 'B' and resid 706 through 708 Processing sheet with id=AB5, first strand: chain 'B' and resid 726 through 727 removed outlier: 3.549A pdb=" N ILE B 726 " --> pdb=" O THR B 733 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB8, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.852A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N SER C 556 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 503 " --> pdb=" O THR C 604 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.485A 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 'C' and resid 734 through 735 Processing sheet with id=AC4, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC5, first strand: chain 'D' and resid 412 through 415 removed outlier: 4.023A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 524 through 527 removed outlier: 6.289A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 581 through 582 Processing sheet with id=AC8, first strand: chain 'D' and resid 629 through 631 removed outlier: 6.359A pdb=" N HIS D 629 " --> pdb=" O LYS D 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD1, first strand: chain 'D' and resid 726 through 727 Processing sheet with id=AD2, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD3, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AD4, first strand: chain 'E' and resid 526 through 527 removed outlier: 6.721A pdb=" N THR E 499 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR E 604 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE E 501 " --> pdb=" O THR E 604 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AD6, first strand: chain 'E' and resid 628 through 631 removed outlier: 6.439A pdb=" N HIS E 629 " --> pdb=" O LYS E 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 707 through 708 Processing sheet with id=AD8, first strand: chain 'E' and resid 726 through 728 Processing sheet with id=AD9, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AE1, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AE2, first strand: chain 'F' and resid 524 through 526 removed outlier: 6.854A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N SER F 556 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 581 through 583 Processing sheet with id=AE4, first strand: chain 'F' and resid 629 through 631 Processing sheet with id=AE5, first strand: chain 'F' and resid 706 through 708 Processing sheet with id=AE6, first strand: chain 'F' and resid 726 through 727 removed outlier: 3.500A pdb=" N THR F 733 " --> pdb=" O ILE F 726 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2385 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: 3.60 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6750 1.34 - 1.46: 4531 1.46 - 1.58: 9515 1.58 - 1.69: 34 1.69 - 1.81: 116 Bond restraints: 20946 Sorted by residual: bond pdb=" N3B ANP C 802 " pdb=" PG ANP C 802 " ideal model delta sigma weight residual 1.795 1.637 0.158 2.00e-02 2.50e+03 6.26e+01 bond pdb=" N3B ANP F 803 " pdb=" PG ANP F 803 " ideal model delta sigma weight residual 1.795 1.637 0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 1.795 1.637 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" N3B ANP D 801 " pdb=" PG ANP D 801 " ideal model delta sigma weight residual 1.795 1.638 0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" N3B ANP F 802 " pdb=" PG ANP F 802 " ideal model delta sigma weight residual 1.795 1.639 0.156 2.00e-02 2.50e+03 6.09e+01 ... (remaining 20941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 28185 2.12 - 4.23: 241 4.23 - 6.35: 48 6.35 - 8.47: 9 8.47 - 10.58: 6 Bond angle restraints: 28489 Sorted by residual: angle pdb=" CA PHE B 696 " pdb=" CB PHE B 696 " pdb=" CG PHE B 696 " ideal model delta sigma weight residual 113.80 120.20 -6.40 1.00e+00 1.00e+00 4.10e+01 angle pdb=" C PHE B 696 " pdb=" CA PHE B 696 " pdb=" CB PHE B 696 " ideal model delta sigma weight residual 110.94 102.05 8.89 1.65e+00 3.67e-01 2.91e+01 angle pdb=" PA ANP A 802 " pdb=" O3A ANP A 802 " pdb=" PB ANP A 802 " ideal model delta sigma weight residual 125.41 135.99 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " pdb=" O2G ANP A 802 " ideal model delta sigma weight residual 101.05 110.96 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N3B ANP C 802 " pdb=" PG ANP C 802 " pdb=" O2G ANP C 802 " ideal model delta sigma weight residual 101.05 110.45 -9.40 3.00e+00 1.11e-01 9.82e+00 ... (remaining 28484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.87: 11998 31.87 - 63.73: 610 63.73 - 95.60: 92 95.60 - 127.47: 2 127.47 - 159.33: 3 Dihedral angle restraints: 12705 sinusoidal: 4692 harmonic: 8013 Sorted by residual: 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 -148.88 -31.12 0 5.00e+00 4.00e-02 3.87e+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 -149.06 -30.94 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ILE F 681 " pdb=" C ILE F 681 " pdb=" N PRO F 682 " pdb=" CA PRO F 682 " ideal model delta harmonic sigma weight residual -180.00 -149.83 -30.17 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 12702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3012 0.077 - 0.153: 283 0.153 - 0.230: 6 0.230 - 0.307: 0 0.307 - 0.383: 5 Chirality restraints: 3306 Sorted by residual: chirality pdb=" C3' ANP C 802 " pdb=" C2' ANP C 802 " pdb=" C4' ANP C 802 " pdb=" O3' ANP C 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.74 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C3' ANP F 803 " pdb=" C2' ANP F 803 " pdb=" C4' ANP F 803 " pdb=" O3' ANP F 803 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3' ANP A 802 " pdb=" C2' ANP A 802 " pdb=" C4' ANP A 802 " pdb=" O3' ANP A 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 3303 not shown) Planarity restraints: 3640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 695 " 0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ASP B 695 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP B 695 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE B 696 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 482 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C TYR B 482 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR B 482 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU B 483 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 681 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO B 682 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 682 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 682 " -0.023 5.00e-02 4.00e+02 ... (remaining 3637 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 112 2.57 - 3.15: 16465 3.15 - 3.74: 30606 3.74 - 4.32: 44745 4.32 - 4.90: 72375 Nonbonded interactions: 164303 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O2B ANP F 802 " model vdw 1.989 2.170 nonbonded pdb=" OE1 GLU F 483 " pdb=" OH TYR F 679 " model vdw 2.011 3.040 nonbonded pdb=" OE1 GLU D 483 " pdb=" OH TYR D 679 " model vdw 2.089 3.040 nonbonded pdb=" OE1 GLU C 483 " pdb=" OH TYR C 679 " model vdw 2.096 3.040 nonbonded pdb=" NZ LYS B 513 " pdb=" OE2 GLU B 526 " model vdw 2.102 3.120 ... (remaining 164298 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 through 342 or (resid 343 through 344 and (name N or n \ ame CA or name C or name O or name CB )) or resid 345 through 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 and (name N or name CA or name C or name O or name CB )) or (resid 361 and ( \ name N or name CA or name C or name O or name CB )) or resid 362 through 376 or \ (resid 377 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 404 or (resid 405 and (name N or name CA or name C or name \ O or name CB )) or resid 406 through 411 or (resid 412 and (name N or name CA or \ name C or name O or name CB )) or resid 413 through 414 or (resid 415 through 4 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 417 through \ 419 or (resid 420 through 424 and (name N or name CA or name C or name O or nam \ e 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 through 430 or (resid 431 through 433 and (name N or na \ me CA or name C or name O or name CB )) or resid 434 through 444 or (resid 445 t \ hrough 447 and (name N or name CA or name C or name O or name CB )) or resid 448 \ through 452 or (resid 453 through 491 and (name N or name CA or name C or name \ O or name CB )) or (resid 492 through 495 and (name N or name CA or name C or na \ me O or name CB )) or resid 496 or (resid 497 through 502 and (name N or name CA \ or name C or name O or name CB )) or resid 503 or (resid 504 through 507 and (n \ ame N or name CA or name C or name O or name CB )) or resid 508 or (resid 509 an \ d (name N or name CA or name C or name O or name CB )) or resid 510 or (resid 51 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 512 through \ 513 or (resid 514 through 516 and (name N or name CA or name C or name O or name \ CB )) or resid 517 or (resid 518 through 520 and (name N or name CA or name C o \ r name O or name CB )) or resid 521 through 523 or (resid 524 through 527 and (n \ ame N or name CA or name C or name O or name CB )) or resid 528 or (resid 529 th \ rough 531 and (name N or name CA or name C or name O or name CB )) or resid 532 \ or (resid 533 through 538 and (name N or name CA or name C or name O or name CB \ )) or resid 539 or (resid 540 through 541 and (name N or name CA or name C or na \ me O or name CB )) or resid 542 or (resid 543 through 548 and (name N or name CA \ or name C or name O or name CB )) or resid 549 or (resid 550 and (name N or nam \ e CA or name C or name O or name CB )) or resid 551 through 552 or (resid 553 th \ rough 554 and (name N or name CA or name C or name O or name CB )) or resid 555 \ or (resid 556 through 558 and (name N or name CA or name C or name O or name CB \ )) or resid 559 through 566 or (resid 567 through 572 and (name N or name CA or \ name C or name O or name CB )) or resid 573 through 574 or (resid 575 through 57 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 580 or (resi \ d 581 through 582 and (name N or name CA or name C or name O or name CB )) or re \ sid 583 through 584 or (resid 585 through 586 and (name N or name CA or name C o \ r name O or name CB )) or resid 587 or (resid 588 through 591 and (name N or nam \ e CA or name C or name O or name CB )) or resid 592 through 599 or (resid 600 an \ d (name N or name CA or name C or name O or name CB )) or resid 601 through 602 \ or (resid 603 through 604 and (name N or name CA or name C or name O or name CB \ )) or resid 605 through 609 or (resid 610 through 620 and (name N or name CA or \ name C or name O or name CB )) or resid 621 through 624 or (resid 625 and (name \ N or name CA or name C or name O or name CB )) or resid 626 through 627 or (resi \ d 628 through 629 and (name N or name CA or name C or name O or name CB )) or re \ sid 630 through 635 or (resid 636 through 647 and (name N or name CA or name C o \ r name O or name CB )) or resid 648 or (resid 649 through 650 and (name N or nam \ e CA or name C or name O or name CB )) or resid 651 through 652 or (resid 653 an \ d (name N or name CA or name C or name O or name CB )) or resid 654 through 655 \ or (resid 656 and (name N or name CA or name C or name O or name CB )) or resid \ 657 or (resid 658 through 659 and (name N or name CA or name C or name O or name \ CB )) or resid 660 through 662 or (resid 663 through 664 and (name N or name CA \ or name C or name O or name CB )) or resid 665 or (resid 666 through 669 and (n \ ame N or name CA or name C or name O or name CB )) or resid 670 through 672 or ( \ resid 673 and (name N or name CA or name C or name O or name CB )) or resid 674 \ through 675 or (resid 676 through 677 and (name N or name CA or name C or name O \ or name CB )) or resid 678 or (resid 679 through 680 and (name N or name CA or \ name C or name O or name CB )) or resid 684 or (resid 685 through 702 and (name \ N or name CA or name C or name O or name CB )) or resid 703 or (resid 704 throug \ h 723 and (name N or name CA or name C or name O or name CB )) or resid 724 thro \ ugh 729 or (resid 731 through 752 and (name N or name CA or name C or name O or \ name CB )) or resid 753 or (resid 754 through 765 and (name N or name CA or name \ C or name O or name CB )) or (resid 772 through 782 and (name N or name CA or n \ ame C or name O or name CB )))) selection = (chain 'B' and (resid 323 through 342 or (resid 343 through 344 and (name N or n \ ame CA or name C or name O or name CB )) or resid 345 through 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 and (name N or name CA or name C or name O or name CB )) or resid 361 throug \ h 376 or (resid 377 through 378 and (name N or name CA or name C or name O or na \ me CB )) or resid 379 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 through 411 or (resid 412 and (name N or n \ ame CA or name C or name O or name CB )) or resid 413 through 414 or (resid 415 \ through 416 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 7 through 419 or (resid 420 through 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 through 430 or (resid 431 through 433 and (nam \ e N or name CA or name C or name O or name CB )) or resid 434 through 444 or (re \ sid 445 through 447 and (name N or name CA or name C or name O or name CB )) or \ resid 448 through 452 or (resid 453 through 491 and (name N or name CA or name C \ or name O or name CB )) or (resid 492 through 495 and (name N or name CA or nam \ e C or name O or name CB )) or resid 496 or (resid 497 through 502 and (name N o \ r name CA or name C or name O or name CB )) or resid 503 or (resid 504 through 5 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 508 or (res \ id 509 and (name N or name CA or name C or name O or name CB )) or resid 510 or \ (resid 511 and (name N or name CA or name C or name O or name CB )) or resid 512 \ through 513 or (resid 514 through 516 and (name N or name CA or name C or name \ O or name CB )) or resid 517 or (resid 518 through 520 and (name N or name CA or \ name C or name O or name CB )) or resid 521 through 523 or (resid 524 through 5 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 528 or (res \ id 529 through 531 and (name N or name CA or name C or name O or name CB )) or r \ esid 532 or (resid 533 through 538 and (name N or name CA or name C or name O or \ name CB )) or resid 539 or (resid 540 through 541 and (name N or name CA or nam \ e C or name O or name CB )) or resid 542 or (resid 543 through 548 and (name N o \ r name CA or name C or name O or name CB )) or resid 549 or (resid 550 and (name \ N or name CA or name C or name O or name CB )) or resid 551 through 552 or (res \ id 553 through 554 and (name N or name CA or name C or name O or name CB )) or r \ esid 555 or (resid 556 through 558 and (name N or name CA or name C or name O or \ name CB )) or resid 559 through 566 or (resid 567 through 572 and (name N or na \ me CA or name C or name O or name CB )) or resid 573 through 574 or (resid 575 t \ hrough 579 and (name N or name CA or name C or name O or name CB )) or resid 580 \ or (resid 581 through 582 and (name N or name CA or name C or name O or name CB \ )) or resid 583 through 584 or (resid 585 through 586 and (name N or name CA or \ name C or name O or name CB )) or resid 587 or (resid 588 through 591 and (name \ N or name CA or name C or name O or name CB )) or resid 592 through 599 or (res \ id 600 and (name N or name CA or name C or name O or name CB )) or resid 601 thr \ ough 602 or (resid 603 through 604 and (name N or name CA or name C or name O or \ name CB )) or resid 605 through 609 or (resid 610 through 620 and (name N or na \ me CA or name C or name O or name CB )) or resid 621 through 624 or (resid 625 a \ nd (name N or name CA or name C or name O or name CB )) or resid 626 through 627 \ or (resid 628 through 629 and (name N or name CA or name C or name O or name CB \ )) or resid 630 through 635 or (resid 636 through 647 and (name N or name CA or \ name C or name O or name CB )) or resid 648 or (resid 649 through 650 and (name \ N or name CA or name C or name O or name CB )) or resid 651 through 652 or (res \ id 653 and (name N or name CA or name C or name O or name CB )) or resid 654 thr \ ough 655 or (resid 656 and (name N or name CA or name C or name O or name CB )) \ or resid 657 or (resid 658 through 659 and (name N or name CA or name C or name \ O or name CB )) or resid 660 through 662 or (resid 663 through 664 and (name N o \ r name CA or name C or name O or name CB )) or resid 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 through \ 672 or (resid 673 and (name N or name CA or name C or name O or name CB )) or r \ esid 674 through 675 or (resid 676 through 677 and (name N or name CA or name C \ or name O or name CB )) or resid 678 or (resid 679 through 680 and (name N or na \ me CA or name C or name O or name CB )) or resid 684 or (resid 685 through 702 a \ nd (name N or name CA or name C or name O or name CB )) or resid 703 or (resid 7 \ 04 through 723 and (name N or name CA or name C or name O or name CB )) or resid \ 724 or (resid 725 through 752 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 753 through 765 and (name N or name CA or name C or name O or \ name CB )) or (resid 772 through 782 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'C' and (resid 323 through 342 or (resid 343 through 344 and (name N or n \ ame CA or name C or name O or name CB )) or resid 345 through 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 and (name N or name CA or name C or name O or name CB )) or (resid 361 and ( \ name N or name CA or name C or name O or name CB )) or resid 362 through 377 or \ (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ through 404 or (resid 405 and (name N or name CA or name C or name O or name CB \ )) or resid 406 through 411 or (resid 412 and (name N or name CA or name C or n \ ame O or name CB )) or resid 413 through 414 or (resid 415 through 416 and (name \ N or name CA or name C or name O or name CB )) or resid 417 through 419 or (res \ id 420 through 424 and (name N or name CA or name C or name O or name CB )) or r \ esid 425 through 430 or (resid 431 through 433 and (name N or name CA or name C \ or name O or name CB )) or resid 434 through 444 or (resid 445 through 447 and ( \ name N or name CA or name C or name O or name CB )) or resid 448 through 452 or \ (resid 453 through 491 and (name N or name CA or name C or name O or name CB )) \ or (resid 492 through 495 and (name N or name CA or name C or name O or name CB \ )) or resid 496 or (resid 497 through 502 and (name N or name CA or name C or na \ me O or name CB )) or (resid 503 through 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 name CA or name \ C or name O or name CB )) or resid 510 or (resid 511 and (name N or name CA or n \ ame C or name O or name CB )) or resid 512 through 513 or (resid 514 through 516 \ and (name N or name CA or name C or name O or name CB )) or resid 517 or (resid \ 518 through 520 and (name N or name CA or name C or name O or name CB )) or res \ id 521 through 523 or (resid 524 through 527 and (name N or name CA or name C or \ name O or name CB )) or resid 528 or (resid 529 through 531 and (name N or name \ CA or name C or name O or name CB )) or resid 532 or (resid 533 through 538 and \ (name N or name CA or name C or name O or name CB )) or resid 539 or (resid 540 \ through 541 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 42 or (resid 543 through 548 and (name N or name CA or name C or name O or name \ CB )) or resid 549 or (resid 550 and (name N or name CA or name C or name O or n \ ame CB )) or resid 551 through 552 or (resid 553 through 554 and (name N or name \ CA or name C or name O or name CB )) or resid 555 or (resid 556 through 558 and \ (name N or name CA or name C or name O or name CB )) or resid 559 through 566 o \ r (resid 567 through 572 and (name N or name CA or name C or name O or name CB ) \ ) or resid 573 through 574 or (resid 575 through 579 and (name N or name CA or n \ ame C or name O or name CB )) or resid 580 or (resid 581 through 582 and (name N \ or name CA or name C or name O or name CB )) or resid 583 through 584 or (resid \ 585 through 586 and (name N or name CA or name C or name O or name CB )) or res \ id 587 or (resid 588 through 591 and (name N or name CA or name C or name O or n \ ame CB )) or resid 592 through 599 or (resid 600 and (name N or name CA or name \ C or name O or name CB )) or resid 601 through 602 or (resid 603 through 604 and \ (name N or name CA or name C or name O or name CB )) or resid 605 through 609 o \ r (resid 610 through 620 and (name N or name CA or name C or name O or name CB ) \ ) or resid 621 through 624 or (resid 625 and (name N or name CA or name C or nam \ e O or name CB )) or resid 626 through 627 or (resid 628 through 629 and (name N \ or name CA or name C or name O or name CB )) or resid 630 through 635 or (resid \ 636 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 or (resid 649 through 650 and (name N or name CA or name C or name O or n \ ame CB )) or resid 651 through 652 or (resid 653 and (name N or name CA or name \ C or name O or name CB )) or resid 654 through 655 or (resid 656 and (name N or \ name CA or name C or name O or name CB )) or resid 657 or (resid 658 through 659 \ and (name N or name CA or name C or name O or name CB )) or resid 660 through 6 \ 62 or (resid 663 through 664 and (name N or name CA or name C or name O or name \ CB )) or resid 665 or (resid 666 through 669 and (name N or name CA or name C or \ name O or name CB )) or resid 670 through 672 or (resid 673 and (name N or name \ CA or name C or name O or name CB )) or resid 674 through 675 or (resid 676 thr \ ough 677 and (name N or name CA or name C or name O or name CB )) or resid 678 o \ r (resid 679 through 680 and (name N or name CA or name C or name O or name CB ) \ ) or resid 684 or (resid 685 through 702 and (name N or name CA or name C or nam \ e O or name CB )) or resid 703 through 729 or resid 731 through 765 or resid 772 \ through 782)) selection = (chain 'D' and (resid 323 through 342 or (resid 343 through 344 and (name N or n \ ame CA or name C or name O or name CB )) or resid 345 through 358 or resid 361 t \ hrough 376 or (resid 377 through 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 through 404 or (resid 405 and (name N or name CA or n \ ame C or name O or name CB )) or resid 406 through 411 or (resid 412 and (name N \ or name CA or name C or name O or name CB )) or resid 413 through 414 or (resid \ 415 through 416 and (name N or name CA or name C or name O or name CB )) or res \ id 417 through 419 or (resid 420 through 424 and (name N or name CA or name C or \ name O or name CB )) or resid 425 through 431 or (resid 432 through 433 and (na \ me N or name CA or name C or name O or name CB )) or resid 434 through 446 or (r \ esid 447 and (name N or name CA or name C or name O or name CB )) or resid 448 t \ hrough 452 or (resid 453 through 491 and (name N or name CA or name C or name O \ or name CB )) or (resid 492 through 495 and (name N or name CA or name C or name \ O or name CB )) or resid 496 or (resid 497 through 502 and (name N or name CA o \ r name C or name O or name CB )) or resid 503 or (resid 504 through 507 and (nam \ e N or name CA or name C or name O or name CB )) or resid 508 or (resid 509 and \ (name N or name CA or name C or name O or name CB )) or resid 510 or (resid 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 51 \ 3 or (resid 514 through 516 and (name N or name CA or name C or name O or name C \ B )) or resid 517 or (resid 518 through 520 and (name N or name CA or name C or \ name O or name CB )) or resid 521 through 523 or (resid 524 through 527 and (nam \ e N or name CA or name C or name O or name CB )) or resid 528 or (resid 529 thro \ ugh 531 and (name N or name CA or name C or name O or name CB )) or resid 532 or \ (resid 533 through 538 and (name N or name CA or name C or name O or name CB )) \ or resid 539 or (resid 540 through 541 and (name N or name CA or name C or name \ O or name CB )) or resid 542 through 546 or (resid 547 through 548 and (name N \ or name CA or name C or name O or name CB )) or resid 549 or (resid 550 and (nam \ e N or name CA or name C or name O or name CB )) or resid 551 through 552 or (re \ sid 553 through 554 and (name N or name CA or name C or name O or name CB )) or \ resid 555 or (resid 556 through 558 and (name N or name CA or name C or name O o \ r name CB )) or resid 559 through 566 or (resid 567 through 572 and (name N or n \ ame CA or name C or name O or name CB )) or resid 573 through 574 or (resid 575 \ through 579 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 0 or (resid 581 through 582 and (name N or name CA or name C or name O or name C \ B )) or resid 583 through 584 or (resid 585 through 586 and (name N or name CA o \ r name C or name O or name CB )) or resid 587 through 599 or (resid 600 and (nam \ e N or name CA or name C or name O or name CB )) or resid 601 through 603 or (re \ sid 604 and (name N or name CA or name C or name O or name CB )) or resid 605 th \ rough 609 or (resid 610 through 620 and (name N or name CA or name C or name O o \ r name CB )) or resid 621 through 624 or (resid 625 and (name N or name CA or na \ me C or name O or name CB )) or resid 626 through 627 or (resid 628 through 629 \ and (name N or name CA or name C or name O or name CB )) or resid 630 through 63 \ 5 or (resid 636 through 647 and (name N or name CA or name C or name O or name C \ B )) or resid 648 or (resid 649 through 650 and (name N or name CA or name C or \ name O or name CB )) or resid 651 through 652 or (resid 653 and (name N or name \ CA or name C or name O or name CB )) or resid 654 through 658 or (resid 659 and \ (name N or name CA or name C or name O or name CB )) or resid 660 through 663 or \ (resid 664 and (name N or name CA or name C or name O or name CB )) or resid 66 \ 5 or (resid 666 through 669 and (name N or name CA or name C or name O or name C \ B )) or resid 670 through 672 or (resid 673 and (name N or name CA or name C or \ name O or name CB )) or resid 674 through 675 or (resid 676 through 677 and (nam \ e N or name CA or name C or name O or name CB )) or resid 678 or (resid 679 thro \ ugh 680 and (name N or name CA or name C or name O or name CB )) or resid 684 or \ (resid 685 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 name CA or name C or name \ O or name CB )) or (resid 724 through 729 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 731 through 752 and (name N or name CA or name C o \ r name O or name CB )) or (resid 753 through 782 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'E' and (resid 323 through 355 or (resid 356 and (name N or name CA or na \ me 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 415 or (resid \ 416 and (name N or name CA or name C or name O or name CB )) or resid 417 throug \ h 430 or (resid 431 through 433 and (name N or name CA or name C or name O or na \ me CB )) or resid 434 through 533 or (resid 534 through 538 and (name N or name \ CA or name C or name O or name CB )) or (resid 539 through 541 and (name N or na \ me CA or name C or name O or name CB )) or resid 542 through 556 or (resid 557 t \ hrough 558 and (name N or name CA or name C or name O or name CB )) or resid 559 \ through 585 or (resid 586 and (name N or name CA or name C or name O or name CB \ )) or resid 587 or (resid 588 through 591 and (name N or name CA or name C or n \ ame O or name CB )) or resid 592 through 602 or (resid 603 through 604 and (name \ N or name CA or name C or name O or name CB )) or resid 605 through 611 or (res \ id 612 through 620 and (name N or name CA or name C or name O or name CB )) or r \ esid 621 through 636 or (resid 637 through 647 and (name N or name CA or name C \ or name O or name CB )) or resid 648 through 652 or (resid 653 and (name N or na \ me CA or name C or name O or name CB )) or resid 654 through 655 or (resid 656 a \ nd (name N or name CA or name C or name O or name CB )) or resid 657 through 729 \ or resid 731 through 765 or resid 772 through 782)) selection = (chain 'F' and (resid 323 through 342 or (resid 343 through 344 and (name N or n \ ame CA or name C or name O or name CB )) or resid 345 through 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 and (name N or name CA or name C or name O or name CB )) or resid 361 throug \ h 404 or (resid 405 and (name N or name CA or name C or name O or name CB )) or \ resid 406 through 411 or (resid 412 and (name N or name CA or name C or name O o \ r name CB )) or resid 413 through 414 or (resid 415 through 416 and (name N or n \ ame CA or name C or name O or name CB )) or resid 417 through 419 or (resid 420 \ through 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 or (resid 426 and (name N or name CA or name C or name O or name CB )) or resi \ d 427 through 430 or (resid 431 through 433 and (name N or name CA or name C or \ name O or name CB )) or resid 434 through 444 or (resid 445 through 447 and (nam \ e N or name CA or name C or name O or name CB )) or resid 448 through 452 or (re \ sid 453 through 491 and (name N or name CA or name C or name O or name CB )) or \ (resid 492 through 495 and (name N or name CA or name C or name O or name CB )) \ or resid 496 or (resid 497 through 502 and (name N or name CA or name C or name \ O or name CB )) or resid 503 or (resid 504 through 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 name C \ A or name C or name O or name CB )) or resid 510 or (resid 511 and (name N or na \ me CA or name C or name O or name CB )) or resid 512 through 513 or (resid 514 t \ hrough 516 and (name N or name CA or name C or name O or name CB )) or resid 517 \ or (resid 518 through 520 and (name N or name CA or name C or name O or name CB \ )) or resid 521 through 523 or (resid 524 through 527 and (name N or name CA or \ name C or name O or name CB )) or resid 528 or (resid 529 through 531 and (name \ N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 throu \ gh 538 and (name N or name CA or name C or name O or name CB )) or resid 539 or \ (resid 540 through 541 and (name N or name CA or name C or name O or name CB )) \ or resid 542 or (resid 543 through 548 and (name N or name CA or name C or name \ O or name CB )) or resid 549 or (resid 550 and (name N or name CA or name C or n \ ame O or name CB )) or resid 551 through 552 or (resid 553 through 554 and (name \ N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 throu \ gh 558 and (name N or name CA or name C or name O or name CB )) or resid 559 thr \ ough 567 or (resid 568 through 572 and (name N or name CA or name C or name O or \ name CB )) or resid 573 through 574 or (resid 575 through 579 and (name N or na \ me CA or name C or name O or name CB )) or resid 580 or (resid 581 through 582 a \ nd (name N or name CA or name C or name O or name CB )) or resid 583 through 584 \ or (resid 585 through 586 and (name N or name CA or name C or name O or name CB \ )) or resid 587 or (resid 588 through 591 and (name N or name CA or name C or n \ ame O or name CB )) or resid 592 through 599 or (resid 600 and (name N or name C \ A or name C or name O or name CB )) or resid 601 through 602 or (resid 603 throu \ gh 604 and (name N or name CA or name C or name O or name CB )) or resid 605 thr \ ough 609 or (resid 610 through 620 and (name N or name CA or name C or name O or \ name CB )) or resid 621 through 624 or (resid 625 and (name N or name CA or nam \ e C or name O or name CB )) or resid 626 through 627 or (resid 628 through 629 a \ nd (name N or name CA or name C or name O or name CB )) or resid 630 through 635 \ or (resid 636 through 647 and (name N or name CA or name C or name O or name CB \ )) or resid 648 or (resid 649 through 650 and (name N or name CA or name C or n \ ame O or name CB )) or resid 651 through 657 or (resid 658 through 659 and (name \ N or name CA or name C or name O or name CB )) or resid 660 through 662 or (res \ id 663 through 664 and (name N or name CA or name C or name O or name CB )) or r \ esid 665 or (resid 666 through 669 and (name N or name CA or name C or name O or \ name CB )) or resid 670 through 672 or (resid 673 and (name N or name CA or nam \ e C or name O or name CB )) or resid 674 through 675 or (resid 676 through 677 a \ nd (name N or name CA or name C or name O or name CB )) or resid 678 or (resid 6 \ 79 through 680 and (name N or name CA or name C or name O or name CB )) or resid \ 684 or (resid 685 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 or (resid 725 through 729 and (name N or na \ me CA or name C or name O or name CB )) or (resid 731 through 752 and (name N or \ name CA or name C or name O or name CB )) or resid 753 or (resid 754 through 76 \ 5 and (name N or name CA or name C or name O or name CB )) or (resid 772 through \ 782 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.280 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 20948 Z= 0.206 Angle : 0.538 10.583 28489 Z= 0.274 Chirality : 0.043 0.383 3306 Planarity : 0.003 0.041 3640 Dihedral : 18.905 159.333 7491 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.63 % Rotamer: Outliers : 0.15 % Allowed : 25.35 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 2703 helix: 0.83 (0.17), residues: 1032 sheet: 0.09 (0.27), residues: 423 loop : -0.24 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.016 0.001 TYR A 482 PHE 0.015 0.001 PHE B 524 TRP 0.006 0.001 TRP F 350 HIS 0.005 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.21 (20946) covalent geometry : angle 0.53839 / 0.27 (28489) hydrogen bonds : bond 0.15508 / 9.91 ( 832) hydrogen bonds : angle 5.99075 / 4.16 ( 2385) Misc. bond : bond 0.00125 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: C 387 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7433 (ttp-110) outliers start: 3 outliers final: 1 residues processed: 251 average time/residue: 0.5964 time to fit residues: 170.2787 Evaluate side-chains 241 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 632 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 358 ASN F 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.181866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116737 restraints weight = 20163.605| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.41 r_work: 0.3049 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20948 Z= 0.161 Angle : 0.568 6.543 28489 Z= 0.303 Chirality : 0.046 0.263 3306 Planarity : 0.004 0.043 3640 Dihedral : 13.099 158.032 3118 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % Rotamer: Outliers : 3.14 % Allowed : 23.23 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % 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: 0.48 (0.16), residues: 2703 helix: 1.03 (0.17), residues: 1060 sheet: 0.11 (0.28), residues: 368 loop : -0.12 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.018 0.001 TYR A 482 PHE 0.022 0.002 PHE F 524 TRP 0.007 0.001 TRP F 350 HIS 0.007 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (20946) covalent geometry : angle 0.56830 / 0.30 (28489) hydrogen bonds : bond 0.04809 / 3.21 ( 832) hydrogen bonds : angle 4.81524 / 3.40 ( 2385) Misc. bond : bond 0.00357 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 448 ASP cc_start: 0.7948 (p0) cc_final: 0.7743 (p0) REVERT: A 677 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8112 (tppp) REVERT: B 612 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.8024 (tmm-80) REVERT: B 695 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: D 447 ASP cc_start: 0.6979 (t0) cc_final: 0.6643 (t0) REVERT: D 684 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7725 (ttp) REVERT: E 356 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7730 (mtpt) REVERT: E 387 ARG cc_start: 0.8137 (ttp-170) cc_final: 0.7936 (ttp80) REVERT: F 646 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.6758 (m-30) outliers start: 62 outliers final: 16 residues processed: 289 average time/residue: 0.5469 time to fit residues: 180.7231 Evaluate side-chains 246 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 646 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 125 optimal weight: 4.9990 chunk 222 optimal weight: 50.0000 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 144 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 216 optimal weight: 0.3980 chunk 257 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS B 680 HIS F 660 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.182248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115793 restraints weight = 20210.395| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.59 r_work: 0.3032 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20948 Z= 0.152 Angle : 0.542 6.260 28489 Z= 0.290 Chirality : 0.045 0.270 3306 Planarity : 0.004 0.045 3640 Dihedral : 11.582 157.811 3115 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.97 % Rotamer: Outliers : 3.24 % Allowed : 23.48 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % 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: 0.56 (0.16), residues: 2703 helix: 1.12 (0.17), residues: 1054 sheet: 0.19 (0.29), residues: 338 loop : -0.10 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.016 0.001 TYR A 482 PHE 0.020 0.002 PHE F 524 TRP 0.006 0.001 TRP F 350 HIS 0.008 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (20946) covalent geometry : angle 0.54219 / 0.29 (28489) hydrogen bonds : bond 0.04502 / 3.01 ( 832) hydrogen bonds : angle 4.56736 / 3.25 ( 2385) Misc. bond : bond 0.00235 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 241 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 677 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8125 (tppp) REVERT: C 620 ARG cc_start: 0.7467 (ptp-170) cc_final: 0.7086 (ptp-170) REVERT: C 683 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7432 (mm) REVERT: D 447 ASP cc_start: 0.6926 (t0) cc_final: 0.6482 (t0) REVERT: E 417 ASN cc_start: 0.8193 (m-40) cc_final: 0.7330 (p0) REVERT: F 324 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7939 (m-40) REVERT: F 646 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.6731 (m-30) REVERT: F 680 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7978 (t70) REVERT: F 695 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8011 (p0) outliers start: 64 outliers final: 27 residues processed: 285 average time/residue: 0.5411 time to fit residues: 177.3796 Evaluate side-chains 264 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 563 CYS Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 636 ARG Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 107 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 140 optimal weight: 0.0370 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN A 680 HIS B 680 HIS C 680 HIS D 324 ASN F 660 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.184479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120321 restraints weight = 20230.788| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.49 r_work: 0.3051 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20948 Z= 0.105 Angle : 0.485 6.114 28489 Z= 0.260 Chirality : 0.043 0.251 3306 Planarity : 0.004 0.040 3640 Dihedral : 10.582 156.401 3115 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer: Outliers : 3.09 % Allowed : 23.48 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % 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: 0.75 (0.16), residues: 2703 helix: 1.31 (0.17), residues: 1058 sheet: 0.25 (0.29), residues: 358 loop : -0.01 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 625 TYR 0.017 0.001 TYR A 482 PHE 0.015 0.001 PHE F 524 TRP 0.006 0.001 TRP F 350 HIS 0.006 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (20946) covalent geometry : angle 0.48529 / 0.26 (28489) hydrogen bonds : bond 0.03414 / 2.28 ( 832) hydrogen bonds : angle 4.37148 / 3.12 ( 2385) Misc. bond : bond 0.00205 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 387 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7492 (ttp-110) REVERT: C 620 ARG cc_start: 0.7602 (ptp-170) cc_final: 0.7227 (ptp-170) REVERT: D 447 ASP cc_start: 0.7016 (t0) cc_final: 0.6606 (t0) REVERT: D 684 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7609 (ttp) REVERT: E 417 ASN cc_start: 0.8244 (m-40) cc_final: 0.7368 (p0) REVERT: F 646 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.6830 (m-30) outliers start: 61 outliers final: 25 residues processed: 284 average time/residue: 0.5207 time to fit residues: 171.1660 Evaluate side-chains 254 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 563 CYS Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 714 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 200 optimal weight: 40.0000 chunk 62 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 176 optimal weight: 20.0000 chunk 243 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 680 HIS D 324 ASN D 594 ASN F 660 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.179933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113353 restraints weight = 20119.448| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.55 r_work: 0.2977 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 20948 Z= 0.291 Angle : 0.670 9.746 28489 Z= 0.354 Chirality : 0.052 0.299 3306 Planarity : 0.005 0.050 3640 Dihedral : 11.749 158.542 3115 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 3.95 % Allowed : 23.13 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % 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: 2703 helix: 0.88 (0.16), residues: 1054 sheet: 0.09 (0.27), residues: 406 loop : -0.22 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 665 TYR 0.018 0.002 TYR A 679 PHE 0.030 0.003 PHE F 524 TRP 0.007 0.002 TRP C 675 HIS 0.011 0.002 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.29 (20946) covalent geometry : angle 0.67009 / 0.35 (28489) hydrogen bonds : bond 0.06223 / 4.16 ( 832) hydrogen bonds : angle 4.68712 / 3.34 ( 2385) Misc. bond : bond 0.00298 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 242 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 677 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8150 (tppp) REVERT: C 367 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8418 (tp) REVERT: C 620 ARG cc_start: 0.7493 (ptp-170) cc_final: 0.7087 (ptp-170) REVERT: D 447 ASP cc_start: 0.7023 (t0) cc_final: 0.6527 (t0) REVERT: E 417 ASN cc_start: 0.8221 (m-40) cc_final: 0.7371 (p0) REVERT: F 324 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.7750 (t0) REVERT: F 646 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.6571 (m-30) outliers start: 78 outliers final: 44 residues processed: 297 average time/residue: 0.5420 time to fit residues: 185.3353 Evaluate side-chains 287 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain E residue 621 ILE Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 563 CYS Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 636 ARG Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 714 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 111 optimal weight: 0.4980 chunk 182 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN B 680 HIS C 529 GLN C 680 HIS D 324 ASN D 680 HIS F 324 ASN F 660 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.184178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115628 restraints weight = 20065.336| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.29 r_work: 0.3082 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20948 Z= 0.102 Angle : 0.491 6.207 28489 Z= 0.263 Chirality : 0.043 0.256 3306 Planarity : 0.004 0.049 3640 Dihedral : 10.641 156.203 3115 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 2.43 % Allowed : 24.90 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 2703 helix: 1.26 (0.17), residues: 1048 sheet: 0.16 (0.29), residues: 364 loop : -0.07 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 387 TYR 0.016 0.001 TYR A 482 PHE 0.014 0.001 PHE A 561 TRP 0.006 0.001 TRP F 350 HIS 0.006 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (20946) covalent geometry : angle 0.49070 / 0.26 (28489) hydrogen bonds : bond 0.03400 / 2.27 ( 832) hydrogen bonds : angle 4.40191 / 3.15 ( 2385) Misc. bond : bond 0.00197 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8596 (tpt) cc_final: 0.8355 (mmm) REVERT: B 435 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: C 620 ARG cc_start: 0.7551 (ptp-170) cc_final: 0.7162 (ptp-170) REVERT: D 447 ASP cc_start: 0.7006 (t0) cc_final: 0.6548 (t0) REVERT: E 417 ASN cc_start: 0.8172 (m-40) cc_final: 0.7284 (p0) REVERT: F 646 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.6772 (m-30) outliers start: 48 outliers final: 27 residues processed: 269 average time/residue: 0.5530 time to fit residues: 171.5899 Evaluate side-chains 252 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 563 CYS Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 714 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 203 optimal weight: 30.0000 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 84 optimal weight: 0.0010 chunk 137 optimal weight: 6.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN A 680 HIS B 680 HIS C 529 GLN C 680 HIS D 324 ASN D 680 HIS F 324 ASN F 660 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.181562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115776 restraints weight = 20254.718| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.57 r_work: 0.3039 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20948 Z= 0.144 Angle : 0.527 6.332 28489 Z= 0.281 Chirality : 0.045 0.265 3306 Planarity : 0.004 0.053 3640 Dihedral : 10.668 156.222 3115 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 2.94 % Allowed : 24.54 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % 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: 0.64 (0.16), residues: 2703 helix: 1.24 (0.17), residues: 1048 sheet: 0.13 (0.29), residues: 360 loop : -0.06 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 387 TYR 0.019 0.001 TYR A 482 PHE 0.020 0.002 PHE F 524 TRP 0.006 0.001 TRP F 350 HIS 0.008 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (20946) covalent geometry : angle 0.52733 / 0.28 (28489) hydrogen bonds : bond 0.04236 / 2.84 ( 832) hydrogen bonds : angle 4.38196 / 3.14 ( 2385) Misc. bond : bond 0.00229 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ARG cc_start: 0.8226 (mtm110) cc_final: 0.7638 (ttp-110) REVERT: C 620 ARG cc_start: 0.7561 (ptp-170) cc_final: 0.7160 (ptp-170) REVERT: C 683 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7530 (mm) REVERT: D 447 ASP cc_start: 0.7019 (t0) cc_final: 0.6563 (t0) REVERT: D 684 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7802 (ttp) REVERT: E 417 ASN cc_start: 0.8232 (m-40) cc_final: 0.7304 (p0) REVERT: F 646 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.6733 (m-30) outliers start: 58 outliers final: 33 residues processed: 274 average time/residue: 0.5658 time to fit residues: 178.4169 Evaluate side-chains 269 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 563 CYS Chi-restraints excluded: chain F residue 646 ASP Chi-restraints excluded: chain F residue 714 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 65 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN A 680 HIS B 680 HIS C 680 HIS D 324 ASN D 680 HIS F 324 ASN F 660 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116859 restraints weight = 20117.944| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.75 r_work: 0.3039 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20948 Z= 0.125 Angle : 0.504 6.827 28489 Z= 0.269 Chirality : 0.044 0.256 3306 Planarity : 0.004 0.044 3640 Dihedral : 10.362 155.247 3115 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.11 % Rotamer: Outliers : 2.83 % Allowed : 24.70 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.20 % 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: 0.70 (0.16), residues: 2703 helix: 1.30 (0.17), residues: 1050 sheet: 0.13 (0.29), residues: 360 loop : -0.03 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 387 TYR 0.017 0.001 TYR A 482 PHE 0.017 0.001 PHE F 524 TRP 0.006 0.001 TRP F 350 HIS 0.007 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (20946) covalent geometry : angle 0.50418 / 0.27 (28489) hydrogen bonds : bond 0.03825 / 2.56 ( 832) hydrogen bonds : angle 4.32616 / 3.10 ( 2385) Misc. bond : bond 0.00205 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7461 (ttp-110) REVERT: A 462 MET cc_start: 0.8669 (tpt) cc_final: 0.8453 (mmm) REVERT: C 620 ARG cc_start: 0.7587 (ptp-170) cc_final: 0.7193 (ptp-170) REVERT: C 683 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7547 (mm) REVERT: D 447 ASP cc_start: 0.7039 (t0) cc_final: 0.6607 (t0) REVERT: D 583 ILE cc_start: 0.5419 (OUTLIER) cc_final: 0.5111 (mm) REVERT: D 684 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7708 (ttp) REVERT: D 702 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6503 (tp) REVERT: E 417 ASN cc_start: 0.8171 (m-40) cc_final: 0.7266 (p0) REVERT: F 646 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.6628 (m-30) outliers start: 56 outliers final: 33 residues processed: 278 average time/residue: 0.5585 time to fit residues: 179.1158 Evaluate side-chains 270 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 563 CYS Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 646 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 152 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 212 optimal weight: 30.0000 chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 220 optimal weight: 50.0000 chunk 214 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 256 optimal weight: 0.0770 chunk 116 optimal weight: 1.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN A 680 HIS B 680 HIS C 680 HIS D 324 ASN D 680 HIS F 324 ASN F 660 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.183871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113282 restraints weight = 19999.842| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.91 r_work: 0.3075 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20948 Z= 0.120 Angle : 0.499 6.752 28489 Z= 0.266 Chirality : 0.044 0.254 3306 Planarity : 0.004 0.044 3640 Dihedral : 10.121 154.545 3115 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 2.48 % Allowed : 25.05 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % 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: 0.74 (0.16), residues: 2703 helix: 1.32 (0.17), residues: 1050 sheet: 0.15 (0.29), residues: 360 loop : 0.00 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 625 TYR 0.017 0.001 TYR A 482 PHE 0.017 0.001 PHE F 524 TRP 0.006 0.001 TRP F 350 HIS 0.007 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (20946) covalent geometry : angle 0.49931 / 0.27 (28489) hydrogen bonds : bond 0.03752 / 2.51 ( 832) hydrogen bonds : angle 4.28230 / 3.07 ( 2385) Misc. bond : bond 0.00203 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ARG cc_start: 0.8232 (mtm110) cc_final: 0.7492 (ttp-110) REVERT: A 453 GLU cc_start: 0.8622 (tt0) cc_final: 0.8035 (tt0) REVERT: A 462 MET cc_start: 0.8620 (tpt) cc_final: 0.8401 (mmm) REVERT: C 620 ARG cc_start: 0.7606 (ptp-170) cc_final: 0.7215 (ptp-170) REVERT: C 683 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7569 (mm) REVERT: D 447 ASP cc_start: 0.7029 (t0) cc_final: 0.6641 (t0) REVERT: D 583 ILE cc_start: 0.5543 (OUTLIER) cc_final: 0.5212 (mm) REVERT: D 684 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7653 (ttp) REVERT: D 702 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6511 (tp) REVERT: E 417 ASN cc_start: 0.8234 (m-40) cc_final: 0.7325 (p0) REVERT: F 646 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.6621 (m-30) outliers start: 49 outliers final: 34 residues processed: 269 average time/residue: 0.5547 time to fit residues: 172.2389 Evaluate side-chains 273 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 563 CYS Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 178 optimal weight: 30.0000 chunk 180 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 264 optimal weight: 0.0770 chunk 251 optimal weight: 4.9990 chunk 203 optimal weight: 0.0370 chunk 16 optimal weight: 1.9990 chunk 249 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN A 680 HIS B 680 HIS C 680 HIS D 324 ASN D 680 HIS F 324 ASN F 660 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.185835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117212 restraints weight = 20180.421| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.13 r_work: 0.3111 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20948 Z= 0.092 Angle : 0.462 6.480 28489 Z= 0.247 Chirality : 0.042 0.235 3306 Planarity : 0.004 0.044 3640 Dihedral : 9.602 152.701 3115 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.63 % Favored : 97.34 % Rotamer: Outliers : 2.13 % Allowed : 25.40 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % 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: 0.87 (0.16), residues: 2703 helix: 1.43 (0.17), residues: 1053 sheet: 0.17 (0.29), residues: 364 loop : 0.08 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 625 TYR 0.018 0.001 TYR A 482 PHE 0.013 0.001 PHE A 698 TRP 0.006 0.001 TRP F 350 HIS 0.007 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (20946) covalent geometry : angle 0.46201 / 0.25 (28489) hydrogen bonds : bond 0.02969 / 1.98 ( 832) hydrogen bonds : angle 4.17697 / 2.99 ( 2385) Misc. bond : bond 0.00180 / 0.11 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5406 Ramachandran restraints generated. 2703 Oldfield, 0 Emsley, 2703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7355 (ttp-110) REVERT: A 453 GLU cc_start: 0.8599 (tt0) cc_final: 0.8029 (tt0) REVERT: C 620 ARG cc_start: 0.7542 (ptp-170) cc_final: 0.7154 (ptp-170) REVERT: C 683 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7514 (mm) REVERT: D 387 ARG cc_start: 0.7939 (mpp-170) cc_final: 0.6868 (ttp80) REVERT: D 447 ASP cc_start: 0.6989 (t0) cc_final: 0.6601 (t0) REVERT: D 684 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7239 (ttp) REVERT: E 417 ASN cc_start: 0.8221 (m-40) cc_final: 0.7317 (p0) REVERT: E 670 TYR cc_start: 0.5862 (t80) cc_final: 0.5081 (t80) outliers start: 42 outliers final: 27 residues processed: 272 average time/residue: 0.5642 time to fit residues: 176.1126 Evaluate side-chains 262 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 628 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 18 optimal weight: 2.9990 chunk 179 optimal weight: 30.0000 chunk 232 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 209 optimal weight: 50.0000 chunk 107 optimal weight: 0.0050 chunk 250 optimal weight: 0.3980 chunk 96 optimal weight: 0.5980 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN A 680 HIS B 680 HIS C 680 HIS D 324 ASN D 680 HIS F 324 ASN F 660 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.184147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118640 restraints weight = 20204.029| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.62 r_work: 0.3063 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20948 Z= 0.119 Angle : 0.495 7.618 28489 Z= 0.263 Chirality : 0.043 0.243 3306 Planarity : 0.004 0.044 3640 Dihedral : 9.668 152.507 3115 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.15 % Rotamer: Outliers : 2.28 % Allowed : 25.35 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % 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: 0.84 (0.16), residues: 2703 helix: 1.40 (0.17), residues: 1051 sheet: 0.20 (0.29), residues: 360 loop : 0.07 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 595 TYR 0.018 0.001 TYR A 482 PHE 0.018 0.001 PHE F 524 TRP 0.007 0.001 TRP E 355 HIS 0.008 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (20946) covalent geometry : angle 0.49521 / 0.26 (28489) hydrogen bonds : bond 0.03678 / 2.46 ( 832) hydrogen bonds : angle 4.21083 / 3.02 ( 2385) Misc. bond : bond 0.00203 / 0.12 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9210.06 seconds wall clock time: 156 minutes 55.69 seconds (9415.69 seconds total)