Starting phenix.real_space_refine on Tue Jun 17 22:53:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh0_37524/06_2025/8wh0_37524_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh0_37524/06_2025/8wh0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wh0_37524/06_2025/8wh0_37524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh0_37524/06_2025/8wh0_37524.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh0_37524/06_2025/8wh0_37524_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh0_37524/06_2025/8wh0_37524_neut.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG: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: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG: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: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 6, 'ASP:plan': 7} 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: {'GLN:plan1': 3, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 10, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 9, 'ARG:plan': 6} 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: {'GLN:plan1': 5, 'HIS:plan': 6, 'TYR:plan': 12, 'ASN:plan1': 10, 'ASP:plan': 19, 'PHE:plan': 19, 'GLU:plan': 19, 'ARG:plan': 12} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG: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: 12.91, per 1000 atoms: 0.63 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: 5.35 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 3.14 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: 7.04 Time building geometry restraints manager: 6.25 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: 28184 2.12 - 4.23: 242 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: 3015 0.077 - 0.153: 280 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: 1.360 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: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 48.630 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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= 0.198 Angle : 0.536 10.583 28489 Z= 0.270 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 : 11.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (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 TRP 0.006 0.001 TRP F 350 HIS 0.005 0.001 HIS A 680 PHE 0.015 0.001 PHE B 524 TYR 0.016 0.001 TYR A 482 ARG 0.002 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.15508 ( 832) hydrogen bonds : angle 5.99075 ( 2385) covalent geometry : bond 0.00405 (20946) covalent geometry : angle 0.53649 (28489) Misc. bond : bond 0.00125 ( 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 : 2.478 Fit side-chains 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: 1.2638 time to fit residues: 360.9764 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 : 2.248 ------------------------------------------------------------------------------- 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 227 optimal weight: 1.9990 chunk 204 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 660 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115524 restraints weight = 20112.655| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.55 r_work: 0.2999 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20948 Z= 0.216 Angle : 0.622 7.598 28489 Z= 0.330 Chirality : 0.048 0.197 3306 Planarity : 0.005 0.047 3640 Dihedral : 12.788 156.196 3118 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.41 % Rotamer: Outliers : 3.59 % Allowed : 22.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2703 helix: 0.90 (0.17), residues: 1058 sheet: 0.13 (0.27), residues: 398 loop : -0.19 (0.16), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 350 HIS 0.008 0.001 HIS A 680 PHE 0.023 0.002 PHE F 524 TYR 0.031 0.002 TYR E 670 ARG 0.003 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05524 ( 832) hydrogen bonds : angle 4.86158 ( 2385) covalent geometry : bond 0.00529 (20946) covalent geometry : angle 0.62174 (28489) Misc. bond : bond 0.00276 ( 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 317 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 246 time to evaluate : 2.529 Fit side-chains REVERT: A 677 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8167 (tppp) REVERT: B 612 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.8094 (tmm-80) REVERT: D 447 ASP cc_start: 0.7057 (t0) cc_final: 0.6743 (t0) REVERT: D 707 VAL cc_start: 0.7053 (OUTLIER) cc_final: 0.6660 (t) REVERT: F 646 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.6734 (m-30) outliers start: 71 outliers final: 21 residues processed: 299 average time/residue: 1.2111 time to fit residues: 415.7914 Evaluate side-chains 258 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 680 HIS Chi-restraints excluded: chain B residue 474 GLU 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 C residue 497 CYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 707 VAL 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 563 CYS 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 201 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 HIS C 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 = 0.4021 r_free = 0.4021 target = 0.180874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110987 restraints weight = 20085.366| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.50 r_work: 0.3027 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20948 Z= 0.171 Angle : 0.562 6.218 28489 Z= 0.300 Chirality : 0.046 0.196 3306 Planarity : 0.005 0.047 3640 Dihedral : 11.460 154.668 3115 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.14 % Favored : 96.74 % Rotamer: Outliers : 3.39 % Allowed : 23.38 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2703 helix: 1.03 (0.17), residues: 1049 sheet: 0.32 (0.31), residues: 314 loop : -0.16 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 350 HIS 0.008 0.001 HIS C 680 PHE 0.021 0.002 PHE F 524 TYR 0.035 0.002 TYR E 670 ARG 0.004 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 832) hydrogen bonds : angle 4.60700 ( 2385) covalent geometry : bond 0.00416 (20946) covalent geometry : angle 0.56153 (28489) Misc. bond : bond 0.00241 ( 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 304 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 2.768 Fit side-chains revert: symmetry clash REVERT: A 637 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: A 765 LYS cc_start: 0.5178 (OUTLIER) cc_final: 0.3475 (pttt) REVERT: C 620 ARG cc_start: 0.7493 (ptp-170) cc_final: 0.7135 (ptp-170) REVERT: D 447 ASP cc_start: 0.6950 (t0) cc_final: 0.6545 (t0) REVERT: D 684 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7772 (ttp) REVERT: E 387 ARG cc_start: 0.8070 (tmm160) cc_final: 0.7866 (ttp80) REVERT: F 324 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7968 (m-40) REVERT: F 646 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.6695 (m-30) REVERT: F 695 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7993 (p0) outliers start: 67 outliers final: 29 residues processed: 285 average time/residue: 1.1619 time to fit residues: 380.8442 Evaluate side-chains 266 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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 637 GLU Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN 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 530 THR 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 578 THR 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 E residue 674 LYS 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 628 THR Chi-restraints excluded: chain F residue 636 ARG Chi-restraints excluded: chain F residue 646 ASP 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 144 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 164 optimal weight: 0.2980 chunk 204 optimal weight: 9.9990 chunk 130 optimal weight: 0.0870 chunk 95 optimal weight: 0.8980 chunk 265 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 680 HIS B 680 HIS C 680 HIS D 324 ASN D 594 ASN D 680 HIS E 358 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 = 0.4055 r_free = 0.4055 target = 0.184192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120488 restraints weight = 20133.641| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.43 r_work: 0.3055 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20948 Z= 0.111 Angle : 0.493 6.283 28489 Z= 0.264 Chirality : 0.043 0.171 3306 Planarity : 0.004 0.041 3640 Dihedral : 10.452 153.044 3115 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.11 % Rotamer: Outliers : 3.54 % Allowed : 23.28 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2703 helix: 1.25 (0.17), residues: 1049 sheet: 0.18 (0.29), residues: 364 loop : -0.05 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 350 HIS 0.006 0.001 HIS C 680 PHE 0.016 0.001 PHE B 524 TYR 0.037 0.001 TYR E 670 ARG 0.007 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 832) hydrogen bonds : angle 4.39309 ( 2385) covalent geometry : bond 0.00253 (20946) covalent geometry : angle 0.49284 (28489) Misc. bond : bond 0.00192 ( 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 311 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 2.369 Fit side-chains REVERT: A 462 MET cc_start: 0.8617 (tpt) cc_final: 0.8393 (mmm) REVERT: A 637 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: A 765 LYS cc_start: 0.5486 (OUTLIER) cc_final: 0.3679 (pttm) REVERT: C 620 ARG cc_start: 0.7593 (ptp-170) cc_final: 0.7229 (ptp-170) REVERT: D 447 ASP cc_start: 0.7017 (t0) cc_final: 0.6646 (t0) REVERT: D 684 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7653 (ttp) REVERT: E 348 ILE cc_start: 0.8607 (pt) cc_final: 0.8379 (pt) REVERT: E 417 ASN cc_start: 0.8242 (m-40) cc_final: 0.7364 (p0) REVERT: F 646 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.6801 (m-30) outliers start: 70 outliers final: 30 residues processed: 296 average time/residue: 1.0962 time to fit residues: 374.1785 Evaluate side-chains 267 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 2.215 ------------------------------------------------------------------------------- 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 617 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 474 GLU 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 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 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 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 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 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 20 optimal weight: 0.0870 chunk 58 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 264 optimal weight: 0.0050 chunk 105 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 overall best weight: 1.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.183822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118008 restraints weight = 20119.198| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.36 r_work: 0.3043 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 0.039 20948 Z= 0.123 Angle : 0.502 6.627 28489 Z= 0.269 Chirality : 0.043 0.168 3306 Planarity : 0.004 0.043 3640 Dihedral : 10.266 152.173 3115 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 3.34 % Allowed : 23.58 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 2703 helix: 1.31 (0.17), residues: 1048 sheet: 0.18 (0.29), residues: 364 loop : -0.02 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 350 HIS 0.007 0.001 HIS C 680 PHE 0.017 0.001 PHE F 524 TYR 0.040 0.001 TYR E 670 ARG 0.006 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 832) hydrogen bonds : angle 4.36362 ( 2385) covalent geometry : bond 0.00292 (20946) covalent geometry : angle 0.50235 (28489) Misc. bond : bond 0.00201 ( 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 301 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 235 time to evaluate : 2.456 Fit side-chains REVERT: A 387 ARG cc_start: 0.8259 (mtm110) cc_final: 0.7496 (ttp-110) REVERT: A 453 GLU cc_start: 0.8658 (tt0) cc_final: 0.8061 (tt0) REVERT: A 677 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8220 (tppp) REVERT: A 765 LYS cc_start: 0.5489 (OUTLIER) cc_final: 0.3677 (pttm) REVERT: B 435 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8433 (mtmm) REVERT: C 620 ARG cc_start: 0.7615 (ptp-170) cc_final: 0.7234 (ptp-170) REVERT: D 447 ASP cc_start: 0.7053 (t0) cc_final: 0.6660 (t0) REVERT: D 684 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7668 (ttp) REVERT: E 417 ASN cc_start: 0.8252 (m-40) cc_final: 0.7364 (p0) REVERT: F 646 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.6808 (m-30) outliers start: 66 outliers final: 37 residues processed: 284 average time/residue: 1.1719 time to fit residues: 384.4187 Evaluate side-chains 275 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR 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 A residue 765 LYS 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 474 GLU 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 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 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 684 MET Chi-restraints excluded: chain E residue 413 LEU 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 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 628 THR 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 234 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 131 optimal weight: 40.0000 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 228 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4057 r_free = 0.4057 target = 0.184417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119825 restraints weight = 20109.304| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.29 r_work: 0.3060 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1362 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= 0.113 Angle : 0.488 6.697 28489 Z= 0.261 Chirality : 0.043 0.168 3306 Planarity : 0.004 0.042 3640 Dihedral : 9.965 150.907 3115 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 3.14 % Allowed : 23.99 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.16), residues: 2703 helix: 1.38 (0.17), residues: 1048 sheet: 0.21 (0.30), residues: 350 loop : 0.02 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 350 HIS 0.007 0.001 HIS C 680 PHE 0.016 0.001 PHE B 524 TYR 0.047 0.001 TYR E 670 ARG 0.004 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 832) hydrogen bonds : angle 4.30033 ( 2385) covalent geometry : bond 0.00263 (20946) covalent geometry : angle 0.48756 (28489) Misc. bond : bond 0.00191 ( 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 299 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 237 time to evaluate : 2.307 Fit side-chains revert: symmetry clash REVERT: A 387 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7488 (ttp-110) REVERT: A 453 GLU cc_start: 0.8640 (tt0) cc_final: 0.8044 (tt0) REVERT: A 462 MET cc_start: 0.8641 (tpt) cc_final: 0.8427 (mmm) REVERT: A 637 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: A 765 LYS cc_start: 0.5507 (OUTLIER) cc_final: 0.3761 (pttm) REVERT: C 620 ARG cc_start: 0.7586 (ptp-170) cc_final: 0.7187 (ptp-170) REVERT: D 447 ASP cc_start: 0.6997 (t0) cc_final: 0.6608 (t0) REVERT: D 522 ASP cc_start: 0.7831 (t0) cc_final: 0.7391 (t0) REVERT: D 684 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7556 (ttp) REVERT: D 702 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6552 (tp) REVERT: E 417 ASN cc_start: 0.8248 (m-40) cc_final: 0.7358 (p0) REVERT: F 755 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6687 (p0) outliers start: 62 outliers final: 38 residues processed: 287 average time/residue: 1.4205 time to fit residues: 472.3090 Evaluate side-chains 274 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 765 LYS 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 474 GLU 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 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 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 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 442 THR 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 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 714 ILE Chi-restraints excluded: chain F residue 755 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 238 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 680 HIS B 680 HIS C 680 HIS D 324 ASN D 680 HIS F 660 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.181035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115206 restraints weight = 20105.402| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.65 r_work: 0.3016 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20948 Z= 0.171 Angle : 0.554 6.905 28489 Z= 0.294 Chirality : 0.046 0.200 3306 Planarity : 0.004 0.045 3640 Dihedral : 10.379 151.445 3115 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.89 % Rotamer: Outliers : 3.85 % Allowed : 23.43 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2703 helix: 1.18 (0.17), residues: 1049 sheet: 0.15 (0.29), residues: 360 loop : -0.07 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 350 HIS 0.009 0.001 HIS C 680 PHE 0.022 0.002 PHE F 524 TYR 0.045 0.002 TYR E 670 ARG 0.003 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 832) hydrogen bonds : angle 4.43954 ( 2385) covalent geometry : bond 0.00418 (20946) covalent geometry : angle 0.55390 (28489) Misc. bond : bond 0.00244 ( 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 312 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 236 time to evaluate : 3.176 Fit side-chains revert: symmetry clash REVERT: A 453 GLU cc_start: 0.8630 (tt0) cc_final: 0.8040 (tt0) REVERT: A 637 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: A 677 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8198 (tppp) REVERT: C 367 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8503 (tp) REVERT: C 620 ARG cc_start: 0.7586 (ptp-170) cc_final: 0.7173 (ptp-170) REVERT: D 447 ASP cc_start: 0.7021 (t0) cc_final: 0.6571 (t0) REVERT: D 684 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7854 (ttp) REVERT: D 702 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6493 (tp) REVERT: E 417 ASN cc_start: 0.8257 (m-40) cc_final: 0.7408 (p0) REVERT: F 324 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7902 (m-40) REVERT: F 646 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.6947 (m-30) outliers start: 76 outliers final: 38 residues processed: 290 average time/residue: 1.5414 time to fit residues: 520.3043 Evaluate side-chains 280 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR 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 637 GLU 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 474 GLU 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 363 LEU 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 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 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 452 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 602 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 97 optimal weight: 1.9990 chunk 222 optimal weight: 50.0000 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 198 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN C 680 HIS D 324 ASN D 680 HIS F 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.179462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113156 restraints weight = 20267.500| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.55 r_work: 0.3004 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20948 Z= 0.235 Angle : 0.623 7.950 28489 Z= 0.331 Chirality : 0.048 0.266 3306 Planarity : 0.005 0.058 3640 Dihedral : 11.185 153.118 3115 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 3.39 % Allowed : 23.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2703 helix: 0.94 (0.17), residues: 1054 sheet: 0.17 (0.28), residues: 376 loop : -0.20 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 350 HIS 0.010 0.002 HIS C 680 PHE 0.026 0.002 PHE F 524 TYR 0.041 0.002 TYR E 670 ARG 0.011 0.001 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.05649 ( 832) hydrogen bonds : angle 4.58453 ( 2385) covalent geometry : bond 0.00582 (20946) covalent geometry : angle 0.62278 (28489) Misc. bond : bond 0.00336 ( 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 309 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 242 time to evaluate : 4.597 Fit side-chains revert: symmetry clash REVERT: A 387 ARG cc_start: 0.8284 (mtm110) cc_final: 0.7715 (ttp-110) REVERT: A 462 MET cc_start: 0.8713 (tpt) cc_final: 0.8478 (mmm) REVERT: A 637 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: A 649 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8496 (mtpm) REVERT: A 677 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8259 (tppp) REVERT: C 620 ARG cc_start: 0.7626 (ptp-170) cc_final: 0.7213 (ptp-170) REVERT: D 447 ASP cc_start: 0.7065 (t0) cc_final: 0.6605 (t0) REVERT: D 522 ASP cc_start: 0.7879 (t0) cc_final: 0.7460 (t0) REVERT: D 702 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6325 (tp) REVERT: E 417 ASN cc_start: 0.8285 (m-40) cc_final: 0.7528 (p0) REVERT: F 324 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.7959 (m-40) outliers start: 67 outliers final: 41 residues processed: 292 average time/residue: 1.8673 time to fit residues: 634.1499 Evaluate side-chains 289 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 3.255 ------------------------------------------------------------------------------- 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 431 ASP Chi-restraints excluded: chain A residue 435 LYS 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 637 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 677 LYS 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 474 GLU 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 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 702 ILE Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 452 VAL 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 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 636 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 183 optimal weight: 0.3980 chunk 200 optimal weight: 0.0040 chunk 204 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 197 optimal weight: 40.0000 chunk 221 optimal weight: 30.0000 chunk 126 optimal weight: 0.0970 chunk 48 optimal weight: 0.7980 chunk 118 optimal weight: 0.0370 chunk 159 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.2468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 680 HIS B 324 ASN B 680 HIS C 680 HIS D 324 ASN D 680 HIS E 324 ASN F 324 ASN F 660 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.186990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122812 restraints weight = 20235.189| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.45 r_work: 0.3097 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20948 Z= 0.088 Angle : 0.461 7.597 28489 Z= 0.246 Chirality : 0.041 0.168 3306 Planarity : 0.004 0.047 3640 Dihedral : 9.416 149.990 3115 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer: Outliers : 1.92 % Allowed : 25.30 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2703 helix: 1.36 (0.17), residues: 1054 sheet: 0.20 (0.29), residues: 357 loop : 0.07 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 350 HIS 0.005 0.001 HIS D 680 PHE 0.009 0.001 PHE A 561 TYR 0.043 0.001 TYR E 670 ARG 0.010 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.02632 ( 832) hydrogen bonds : angle 4.17724 ( 2385) covalent geometry : bond 0.00192 (20946) covalent geometry : angle 0.46052 (28489) Misc. bond : bond 0.00201 ( 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 281 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 2.396 Fit side-chains revert: symmetry clash REVERT: A 387 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7285 (ttp-110) REVERT: A 453 GLU cc_start: 0.8622 (tt0) cc_final: 0.8045 (tt0) REVERT: A 462 MET cc_start: 0.8642 (tpt) cc_final: 0.8379 (mmm) REVERT: A 637 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: C 620 ARG cc_start: 0.7565 (ptp-170) cc_final: 0.7207 (ptp-170) REVERT: D 447 ASP cc_start: 0.7007 (t0) cc_final: 0.6650 (t0) REVERT: D 522 ASP cc_start: 0.7796 (t0) cc_final: 0.7444 (t0) REVERT: D 679 TYR cc_start: 0.8187 (m-80) cc_final: 0.7963 (m-80) REVERT: D 684 MET cc_start: 0.7883 (ttm) cc_final: 0.7618 (ttp) REVERT: E 417 ASN cc_start: 0.8344 (m-40) cc_final: 0.7519 (p0) REVERT: F 646 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.6951 (m-30) outliers start: 38 outliers final: 15 residues processed: 275 average time/residue: 1.5011 time to fit residues: 478.3958 Evaluate side-chains 249 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 581 CYS 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 525 VAL 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 264 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 178 optimal weight: 40.0000 chunk 149 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 680 HIS B 680 HIS C 680 HIS D 324 ASN D 680 HIS F 660 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114788 restraints weight = 20126.814| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.52 r_work: 0.2997 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20948 Z= 0.184 Angle : 0.571 10.130 28489 Z= 0.303 Chirality : 0.046 0.218 3306 Planarity : 0.004 0.054 3640 Dihedral : 10.137 151.180 3115 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 1.62 % Allowed : 25.66 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2703 helix: 1.17 (0.17), residues: 1056 sheet: 0.13 (0.29), residues: 360 loop : -0.03 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 355 HIS 0.011 0.001 HIS C 680 PHE 0.023 0.002 PHE F 524 TYR 0.043 0.002 TYR E 670 ARG 0.008 0.001 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 832) hydrogen bonds : angle 4.37776 ( 2385) covalent geometry : bond 0.00453 (20946) covalent geometry : angle 0.57138 (28489) Misc. bond : bond 0.00261 ( 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 270 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 2.314 Fit side-chains revert: symmetry clash REVERT: A 387 ARG cc_start: 0.8280 (mtm110) cc_final: 0.7631 (ttp-110) REVERT: A 637 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 649 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8525 (mtpm) REVERT: B 526 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8408 (tp30) REVERT: C 620 ARG cc_start: 0.7593 (ptp-170) cc_final: 0.7180 (ptp-170) REVERT: D 447 ASP cc_start: 0.7042 (t0) cc_final: 0.6637 (t0) REVERT: D 522 ASP cc_start: 0.7795 (t0) cc_final: 0.7447 (t0) REVERT: E 356 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7847 (mtpt) REVERT: E 417 ASN cc_start: 0.8337 (m-40) cc_final: 0.7497 (p0) REVERT: F 646 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7007 (m-30) outliers start: 32 outliers final: 17 residues processed: 264 average time/residue: 1.1859 time to fit residues: 358.6244 Evaluate side-chains 255 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 2.326 ------------------------------------------------------------------------------- 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 637 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 581 CYS 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 525 VAL 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 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 220 optimal weight: 50.0000 chunk 243 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.183574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114521 restraints weight = 20115.963| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.32 r_work: 0.3044 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1535 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= 0.123 Angle : 0.513 12.802 28489 Z= 0.272 Chirality : 0.043 0.178 3306 Planarity : 0.004 0.049 3640 Dihedral : 9.782 150.149 3115 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 1.62 % Allowed : 25.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2703 helix: 1.29 (0.17), residues: 1048 sheet: 0.17 (0.29), residues: 360 loop : 0.02 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 350 HIS 0.007 0.001 HIS C 680 PHE 0.017 0.001 PHE F 524 TYR 0.043 0.001 TYR E 670 ARG 0.008 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 832) hydrogen bonds : angle 4.26632 ( 2385) covalent geometry : bond 0.00292 (20946) covalent geometry : angle 0.51256 (28489) Misc. bond : bond 0.00206 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20439.14 seconds wall clock time: 362 minutes 31.59 seconds (21751.59 seconds total)