Starting phenix.real_space_refine on Sun Jul 5 02:43:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9im1_60679/07_2026/9im1_60679.cif Found real_map, /net/cci-nas-00/data/ceres_data/9im1_60679/07_2026/9im1_60679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9im1_60679/07_2026/9im1_60679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9im1_60679/07_2026/9im1_60679.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9im1_60679/07_2026/9im1_60679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9im1_60679/07_2026/9im1_60679.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 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 19 5.49 5 Mg 3 5.21 5 S 119 5.16 5 C 15893 2.51 5 N 4207 2.21 5 O 4726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24967 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4456 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 523} Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3748 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 441} Chain: "C" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3748 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 441} Chain: "D" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3748 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 441} Chain: "F" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3413 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 20, 'TRANS': 402} Chain breaks: 2 Chain: "E" Number of atoms: 5584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5584 Classifications: {'peptide': 689} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Chain: "X" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.31, per 1000 atoms: 0.17 Number of scatterers: 24967 At special positions: 0 Unit cell: (134.64, 132, 167.2, 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 119 16.00 P 19 15.00 Mg 3 11.99 O 4726 8.00 N 4207 7.00 C 15893 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 46 sheets defined 44.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.626A pdb=" N PHE A 243 " --> pdb=" O PHE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.758A pdb=" N ILE A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.758A pdb=" N ASN A 262 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 263 " --> pdb=" O ASN A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.519A pdb=" N CYS A 314 " --> pdb=" O PRO A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.676A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.678A pdb=" N LEU A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 381 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: 3.684A 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 579 removed outlier: 3.507A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.586A pdb=" N ASN A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 696 through 703 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 735 through 747 removed outlier: 3.504A pdb=" N PHE A 739 " --> pdb=" O PRO A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 764 removed outlier: 3.523A pdb=" N PHE A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 783 Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.957A 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: 3.714A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.673A pdb=" N ASN B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.641A pdb=" N SER B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 removed outlier: 3.521A pdb=" N THR B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.527A pdb=" N THR B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.611A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) 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 640 Processing helix chain 'B' and resid 654 through 661 removed outlier: 3.536A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.505A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 679 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.908A pdb=" N GLY B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR B 704 " --> pdb=" O LEU B 700 " (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 721 removed outlier: 3.538A pdb=" N LEU B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 737 No H-bonds generated for 'chain 'B' and resid 735 through 737' Processing helix chain 'B' and resid 738 through 744 removed outlier: 4.031A pdb=" N LYS B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 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 336 removed outlier: 3.546A pdb=" N ASN C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 376 through 381 removed outlier: 4.000A 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: 3.582A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.713A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.667A pdb=" N THR C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 removed outlier: 3.519A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) 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 removed outlier: 3.585A pdb=" N LYS C 678 " --> pdb=" O LYS C 674 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 679 " --> pdb=" O TRP C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 695 removed outlier: 3.517A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE C 693 " --> pdb=" O PRO C 690 " (cutoff:3.500A) Proline residue: C 694 - end of helix No H-bonds generated for 'chain 'C' and resid 689 through 695' Processing helix chain 'C' and resid 696 through 703 Processing helix chain 'C' and resid 710 through 715 Proline residue: C 715 - end of helix Processing helix chain 'C' and resid 716 through 724 removed outlier: 3.703A pdb=" N LEU C 720 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 722 " --> pdb=" O THR C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 745 removed outlier: 4.197A pdb=" N GLN C 741 " --> pdb=" O THR C 737 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS C 742 " --> pdb=" O THR C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.678A pdb=" N GLU C 757 " --> pdb=" O GLY C 753 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 761 " --> pdb=" O GLU C 757 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 783 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.690A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.817A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.582A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.813A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU D 460 " --> pdb=" O PRO D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.872A pdb=" N LEU D 486 " --> pdb=" O TYR D 482 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.557A pdb=" N THR D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.600A pdb=" N ALA D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.560A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 619 removed outlier: 3.519A pdb=" N ARG D 619 " --> pdb=" O ALA D 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 619' Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.789A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 removed outlier: 3.684A pdb=" N LEU D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 703 removed outlier: 4.274A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 723 removed outlier: 3.628A pdb=" N LEU D 720 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 721 " --> pdb=" O MET D 717 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS D 722 " --> pdb=" O THR D 718 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 723 " --> pdb=" O ASP D 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 716 through 723' Processing helix chain 'D' and resid 736 through 745 removed outlier: 4.609A pdb=" N GLN D 741 " --> pdb=" O THR D 737 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS D 742 " --> pdb=" O THR D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 removed outlier: 3.512A pdb=" N PHE D 752 " --> pdb=" O ASN D 748 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS D 754 " --> pdb=" O ARG D 750 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 254 removed outlier: 3.503A pdb=" N ALA F 246 " --> pdb=" O SER F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.623A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.694A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 399 Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.750A pdb=" N ASP F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 removed outlier: 3.910A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 489 removed outlier: 4.328A pdb=" N LYS F 477 " --> pdb=" O ASP F 473 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN F 478 " --> pdb=" O GLU F 474 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU F 480 " --> pdb=" O LYS F 476 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU F 481 " --> pdb=" O LYS F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 521 removed outlier: 3.755A pdb=" N LYS F 513 " --> pdb=" O LYS F 509 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 514 " --> pdb=" O SER F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 547 removed outlier: 3.598A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.681A pdb=" N ILE F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.685A pdb=" N MET F 618 " --> pdb=" O ASP F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 662 Processing helix chain 'F' and resid 664 through 680 removed outlier: 3.594A pdb=" N PHE F 668 " --> pdb=" O TYR F 664 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F 671 " --> pdb=" O ALA F 667 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 26 Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 78 through 104 Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.961A pdb=" N ASN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.214A pdb=" N ARG E 152 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 169 removed outlier: 3.713A pdb=" N SER E 168 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.884A pdb=" N VAL E 173 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 208 removed outlier: 3.658A pdb=" N LEU E 208 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.704A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 372 removed outlier: 3.659A pdb=" N LYS E 366 " --> pdb=" O PRO E 362 " (cutoff:3.500A) 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 381 removed outlier: 3.795A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 399 Processing helix chain 'E' and resid 431 through 436 removed outlier: 3.514A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.811A pdb=" N LYS E 450 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 469 Processing helix chain 'E' and resid 475 through 488 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 528 through 533 removed outlier: 3.958A pdb=" N ILE E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 548 removed outlier: 3.808A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 579 removed outlier: 3.739A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 619 No H-bonds generated for 'chain 'E' and resid 617 through 619' Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 641 Processing helix chain 'E' and resid 653 through 661 removed outlier: 3.736A pdb=" N GLY E 657 " --> pdb=" O GLU E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 681 removed outlier: 3.667A pdb=" N ILE E 681 " --> pdb=" O LYS E 677 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 704 Processing helix chain 'E' and resid 710 through 715 Proline residue: E 715 - end of helix Processing helix chain 'E' and resid 716 through 723 Processing helix chain 'E' and resid 735 through 747 removed outlier: 3.682A pdb=" N TYR E 746 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 Processing helix chain 'E' and resid 754 through 761 Processing helix chain 'E' and resid 779 through 783 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 299 Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.845A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER A 556 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA6, first strand: chain 'A' and resid 628 through 631 Processing sheet with id=AA7, first strand: chain 'A' and resid 706 through 708 Processing sheet with id=AA8, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA9, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AB1, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AB2, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB3, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.949A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N SER B 556 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR B 499 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N THR B 604 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE B 501 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB5, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.288A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 706 through 707 Processing sheet with id=AB7, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AB8, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.673A pdb=" N LYS B 765 " --> pdb=" O TYR B 773 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AC1, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AC2, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.905A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N SER C 556 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 631 removed outlier: 6.305A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AC6, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AC7, first strand: chain 'C' and resid 765 through 766 Processing sheet with id=AC8, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC9, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AD1, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.939A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 499 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 628 through 631 Processing sheet with id=AD3, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AD4, first strand: chain 'D' and resid 726 through 728 removed outlier: 3.816A pdb=" N TYR D 773 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS D 765 " --> pdb=" O TYR D 773 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 294 through 299 removed outlier: 3.603A pdb=" N LYS F 317 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AD7, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AD8, first strand: chain 'F' and resid 524 through 527 removed outlier: 6.789A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N PHE F 501 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 581 through 582 removed outlier: 3.743A pdb=" N VAL F 582 " --> pdb=" O ASN F 594 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASN F 594 " --> pdb=" O VAL F 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.583A pdb=" N PHE E 12 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 55 " --> pdb=" O PHE E 12 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 65 through 73 removed outlier: 10.725A pdb=" N VAL E 65 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASP E 139 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE E 67 " --> pdb=" O PHE E 137 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET E 69 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE E 136 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER E 121 " --> pdb=" O ILE E 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 65 through 73 removed outlier: 10.725A pdb=" N VAL E 65 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASP E 139 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE E 67 " --> pdb=" O PHE E 137 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET E 69 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N TYR E 219 " --> pdb=" O PHE E 137 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP E 139 " --> pdb=" O TYR E 219 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=AE5, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AE6, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AE7, first strand: chain 'E' and resid 524 through 527 removed outlier: 6.742A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR E 499 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR E 604 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE E 501 " --> pdb=" O THR E 604 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 622 " --> pdb=" O LEU E 498 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 581 through 582 Processing sheet with id=AE9, first strand: chain 'E' and resid 706 through 708 Processing sheet with id=AF1, first strand: chain 'E' and resid 765 through 766 removed outlier: 3.771A pdb=" N LYS E 765 " --> pdb=" O TYR E 773 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2367 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: 4.70 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7889 1.34 - 1.46: 5146 1.46 - 1.58: 12271 1.58 - 1.70: 32 1.70 - 1.82: 172 Bond restraints: 25510 Sorted by residual: bond pdb=" CB PRO F 320 " pdb=" CG PRO F 320 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.98e+00 bond pdb=" CB GLN A 775 " pdb=" CG GLN A 775 " ideal model delta sigma weight residual 1.520 1.599 -0.079 3.00e-02 1.11e+03 6.97e+00 bond pdb=" C3' DT X 5 " pdb=" C2' DT X 5 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.01e+00 bond pdb=" C3' DT X 4 " pdb=" C2' DT X 4 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.86e+00 bond pdb=" CB PRO F 690 " pdb=" CG PRO F 690 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.71e+00 ... (remaining 25505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 34215 3.36 - 6.73: 258 6.73 - 10.09: 47 10.09 - 13.46: 9 13.46 - 16.82: 3 Bond angle restraints: 34532 Sorted by residual: angle pdb=" CA PRO F 320 " pdb=" N PRO F 320 " pdb=" CD PRO F 320 " ideal model delta sigma weight residual 112.00 101.39 10.61 1.40e+00 5.10e-01 5.74e+01 angle pdb=" CA GLN A 775 " pdb=" CB GLN A 775 " pdb=" CG GLN A 775 " ideal model delta sigma weight residual 114.10 128.32 -14.22 2.00e+00 2.50e-01 5.05e+01 angle pdb=" CA PRO F 690 " pdb=" N PRO F 690 " pdb=" CD PRO F 690 " ideal model delta sigma weight residual 112.00 102.33 9.67 1.40e+00 5.10e-01 4.78e+01 angle pdb=" CB GLN A 775 " pdb=" CG GLN A 775 " pdb=" CD GLN A 775 " ideal model delta sigma weight residual 112.60 123.47 -10.87 1.70e+00 3.46e-01 4.09e+01 angle pdb=" CB GLN B 775 " pdb=" CG GLN B 775 " pdb=" CD GLN B 775 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.70e+00 3.46e-01 2.78e+01 ... (remaining 34527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 13984 17.53 - 35.05: 1225 35.05 - 52.58: 270 52.58 - 70.10: 60 70.10 - 87.63: 30 Dihedral angle restraints: 15569 sinusoidal: 6568 harmonic: 9001 Sorted by residual: dihedral pdb=" CA ARG F 627 " pdb=" C ARG F 627 " pdb=" N THR F 628 " pdb=" CA THR F 628 " ideal model delta harmonic sigma weight residual 180.00 151.50 28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA TYR E 679 " pdb=" C TYR E 679 " pdb=" N HIS E 680 " pdb=" CA HIS E 680 " ideal model delta harmonic sigma weight residual -180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA PRO F 320 " pdb=" C PRO F 320 " pdb=" N LEU F 321 " pdb=" CA LEU F 321 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 15566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3318 0.065 - 0.129: 513 0.129 - 0.194: 31 0.194 - 0.258: 7 0.258 - 0.323: 1 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CG LEU D 720 " pdb=" CB LEU D 720 " pdb=" CD1 LEU D 720 " pdb=" CD2 LEU D 720 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CG LEU F 577 " pdb=" CB LEU F 577 " pdb=" CD1 LEU F 577 " pdb=" CD2 LEU F 577 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB VAL E 93 " pdb=" CA VAL E 93 " pdb=" CG1 VAL E 93 " pdb=" CG2 VAL E 93 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3867 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 675 " -0.038 2.00e-02 2.50e+03 3.90e-02 3.81e+01 pdb=" CG TRP E 675 " 0.104 2.00e-02 2.50e+03 pdb=" CD1 TRP E 675 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP E 675 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 675 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 675 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 675 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 675 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 675 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP E 675 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 689 " 0.085 5.00e-02 4.00e+02 1.22e-01 2.40e+01 pdb=" N PRO F 690 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO F 690 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO F 690 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 361 " -0.047 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO E 362 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 362 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 362 " -0.038 5.00e-02 4.00e+02 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 243 2.59 - 3.16: 20924 3.16 - 3.74: 37277 3.74 - 4.32: 52049 4.32 - 4.90: 85040 Nonbonded interactions: 195533 Sorted by model distance: nonbonded pdb=" O2B ATP C 801 " pdb="MG MG C 802 " model vdw 2.007 2.170 nonbonded pdb=" O2B ATP B 801 " pdb="MG MG B 802 " model vdw 2.022 2.170 nonbonded pdb=" O PRO A 735 " pdb=" OG1 THR A 738 " model vdw 2.089 3.040 nonbonded pdb=" O3G ATP B 801 " pdb="MG MG B 802 " model vdw 2.098 2.170 nonbonded pdb=" O3G ATP A 801 " pdb="MG MG A 802 " model vdw 2.102 2.170 ... (remaining 195528 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 'B' and resid 323 through 785) selection = (chain 'C' and resid 323 through 785) selection = (chain 'D' and resid 323 through 785) } 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: 9.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.010 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 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 25510 Z= 0.154 Angle : 0.774 16.824 34532 Z= 0.404 Chirality : 0.046 0.323 3870 Planarity : 0.005 0.122 4372 Dihedral : 14.387 87.627 9725 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.53 % Allowed : 15.14 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3034 helix: 0.11 (0.16), residues: 1065 sheet: 0.35 (0.27), residues: 423 loop : 0.08 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 663 TYR 0.029 0.001 TYR D 725 PHE 0.048 0.001 PHE C 739 TRP 0.104 0.002 TRP E 675 HIS 0.006 0.001 HIS C 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (25510) covalent geometry : angle 0.77426 / 0.40 (34532) hydrogen bonds : bond 0.17266 / 12.15 ( 839) hydrogen bonds : angle 6.37381 / 4.50 ( 2367) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 356 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9105 (mttp) REVERT: C 775 GLN cc_start: 0.7201 (mp10) cc_final: 0.6978 (mp10) REVERT: D 650 LEU cc_start: 0.8823 (mm) cc_final: 0.8502 (tm) REVERT: D 681 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9157 (pt) REVERT: D 716 LEU cc_start: 0.9634 (tm) cc_final: 0.9408 (mm) REVERT: D 717 MET cc_start: 0.8470 (mmm) cc_final: 0.7748 (mmm) REVERT: F 547 MET cc_start: 0.8912 (ppp) cc_final: 0.8710 (ppp) REVERT: E 197 MET cc_start: 0.8138 (mpm) cc_final: 0.6853 (ttm) REVERT: E 547 MET cc_start: 0.8705 (pp-130) cc_final: 0.8016 (ppp) outliers start: 15 outliers final: 4 residues processed: 175 average time/residue: 0.6238 time to fit residues: 125.6002 Evaluate side-chains 152 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 763 HIS Chi-restraints excluded: chain F residue 578 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.0040 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN B 660 GLN C 374 GLN C 629 HIS C 660 GLN D 353 ASN ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 605 ASN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.122128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.069980 restraints weight = 63882.117| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.86 r_work: 0.2768 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25510 Z= 0.186 Angle : 0.645 12.675 34532 Z= 0.329 Chirality : 0.045 0.324 3870 Planarity : 0.004 0.064 4372 Dihedral : 8.390 83.563 3507 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.78 % Allowed : 11.83 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3034 helix: 0.46 (0.16), residues: 1101 sheet: 0.32 (0.27), residues: 417 loop : 0.08 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 570 TYR 0.019 0.001 TYR A 482 PHE 0.029 0.001 PHE A 739 TRP 0.046 0.002 TRP E 675 HIS 0.004 0.001 HIS C 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (25510) covalent geometry : angle 0.64487 / 0.33 (34532) hydrogen bonds : bond 0.04806 / 3.33 ( 839) hydrogen bonds : angle 4.93796 / 3.47 ( 2367) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 LYS cc_start: 0.9595 (OUTLIER) cc_final: 0.9199 (tttm) REVERT: A 762 ARG cc_start: 0.9092 (tmm160) cc_final: 0.8802 (pmt-80) REVERT: A 775 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8278 (tm130) REVERT: B 725 TYR cc_start: 0.7464 (m-80) cc_final: 0.7255 (m-80) REVERT: C 529 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8627 (pp30) REVERT: C 684 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7042 (tmm) REVERT: C 773 TYR cc_start: 0.8804 (p90) cc_final: 0.8577 (p90) REVERT: C 775 GLN cc_start: 0.7963 (mp10) cc_final: 0.7531 (mp10) REVERT: D 557 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8158 (pp20) REVERT: D 650 LEU cc_start: 0.8888 (mm) cc_final: 0.8444 (tm) REVERT: D 684 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8171 (tpp) REVERT: D 727 LEU cc_start: 0.8035 (mm) cc_final: 0.7822 (tm) REVERT: F 320 PRO cc_start: 0.5767 (Cg_endo) cc_final: 0.5411 (Cg_exo) REVERT: F 458 MET cc_start: 0.7342 (pmm) cc_final: 0.7113 (pmm) REVERT: E 150 MET cc_start: 0.8452 (ttm) cc_final: 0.8147 (mmm) REVERT: E 413 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8830 (tm) REVERT: E 547 MET cc_start: 0.8313 (pp-130) cc_final: 0.7905 (ppp) outliers start: 50 outliers final: 13 residues processed: 202 average time/residue: 0.5851 time to fit residues: 136.2323 Evaluate side-chains 160 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 563 CYS Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 486 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 289 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 214 optimal weight: 20.0000 chunk 236 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 173 optimal weight: 0.0770 chunk 280 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 204 optimal weight: 0.0970 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN B 761 ASN C 374 GLN C 475 ASN ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN E 328 ASN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.123805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.071605 restraints weight = 64210.374| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.93 r_work: 0.2816 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 25510 Z= 0.102 Angle : 0.568 13.440 34532 Z= 0.286 Chirality : 0.042 0.276 3870 Planarity : 0.004 0.063 4372 Dihedral : 7.971 85.412 3495 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.35 % Allowed : 13.11 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3034 helix: 0.67 (0.16), residues: 1111 sheet: 0.39 (0.27), residues: 417 loop : 0.09 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 344 TYR 0.018 0.001 TYR B 773 PHE 0.034 0.001 PHE C 739 TRP 0.026 0.001 TRP E 675 HIS 0.005 0.001 HIS C 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (25510) covalent geometry : angle 0.56817 / 0.29 (34532) hydrogen bonds : bond 0.03508 / 2.43 ( 839) hydrogen bonds : angle 4.51242 / 3.18 ( 2367) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 LYS cc_start: 0.9590 (OUTLIER) cc_final: 0.9170 (tttm) REVERT: B 387 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8408 (mtm180) REVERT: B 725 TYR cc_start: 0.7649 (m-80) cc_final: 0.7253 (m-80) REVERT: C 529 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8641 (pp30) REVERT: C 684 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7002 (tmm) REVERT: C 773 TYR cc_start: 0.8858 (p90) cc_final: 0.8522 (p90) REVERT: C 775 GLN cc_start: 0.8163 (mp10) cc_final: 0.7508 (mp10) REVERT: D 557 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8273 (pp20) REVERT: D 650 LEU cc_start: 0.8795 (mm) cc_final: 0.8383 (tm) REVERT: D 684 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8247 (tpp) REVERT: F 320 PRO cc_start: 0.5843 (Cg_endo) cc_final: 0.5501 (Cg_exo) REVERT: F 458 MET cc_start: 0.7543 (pmm) cc_final: 0.7219 (pmm) REVERT: F 547 MET cc_start: 0.8840 (ppp) cc_final: 0.8335 (ppp) REVERT: E 150 MET cc_start: 0.8575 (ttm) cc_final: 0.8187 (mmm) REVERT: E 168 SER cc_start: 0.7964 (m) cc_final: 0.7574 (p) REVERT: E 413 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8847 (tm) REVERT: E 458 MET cc_start: 0.8932 (ppp) cc_final: 0.8708 (ppp) REVERT: E 462 MET cc_start: 0.9596 (mmt) cc_final: 0.9233 (mpp) REVERT: E 547 MET cc_start: 0.8466 (pp-130) cc_final: 0.8089 (ppp) outliers start: 38 outliers final: 9 residues processed: 209 average time/residue: 0.5879 time to fit residues: 142.7419 Evaluate side-chains 157 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 440 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 0.0030 chunk 42 optimal weight: 0.9990 chunk 297 optimal weight: 20.0000 chunk 224 optimal weight: 7.9990 chunk 169 optimal weight: 0.0970 chunk 278 optimal weight: 7.9990 chunk 84 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 HIS A 660 GLN A 741 GLN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 660 GLN D 713 HIS ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN E 198 GLN E 713 HIS ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.123703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.071661 restraints weight = 63872.533| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.91 r_work: 0.2822 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25510 Z= 0.098 Angle : 0.557 9.357 34532 Z= 0.277 Chirality : 0.042 0.228 3870 Planarity : 0.003 0.063 4372 Dihedral : 7.748 85.194 3495 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.43 % Allowed : 14.18 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 3034 helix: 0.86 (0.16), residues: 1100 sheet: 0.40 (0.27), residues: 417 loop : 0.14 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 762 TYR 0.015 0.001 TYR C 482 PHE 0.028 0.001 PHE C 739 TRP 0.016 0.001 TRP E 675 HIS 0.004 0.000 HIS C 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (25510) covalent geometry : angle 0.55683 / 0.28 (34532) hydrogen bonds : bond 0.03189 / 2.21 ( 839) hydrogen bonds : angle 4.38598 / 3.09 ( 2367) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5402 (pp) REVERT: A 517 LYS cc_start: 0.9590 (OUTLIER) cc_final: 0.9182 (tttm) REVERT: A 684 MET cc_start: 0.7516 (ttm) cc_final: 0.7282 (ttm) REVERT: B 725 TYR cc_start: 0.7625 (m-80) cc_final: 0.7323 (m-80) REVERT: B 760 ILE cc_start: 0.9375 (mm) cc_final: 0.9076 (pp) REVERT: B 763 HIS cc_start: 0.9123 (m-70) cc_final: 0.8901 (m-70) REVERT: B 775 GLN cc_start: 0.7607 (tp40) cc_final: 0.7272 (tp40) REVERT: C 529 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8597 (pp30) REVERT: C 773 TYR cc_start: 0.8882 (p90) cc_final: 0.8526 (p90) REVERT: C 775 GLN cc_start: 0.8176 (mp10) cc_final: 0.7604 (mp10) REVERT: D 684 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8270 (tpp) REVERT: F 320 PRO cc_start: 0.5528 (Cg_endo) cc_final: 0.5163 (Cg_exo) REVERT: F 547 MET cc_start: 0.8770 (ppp) cc_final: 0.8379 (ppp) REVERT: F 687 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8124 (m-10) REVERT: E 150 MET cc_start: 0.8535 (ttm) cc_final: 0.8175 (mmm) REVERT: E 413 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8840 (tm) REVERT: E 462 MET cc_start: 0.9595 (mmt) cc_final: 0.9303 (mpp) REVERT: E 717 MET cc_start: 0.7422 (tpt) cc_final: 0.7213 (tpp) REVERT: E 729 ASP cc_start: 0.8385 (m-30) cc_final: 0.7968 (p0) outliers start: 40 outliers final: 14 residues processed: 193 average time/residue: 0.5815 time to fit residues: 130.5465 Evaluate side-chains 160 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 745 LYS Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 687 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 440 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 102 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 660 GLN D 713 HIS ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.121525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069095 restraints weight = 63695.072| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.99 r_work: 0.2743 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25510 Z= 0.180 Angle : 0.594 9.430 34532 Z= 0.298 Chirality : 0.043 0.244 3870 Planarity : 0.004 0.062 4372 Dihedral : 7.872 83.507 3495 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.85 % Allowed : 14.71 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3034 helix: 0.91 (0.16), residues: 1090 sheet: 0.36 (0.27), residues: 422 loop : 0.20 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 762 TYR 0.021 0.001 TYR B 482 PHE 0.019 0.001 PHE D 698 TRP 0.013 0.001 TRP E 675 HIS 0.007 0.001 HIS F 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (25510) covalent geometry : angle 0.59373 / 0.30 (34532) hydrogen bonds : bond 0.04225 / 2.90 ( 839) hydrogen bonds : angle 4.50139 / 3.17 ( 2367) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ILE cc_start: 0.6340 (OUTLIER) cc_final: 0.5770 (pp) REVERT: A 517 LYS cc_start: 0.9614 (OUTLIER) cc_final: 0.9219 (tttm) REVERT: B 725 TYR cc_start: 0.7638 (m-80) cc_final: 0.7267 (m-80) REVERT: B 760 ILE cc_start: 0.9389 (mm) cc_final: 0.9064 (pp) REVERT: B 763 HIS cc_start: 0.9078 (m-70) cc_final: 0.8818 (m-70) REVERT: C 529 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8707 (pp30) REVERT: C 700 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9098 (mm) REVERT: C 773 TYR cc_start: 0.8914 (p90) cc_final: 0.8457 (p90) REVERT: C 775 GLN cc_start: 0.8261 (mp10) cc_final: 0.7627 (mp10) REVERT: D 557 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8227 (pp20) REVERT: F 320 PRO cc_start: 0.5302 (Cg_endo) cc_final: 0.4939 (Cg_exo) REVERT: F 687 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8089 (m-10) REVERT: E 150 MET cc_start: 0.8414 (ttm) cc_final: 0.8069 (mmm) REVERT: E 413 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8863 (tm) REVERT: E 547 MET cc_start: 0.8478 (ppp) cc_final: 0.8039 (ppp) REVERT: E 701 LYS cc_start: 0.9342 (mttm) cc_final: 0.8938 (ptpt) REVERT: E 729 ASP cc_start: 0.8452 (m-30) cc_final: 0.8066 (p0) outliers start: 52 outliers final: 20 residues processed: 193 average time/residue: 0.5952 time to fit residues: 132.8847 Evaluate side-chains 165 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 745 LYS Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 575 LYS Chi-restraints excluded: chain F residue 687 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 486 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 176 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 243 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN D 713 HIS F 475 ASN ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 741 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.122606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.069842 restraints weight = 64340.807| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.96 r_work: 0.2772 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25510 Z= 0.117 Angle : 0.571 9.797 34532 Z= 0.282 Chirality : 0.042 0.289 3870 Planarity : 0.004 0.063 4372 Dihedral : 7.820 87.132 3495 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.71 % Allowed : 15.46 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3034 helix: 0.97 (0.16), residues: 1093 sheet: 0.35 (0.27), residues: 421 loop : 0.18 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 762 TYR 0.016 0.001 TYR B 482 PHE 0.034 0.001 PHE C 739 TRP 0.011 0.001 TRP E 675 HIS 0.004 0.001 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (25510) covalent geometry : angle 0.57133 / 0.28 (34532) hydrogen bonds : bond 0.03382 / 2.32 ( 839) hydrogen bonds : angle 4.28866 / 3.04 ( 2367) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5194 (pp) REVERT: A 517 LYS cc_start: 0.9612 (OUTLIER) cc_final: 0.9210 (tttm) REVERT: B 387 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8523 (mtm180) REVERT: B 725 TYR cc_start: 0.7539 (m-80) cc_final: 0.7215 (m-80) REVERT: B 760 ILE cc_start: 0.9346 (mm) cc_final: 0.9053 (pp) REVERT: B 763 HIS cc_start: 0.9166 (m-70) cc_final: 0.8897 (m-70) REVERT: C 529 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8723 (pp30) REVERT: C 700 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9067 (mm) REVERT: C 773 TYR cc_start: 0.8913 (p90) cc_final: 0.8426 (p90) REVERT: C 775 GLN cc_start: 0.8212 (mp10) cc_final: 0.7629 (mp10) REVERT: D 557 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8270 (pp20) REVERT: F 320 PRO cc_start: 0.5357 (Cg_endo) cc_final: 0.5018 (Cg_exo) REVERT: F 462 MET cc_start: 0.8596 (mpt) cc_final: 0.8391 (mpt) REVERT: F 547 MET cc_start: 0.8847 (ppp) cc_final: 0.8159 (ppp) REVERT: F 687 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8279 (m-10) REVERT: E 69 MET cc_start: 0.7810 (tpt) cc_final: 0.7585 (pmm) REVERT: E 150 MET cc_start: 0.8626 (ttm) cc_final: 0.8078 (mmm) REVERT: E 413 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8824 (tm) REVERT: E 462 MET cc_start: 0.9540 (mmt) cc_final: 0.9277 (mpp) REVERT: E 547 MET cc_start: 0.8579 (ppp) cc_final: 0.8139 (ppp) REVERT: E 729 ASP cc_start: 0.8463 (m-30) cc_final: 0.8078 (p0) outliers start: 48 outliers final: 21 residues processed: 187 average time/residue: 0.5466 time to fit residues: 118.5784 Evaluate side-chains 164 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 745 LYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 575 LYS Chi-restraints excluded: chain F residue 687 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 440 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 277 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN B 596 ASN C 660 GLN D 713 HIS ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN E 198 GLN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.121950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.069227 restraints weight = 64200.510| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.98 r_work: 0.2759 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25510 Z= 0.137 Angle : 0.583 11.176 34532 Z= 0.287 Chirality : 0.043 0.273 3870 Planarity : 0.004 0.062 4372 Dihedral : 7.799 88.303 3495 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.03 % Allowed : 15.25 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3034 helix: 1.00 (0.16), residues: 1093 sheet: 0.30 (0.28), residues: 401 loop : 0.16 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 762 TYR 0.018 0.001 TYR B 482 PHE 0.039 0.001 PHE C 739 TRP 0.009 0.001 TRP E 675 HIS 0.004 0.001 HIS C 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (25510) covalent geometry : angle 0.58258 / 0.29 (34532) hydrogen bonds : bond 0.03627 / 2.47 ( 839) hydrogen bonds : angle 4.30267 / 3.05 ( 2367) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 150 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.5691 (pp) REVERT: A 264 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.4516 (mm) REVERT: A 517 LYS cc_start: 0.9615 (OUTLIER) cc_final: 0.9228 (tttm) REVERT: B 387 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8528 (mtm180) REVERT: B 701 LYS cc_start: 0.9550 (tppp) cc_final: 0.9251 (ttpt) REVERT: B 725 TYR cc_start: 0.7521 (m-80) cc_final: 0.7192 (m-10) REVERT: B 760 ILE cc_start: 0.9346 (mm) cc_final: 0.9044 (pp) REVERT: B 763 HIS cc_start: 0.9118 (m-70) cc_final: 0.8822 (m-70) REVERT: C 426 MET cc_start: 0.8952 (mmm) cc_final: 0.8723 (mpp) REVERT: C 529 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8719 (pp30) REVERT: C 660 GLN cc_start: 0.9358 (tp40) cc_final: 0.9152 (mm-40) REVERT: C 700 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9034 (mm) REVERT: C 773 TYR cc_start: 0.8915 (p90) cc_final: 0.8406 (p90) REVERT: C 775 GLN cc_start: 0.8263 (mp10) cc_final: 0.7647 (mp10) REVERT: D 557 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8228 (pp20) REVERT: F 320 PRO cc_start: 0.5087 (Cg_endo) cc_final: 0.4769 (Cg_exo) REVERT: F 462 MET cc_start: 0.8604 (mpt) cc_final: 0.8349 (mpt) REVERT: F 547 MET cc_start: 0.8846 (ppp) cc_final: 0.8247 (ppp) REVERT: F 687 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8116 (m-10) REVERT: E 95 ASN cc_start: 0.6009 (t0) cc_final: 0.5783 (t0) REVERT: E 150 MET cc_start: 0.8450 (ttm) cc_final: 0.8063 (mmm) REVERT: E 413 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8846 (tm) REVERT: E 462 MET cc_start: 0.9553 (mmt) cc_final: 0.9290 (mpp) REVERT: E 547 MET cc_start: 0.8562 (ppp) cc_final: 0.8132 (ppp) REVERT: E 717 MET cc_start: 0.7454 (tpt) cc_final: 0.7212 (tpp) REVERT: E 729 ASP cc_start: 0.8526 (m-30) cc_final: 0.8146 (p0) outliers start: 57 outliers final: 25 residues processed: 189 average time/residue: 0.5442 time to fit residues: 119.7097 Evaluate side-chains 171 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 563 CYS Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 745 LYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 687 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 440 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 285 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 300 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN D 680 HIS D 713 HIS ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 597 HIS E 87 GLN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.121383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068475 restraints weight = 63835.591| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.87 r_work: 0.2747 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25510 Z= 0.162 Angle : 0.595 10.824 34532 Z= 0.296 Chirality : 0.043 0.279 3870 Planarity : 0.004 0.062 4372 Dihedral : 7.850 88.841 3495 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.85 % Allowed : 15.60 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 3034 helix: 0.96 (0.16), residues: 1106 sheet: 0.22 (0.26), residues: 461 loop : 0.20 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 762 TYR 0.019 0.001 TYR B 482 PHE 0.038 0.001 PHE C 739 TRP 0.010 0.001 TRP E 675 HIS 0.007 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (25510) covalent geometry : angle 0.59459 / 0.30 (34532) hydrogen bonds : bond 0.03828 / 2.61 ( 839) hydrogen bonds : angle 4.39363 / 3.11 ( 2367) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.5780 (pp) REVERT: A 264 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.4536 (mm) REVERT: A 517 LYS cc_start: 0.9620 (OUTLIER) cc_final: 0.9229 (tttm) REVERT: B 387 ARG cc_start: 0.8787 (mtm-85) cc_final: 0.8560 (mtm180) REVERT: B 725 TYR cc_start: 0.7482 (m-80) cc_final: 0.7039 (m-10) REVERT: B 760 ILE cc_start: 0.9332 (mm) cc_final: 0.9039 (pp) REVERT: B 763 HIS cc_start: 0.9131 (m-70) cc_final: 0.8842 (m-70) REVERT: C 529 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8765 (pp30) REVERT: C 684 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7196 (tmm) REVERT: C 700 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9050 (mm) REVERT: C 773 TYR cc_start: 0.8919 (p90) cc_final: 0.8397 (p90) REVERT: C 775 GLN cc_start: 0.8280 (mp10) cc_final: 0.7653 (mp10) REVERT: D 557 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8164 (pp20) REVERT: F 320 PRO cc_start: 0.5115 (Cg_endo) cc_final: 0.4797 (Cg_exo) REVERT: F 547 MET cc_start: 0.8838 (ppp) cc_final: 0.8287 (ppp) REVERT: F 687 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: E 95 ASN cc_start: 0.5977 (t0) cc_final: 0.5713 (t0) REVERT: E 150 MET cc_start: 0.8421 (ttm) cc_final: 0.8037 (mmm) REVERT: E 413 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8779 (tm) REVERT: E 462 MET cc_start: 0.9547 (mmt) cc_final: 0.9310 (mpp) REVERT: E 547 MET cc_start: 0.8543 (ppp) cc_final: 0.8144 (ppp) REVERT: E 717 MET cc_start: 0.7520 (tpt) cc_final: 0.7278 (tpp) outliers start: 52 outliers final: 29 residues processed: 186 average time/residue: 0.5632 time to fit residues: 122.6631 Evaluate side-chains 176 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 563 CYS Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 745 LYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 575 LYS Chi-restraints excluded: chain F residue 687 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 440 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 129 optimal weight: 0.8980 chunk 277 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN D 713 HIS ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN E 662 ASN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.121394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068581 restraints weight = 64138.419| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.85 r_work: 0.2739 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25510 Z= 0.168 Angle : 0.616 11.718 34532 Z= 0.303 Chirality : 0.044 0.346 3870 Planarity : 0.004 0.062 4372 Dihedral : 7.853 87.081 3495 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.50 % Allowed : 16.10 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 3034 helix: 0.95 (0.16), residues: 1105 sheet: 0.22 (0.26), residues: 464 loop : 0.16 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 762 TYR 0.020 0.001 TYR B 482 PHE 0.042 0.001 PHE C 739 TRP 0.011 0.001 TRP E 675 HIS 0.004 0.001 HIS B 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (25510) covalent geometry : angle 0.61583 / 0.30 (34532) hydrogen bonds : bond 0.03833 / 2.60 ( 839) hydrogen bonds : angle 4.39951 / 3.12 ( 2367) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6170 (pp) REVERT: A 264 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.4464 (mm) REVERT: A 517 LYS cc_start: 0.9627 (OUTLIER) cc_final: 0.9243 (tttm) REVERT: B 387 ARG cc_start: 0.8814 (mtm-85) cc_final: 0.8570 (mtm180) REVERT: B 701 LYS cc_start: 0.9614 (tppp) cc_final: 0.9399 (tppp) REVERT: B 725 TYR cc_start: 0.7438 (m-80) cc_final: 0.6977 (m-10) REVERT: B 760 ILE cc_start: 0.9340 (mm) cc_final: 0.9037 (pp) REVERT: B 763 HIS cc_start: 0.9094 (m-70) cc_final: 0.8791 (m-70) REVERT: C 529 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8771 (pp30) REVERT: C 684 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7216 (tmm) REVERT: C 700 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9085 (mm) REVERT: C 773 TYR cc_start: 0.8884 (p90) cc_final: 0.8344 (p90) REVERT: C 775 GLN cc_start: 0.8262 (mp10) cc_final: 0.7609 (mp10) REVERT: D 557 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8218 (pp20) REVERT: F 320 PRO cc_start: 0.5045 (Cg_endo) cc_final: 0.4727 (Cg_exo) REVERT: F 547 MET cc_start: 0.8758 (ppp) cc_final: 0.8220 (ppp) REVERT: F 687 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7995 (m-10) REVERT: E 69 MET cc_start: 0.7543 (tpt) cc_final: 0.6854 (mmm) REVERT: E 95 ASN cc_start: 0.6083 (t0) cc_final: 0.5832 (t0) REVERT: E 150 MET cc_start: 0.8349 (ttm) cc_final: 0.7994 (mmm) REVERT: E 413 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8774 (tm) REVERT: E 462 MET cc_start: 0.9541 (mmt) cc_final: 0.9317 (mpp) REVERT: E 547 MET cc_start: 0.8465 (ppp) cc_final: 0.8070 (ppp) outliers start: 42 outliers final: 29 residues processed: 175 average time/residue: 0.5490 time to fit residues: 111.9062 Evaluate side-chains 175 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 563 CYS Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 745 LYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 575 LYS Chi-restraints excluded: chain F residue 687 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 440 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 270 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 216 optimal weight: 0.0570 chunk 79 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN D 713 HIS ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.121484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068641 restraints weight = 64017.226| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.84 r_work: 0.2747 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25510 Z= 0.154 Angle : 0.610 11.828 34532 Z= 0.301 Chirality : 0.044 0.309 3870 Planarity : 0.004 0.062 4372 Dihedral : 7.819 86.852 3495 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.57 % Allowed : 16.17 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 3034 helix: 0.94 (0.16), residues: 1107 sheet: 0.26 (0.26), residues: 460 loop : 0.15 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.021 0.001 TYR B 773 PHE 0.031 0.001 PHE E 102 TRP 0.011 0.001 TRP E 675 HIS 0.004 0.001 HIS B 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (25510) covalent geometry : angle 0.61038 / 0.30 (34532) hydrogen bonds : bond 0.03751 / 2.53 ( 839) hydrogen bonds : angle 4.37918 / 3.11 ( 2367) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.4485 (mm) REVERT: A 517 LYS cc_start: 0.9626 (OUTLIER) cc_final: 0.9240 (tttm) REVERT: B 387 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.8552 (mtm180) REVERT: B 701 LYS cc_start: 0.9619 (tppp) cc_final: 0.9403 (tppp) REVERT: B 725 TYR cc_start: 0.7441 (m-80) cc_final: 0.6997 (m-10) REVERT: B 760 ILE cc_start: 0.9332 (mm) cc_final: 0.9028 (pp) REVERT: B 763 HIS cc_start: 0.9106 (m-70) cc_final: 0.8803 (m-70) REVERT: C 529 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8782 (pp30) REVERT: C 554 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8827 (t80) REVERT: C 684 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7217 (tmm) REVERT: C 700 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9093 (mm) REVERT: C 773 TYR cc_start: 0.8901 (p90) cc_final: 0.8281 (p90) REVERT: C 775 GLN cc_start: 0.8277 (mp10) cc_final: 0.7619 (mp10) REVERT: D 557 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8222 (pp20) REVERT: F 320 PRO cc_start: 0.4847 (Cg_endo) cc_final: 0.4567 (Cg_exo) REVERT: F 515 LEU cc_start: 0.9280 (tp) cc_final: 0.8723 (pp) REVERT: F 547 MET cc_start: 0.8797 (ppp) cc_final: 0.8283 (ppp) REVERT: F 618 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7977 (mpt) REVERT: F 687 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8007 (m-10) REVERT: E 95 ASN cc_start: 0.5974 (t0) cc_final: 0.5672 (t0) REVERT: E 413 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8772 (tm) REVERT: E 462 MET cc_start: 0.9533 (mmt) cc_final: 0.9316 (mpp) REVERT: E 547 MET cc_start: 0.8462 (ppp) cc_final: 0.8071 (ppp) REVERT: E 759 PHE cc_start: 0.8826 (m-10) cc_final: 0.8542 (m-80) outliers start: 44 outliers final: 26 residues processed: 175 average time/residue: 0.5178 time to fit residues: 106.9288 Evaluate side-chains 172 residues out of total 2807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 563 CYS Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 745 LYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 575 LYS Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 687 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 440 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 140 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 258 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN D 713 HIS ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.120872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.068834 restraints weight = 63586.377| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.84 r_work: 0.2744 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25510 Z= 0.169 Angle : 0.623 12.333 34532 Z= 0.306 Chirality : 0.044 0.306 3870 Planarity : 0.004 0.062 4372 Dihedral : 7.824 87.567 3495 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.32 % Allowed : 16.46 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 3034 helix: 0.94 (0.16), residues: 1107 sheet: 0.24 (0.26), residues: 460 loop : 0.13 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 762 TYR 0.020 0.001 TYR B 482 PHE 0.037 0.001 PHE C 739 TRP 0.010 0.001 TRP E 675 HIS 0.014 0.001 HIS D 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (25510) covalent geometry : angle 0.62254 / 0.31 (34532) hydrogen bonds : bond 0.03791 / 2.56 ( 839) hydrogen bonds : angle 4.39010 / 3.11 ( 2367) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8706.57 seconds wall clock time: 149 minutes 2.87 seconds (8942.87 seconds total)