Starting phenix.real_space_refine on Fri Feb 6 23:59:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uqk_26697/02_2026/7uqk_26697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqk_26697/02_2026/7uqk_26697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uqk_26697/02_2026/7uqk_26697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqk_26697/02_2026/7uqk_26697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uqk_26697/02_2026/7uqk_26697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqk_26697/02_2026/7uqk_26697.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 108 5.16 5 C 18652 2.51 5 N 4953 2.21 5 O 5419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29142 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4591 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 32, 'TRANS': 543} Chain breaks: 2 Chain: "B" Number of atoms: 4614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4614 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 32, 'TRANS': 546} Chain breaks: 2 Chain: "C" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4607 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 32, 'TRANS': 545} Chain breaks: 2 Chain: "D" Number of atoms: 4586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4586 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 32, 'TRANS': 543} Chain breaks: 2 Chain: "E" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4448 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 32, 'TRANS': 525} Chain breaks: 4 Chain: "F" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4519 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 32, 'TRANS': 534} Chain breaks: 3 Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1642 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 7.09, per 1000 atoms: 0.24 Number of scatterers: 29142 At special positions: 0 Unit cell: (143.244, 147.384, 158.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 10 15.00 O 5419 8.00 N 4953 7.00 C 18652 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: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6954 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 15 sheets defined 53.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.655A pdb=" N ILE A 416 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.083A pdb=" N LEU A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.558A pdb=" N GLN A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.865A pdb=" N LEU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 486 through 490' Processing helix chain 'A' and resid 495 through 511 removed outlier: 3.652A pdb=" N ARG A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 4.202A pdb=" N LEU A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 547 removed outlier: 3.653A pdb=" N SER A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 608 through 619 removed outlier: 3.686A pdb=" N ILE A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 643 removed outlier: 3.606A pdb=" N PHE A 643 " --> pdb=" O ILE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 649 removed outlier: 4.490A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 649 " --> pdb=" O GLN A 645 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 644 through 649' Processing helix chain 'A' and resid 663 through 674 removed outlier: 3.700A pdb=" N PHE A 667 " --> pdb=" O LYS A 663 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 672 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 removed outlier: 3.641A pdb=" N ARG A 680 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 712 removed outlier: 5.856A pdb=" N ASP A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLN A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 704 " --> pdb=" O GLN A 700 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 Processing helix chain 'A' and resid 754 through 765 removed outlier: 3.873A pdb=" N GLU A 758 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 removed outlier: 3.883A pdb=" N ALA A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 808 Processing helix chain 'A' and resid 814 through 829 Processing helix chain 'A' and resid 838 through 843 Processing helix chain 'A' and resid 847 through 860 Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 884 through 890 removed outlier: 4.420A pdb=" N ASP A 888 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 889 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA A 890 " --> pdb=" O SER A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 910 removed outlier: 3.580A pdb=" N ARG A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 1324 through 1339 removed outlier: 3.653A pdb=" N CYS A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1361 removed outlier: 3.783A pdb=" N ILE A1357 " --> pdb=" O SER A1353 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A1361 " --> pdb=" O ILE A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1378 Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.844A pdb=" N ASP B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 435 through 440 removed outlier: 4.176A pdb=" N TYR B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 471 removed outlier: 3.665A pdb=" N CYS B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.897A pdb=" N LEU B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 547 removed outlier: 4.678A pdb=" N ILE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 599 Processing helix chain 'B' and resid 607 through 618 Processing helix chain 'B' and resid 622 through 642 Processing helix chain 'B' and resid 643 through 647 Processing helix chain 'B' and resid 662 through 673 removed outlier: 3.902A pdb=" N PHE B 666 " --> pdb=" O LYS B 662 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 671 " --> pdb=" O MET B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 711 removed outlier: 5.082A pdb=" N ASP B 698 " --> pdb=" O PRO B 694 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 703 " --> pdb=" O GLN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 730 Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.544A pdb=" N TYR B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE B 758 " --> pdb=" O ARG B 754 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.932A pdb=" N ALA B 787 " --> pdb=" O GLN B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 809 removed outlier: 4.618A pdb=" N GLU B 809 " --> pdb=" O SER B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 827 removed outlier: 3.581A pdb=" N LYS B 827 " --> pdb=" O MET B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 845 removed outlier: 3.819A pdb=" N ASN B 843 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 859 removed outlier: 3.821A pdb=" N ILE B 850 " --> pdb=" O PRO B 846 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 882 removed outlier: 3.937A pdb=" N VAL B 880 " --> pdb=" O ASP B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 889 removed outlier: 3.611A pdb=" N PHE B 888 " --> pdb=" O LEU B 885 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B 889 " --> pdb=" O SER B 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 885 through 889' Processing helix chain 'B' and resid 901 through 917 Processing helix chain 'B' and resid 1323 through 1338 removed outlier: 3.549A pdb=" N ILE B1327 " --> pdb=" O THR B1323 " (cutoff:3.500A) Processing helix chain 'B' and resid 1342 through 1360 removed outlier: 3.707A pdb=" N ILE B1356 " --> pdb=" O SER B1352 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B1360 " --> pdb=" O ILE B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1366 through 1377 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 418 through 435 Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 436 through 440 removed outlier: 3.703A pdb=" N TYR C 439 " --> pdb=" O PRO C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 471 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.749A pdb=" N LEU C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 547 removed outlier: 3.726A pdb=" N SER C 537 " --> pdb=" O GLN C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'C' and resid 568 through 572 Processing helix chain 'C' and resid 587 through 599 removed outlier: 3.538A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 Processing helix chain 'C' and resid 622 through 642 removed outlier: 3.810A pdb=" N LEU C 626 " --> pdb=" O GLY C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 Processing helix chain 'C' and resid 662 through 670 removed outlier: 3.687A pdb=" N PHE C 666 " --> pdb=" O LYS C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 710 removed outlier: 5.270A pdb=" N ASP C 698 " --> pdb=" O PRO C 694 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN C 699 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 703 " --> pdb=" O GLN C 699 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 707 " --> pdb=" O LEU C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 730 Processing helix chain 'C' and resid 753 through 765 removed outlier: 3.918A pdb=" N GLU C 757 " --> pdb=" O PHE C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 793 removed outlier: 3.679A pdb=" N ALA C 787 " --> pdb=" O GLN C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 807 Processing helix chain 'C' and resid 813 through 828 removed outlier: 3.601A pdb=" N ARG C 828 " --> pdb=" O GLU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 845 removed outlier: 4.205A pdb=" N ASN C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 845 " --> pdb=" O TRP C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 858 Processing helix chain 'C' and resid 877 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.539A pdb=" N SER C 886 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP C 887 " --> pdb=" O ILE C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 917 removed outlier: 4.143A pdb=" N LEU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 1323 through 1338 removed outlier: 3.605A pdb=" N ILE C1327 " --> pdb=" O THR C1323 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C1338 " --> pdb=" O LEU C1334 " (cutoff:3.500A) Processing helix chain 'C' and resid 1342 through 1360 removed outlier: 3.814A pdb=" N ILE C1356 " --> pdb=" O SER C1352 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C1360 " --> pdb=" O ILE C1356 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1377 Processing helix chain 'D' and resid 418 through 430 removed outlier: 3.761A pdb=" N ILE D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN D 424 " --> pdb=" O ASN D 420 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET D 428 " --> pdb=" O GLN D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 removed outlier: 4.130A pdb=" N TYR D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 469 removed outlier: 3.516A pdb=" N ALA D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 469 " --> pdb=" O ARG D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.833A pdb=" N ARG D 498 " --> pdb=" O GLY D 494 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D 503 " --> pdb=" O GLN D 499 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 523 Processing helix chain 'D' and resid 532 through 543 removed outlier: 4.491A pdb=" N SER D 537 " --> pdb=" O GLN D 533 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 587 through 598 Processing helix chain 'D' and resid 607 through 618 removed outlier: 3.649A pdb=" N LYS D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 642 Processing helix chain 'D' and resid 662 through 673 removed outlier: 4.407A pdb=" N LEU D 668 " --> pdb=" O SER D 664 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 671 " --> pdb=" O MET D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 680 removed outlier: 3.720A pdb=" N ARG D 679 " --> pdb=" O SER D 676 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER D 680 " --> pdb=" O SER D 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 676 through 680' Processing helix chain 'D' and resid 692 through 697 Processing helix chain 'D' and resid 700 through 712 Processing helix chain 'D' and resid 724 through 728 Processing helix chain 'D' and resid 753 through 758 Processing helix chain 'D' and resid 781 through 793 Processing helix chain 'D' and resid 802 through 806 removed outlier: 3.502A pdb=" N SER D 805 " --> pdb=" O ASP D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 828 removed outlier: 3.702A pdb=" N VAL D 818 " --> pdb=" O ILE D 814 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 819 " --> pdb=" O GLU D 815 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 820 " --> pdb=" O ALA D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 845 removed outlier: 3.925A pdb=" N ASN D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 845 " --> pdb=" O TRP D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 858 Processing helix chain 'D' and resid 876 through 882 Processing helix chain 'D' and resid 883 through 889 removed outlier: 4.400A pdb=" N ASP D 887 " --> pdb=" O ILE D 884 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA D 889 " --> pdb=" O SER D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 917 Processing helix chain 'D' and resid 1323 through 1338 removed outlier: 3.507A pdb=" N CYS D1338 " --> pdb=" O LEU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1342 through 1360 removed outlier: 3.749A pdb=" N SER D1360 " --> pdb=" O ILE D1356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1367 through 1377 Processing helix chain 'E' and resid 411 through 415 removed outlier: 3.739A pdb=" N ASP E 414 " --> pdb=" O ASN E 411 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 415 " --> pdb=" O PHE E 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 411 through 415' Processing helix chain 'E' and resid 430 through 435 removed outlier: 3.713A pdb=" N LEU E 434 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 470 Processing helix chain 'E' and resid 496 through 507 Processing helix chain 'E' and resid 519 through 523 Processing helix chain 'E' and resid 539 through 547 removed outlier: 3.932A pdb=" N ASP E 547 " --> pdb=" O LEU E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 567 removed outlier: 4.044A pdb=" N ALA E 566 " --> pdb=" O ARG E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 572 removed outlier: 3.680A pdb=" N ARG E 572 " --> pdb=" O PRO E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 599 removed outlier: 3.725A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR E 599 " --> pdb=" O LEU E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 616 removed outlier: 3.619A pdb=" N ILE E 611 " --> pdb=" O SER E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 642 removed outlier: 4.047A pdb=" N ARG E 627 " --> pdb=" O GLY E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 671 removed outlier: 3.992A pdb=" N PHE E 666 " --> pdb=" O LYS E 662 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 697 Processing helix chain 'E' and resid 700 through 712 Processing helix chain 'E' and resid 723 through 728 removed outlier: 3.501A pdb=" N ASN E 727 " --> pdb=" O SER E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 764 Processing helix chain 'E' and resid 765 through 767 No H-bonds generated for 'chain 'E' and resid 765 through 767' Processing helix chain 'E' and resid 781 through 793 removed outlier: 3.744A pdb=" N ALA E 787 " --> pdb=" O GLN E 783 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 828 Processing helix chain 'E' and resid 837 through 845 removed outlier: 4.390A pdb=" N ASN E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE E 845 " --> pdb=" O TRP E 841 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 859 Processing helix chain 'E' and resid 877 through 882 Processing helix chain 'E' and resid 884 through 889 removed outlier: 4.450A pdb=" N ASP E 887 " --> pdb=" O ILE E 884 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA E 889 " --> pdb=" O SER E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 917 removed outlier: 4.352A pdb=" N ASN E 911 " --> pdb=" O ARG E 907 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU E 912 " --> pdb=" O TYR E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 1323 through 1338 removed outlier: 3.783A pdb=" N ILE E1327 " --> pdb=" O THR E1323 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS E1338 " --> pdb=" O LEU E1334 " (cutoff:3.500A) Processing helix chain 'E' and resid 1342 through 1360 removed outlier: 3.880A pdb=" N SER E1360 " --> pdb=" O ILE E1356 " (cutoff:3.500A) Processing helix chain 'E' and resid 1366 through 1377 removed outlier: 3.966A pdb=" N ASP E1371 " --> pdb=" O THR E1367 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 415 removed outlier: 3.916A pdb=" N ILE F 415 " --> pdb=" O PHE F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 427 removed outlier: 3.928A pdb=" N LYS F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 435 removed outlier: 3.760A pdb=" N LEU F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 469 Processing helix chain 'F' and resid 492 through 510 removed outlier: 4.515A pdb=" N ALA F 496 " --> pdb=" O TRP F 492 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU F 497 " --> pdb=" O VAL F 493 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG F 498 " --> pdb=" O GLY F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 524 Processing helix chain 'F' and resid 539 through 547 removed outlier: 3.553A pdb=" N LEU F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 567 removed outlier: 4.039A pdb=" N VAL F 567 " --> pdb=" O PRO F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 598 Processing helix chain 'F' and resid 607 through 614 removed outlier: 3.527A pdb=" N ILE F 611 " --> pdb=" O SER F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 624 through 642 Processing helix chain 'F' and resid 643 through 648 removed outlier: 3.873A pdb=" N ARG F 647 " --> pdb=" O PRO F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 668 removed outlier: 3.756A pdb=" N PHE F 666 " --> pdb=" O LYS F 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 711 removed outlier: 3.501A pdb=" N LEU F 696 " --> pdb=" O ILE F 692 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP F 698 " --> pdb=" O PRO F 694 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN F 699 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN F 701 " --> pdb=" O ALA F 697 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN F 702 " --> pdb=" O ASP F 698 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU F 703 " --> pdb=" O GLN F 699 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU F 711 " --> pdb=" O LEU F 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 731 removed outlier: 3.560A pdb=" N PHE F 728 " --> pdb=" O LEU F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 764 removed outlier: 3.598A pdb=" N GLU F 757 " --> pdb=" O PHE F 753 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER F 761 " --> pdb=" O GLU F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 765 through 767 No H-bonds generated for 'chain 'F' and resid 765 through 767' Processing helix chain 'F' and resid 781 through 793 removed outlier: 3.970A pdb=" N ALA F 787 " --> pdb=" O GLN F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 802 through 807 removed outlier: 3.504A pdb=" N LEU F 806 " --> pdb=" O ASP F 802 " (cutoff:3.500A) Processing helix chain 'F' and resid 813 through 828 removed outlier: 3.581A pdb=" N ARG F 828 " --> pdb=" O GLU F 824 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 845 removed outlier: 4.090A pdb=" N ASN F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 846 through 859 removed outlier: 3.533A pdb=" N ILE F 850 " --> pdb=" O PRO F 846 " (cutoff:3.500A) Processing helix chain 'F' and resid 877 through 882 removed outlier: 3.988A pdb=" N ASN F 882 " --> pdb=" O SER F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 885 through 889 removed outlier: 3.967A pdb=" N ALA F 889 " --> pdb=" O SER F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 917 removed outlier: 3.756A pdb=" N TYR F 908 " --> pdb=" O ASN F 904 " (cutoff:3.500A) Processing helix chain 'F' and resid 1323 through 1338 Processing helix chain 'F' and resid 1342 through 1360 removed outlier: 3.546A pdb=" N SER F1360 " --> pdb=" O ILE F1356 " (cutoff:3.500A) Processing helix chain 'F' and resid 1366 through 1377 removed outlier: 3.664A pdb=" N VAL F1370 " --> pdb=" O LYS F1366 " (cutoff:3.500A) Processing helix chain 'G' and resid 955 through 994 removed outlier: 4.123A pdb=" N GLY G 985 " --> pdb=" O ILE G 981 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU G 986 " --> pdb=" O LYS G 982 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU G 989 " --> pdb=" O GLY G 985 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR G 994 " --> pdb=" O PHE G 990 " (cutoff:3.500A) Processing helix chain 'G' and resid 1004 through 1009 removed outlier: 3.731A pdb=" N HIS G1009 " --> pdb=" O ALA G1005 " (cutoff:3.500A) Processing helix chain 'G' and resid 1049 through 1056 removed outlier: 3.700A pdb=" N ASN G1055 " --> pdb=" O GLU G1051 " (cutoff:3.500A) Processing helix chain 'G' and resid 1060 through 1078 removed outlier: 4.306A pdb=" N PHE G1064 " --> pdb=" O GLU G1060 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE G1078 " --> pdb=" O ASP G1074 " (cutoff:3.500A) Processing helix chain 'G' and resid 1080 through 1102 removed outlier: 3.803A pdb=" N GLU G1100 " --> pdb=" O MET G1096 " (cutoff:3.500A) Processing helix chain 'G' and resid 1103 through 1131 Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 485 removed outlier: 6.683A pdb=" N THR A 480 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE A 517 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE A 482 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASP A 519 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG A 484 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 514 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE A 559 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 516 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA A 561 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE A 518 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 451 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THR A 562 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 453 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 798 through 801 removed outlier: 6.395A pdb=" N LEU A 773 " --> pdb=" O CYS A 871 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA A 873 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A 775 " --> pdb=" O ALA A 873 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 479 through 483 Processing sheet with id=AA4, first strand: chain 'B' and resid 731 through 732 removed outlier: 4.281A pdb=" N LYS C 927 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 797 through 800 removed outlier: 6.460A pdb=" N LEU B 772 " --> pdb=" O CYS B 870 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALA B 872 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B 774 " --> pdb=" O ALA B 872 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 479 through 483 removed outlier: 7.990A pdb=" N SER C 513 " --> pdb=" O ILE C 556 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ILE C 558 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE C 515 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA C 560 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE C 517 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 731 through 732 removed outlier: 4.322A pdb=" N LYS D 927 " --> pdb=" O GLU C 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 797 through 800 removed outlier: 6.612A pdb=" N SER C 831 " --> pdb=" O LEU C 867 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C 869 " --> pdb=" O SER C 831 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL C 833 " --> pdb=" O LEU C 869 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU C 871 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 835 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU C 873 " --> pdb=" O ILE C 835 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 482 through 483 removed outlier: 6.570A pdb=" N ARG D 483 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER D 513 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE D 558 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 515 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA D 560 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE D 517 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 797 through 800 removed outlier: 6.044A pdb=" N ASN D 797 " --> pdb=" O VAL D 832 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE D 834 " --> pdb=" O ASN D 797 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLN D 799 " --> pdb=" O PHE D 834 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE D 895 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU D 773 " --> pdb=" O PHE D 895 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 482 through 483 removed outlier: 6.757A pdb=" N GLY E 449 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE E 581 " --> pdb=" O GLY E 449 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU E 451 " --> pdb=" O PHE E 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 797 through 800 removed outlier: 6.315A pdb=" N ASN E 797 " --> pdb=" O VAL E 832 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE E 834 " --> pdb=" O ASN E 797 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN E 799 " --> pdb=" O PHE E 834 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 776 " --> pdb=" O ALA E 872 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 479 through 483 removed outlier: 6.274A pdb=" N THR F 479 " --> pdb=" O ILE F 514 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE F 516 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE F 481 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP F 518 " --> pdb=" O PHE F 481 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG F 483 " --> pdb=" O ASP F 518 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 556 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL F 450 " --> pdb=" O GLY F 559 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR F 561 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE F 452 " --> pdb=" O THR F 561 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 797 through 800 removed outlier: 6.673A pdb=" N SER F 831 " --> pdb=" O LEU F 867 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU F 869 " --> pdb=" O SER F 831 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL F 833 " --> pdb=" O LEU F 869 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU F 871 " --> pdb=" O VAL F 833 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE F 835 " --> pdb=" O LEU F 871 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU F 873 " --> pdb=" O ILE F 835 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU F 772 " --> pdb=" O CYS F 870 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA F 872 " --> pdb=" O LEU F 772 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE F 774 " --> pdb=" O ALA F 872 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 1025 through 1027 removed outlier: 4.264A pdb=" N ILE G1032 " --> pdb=" O PHE G1041 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE G1041 " --> pdb=" O ILE G1032 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4850 1.31 - 1.43: 7285 1.43 - 1.56: 17375 1.56 - 1.69: 19 1.69 - 1.82: 179 Bond restraints: 29708 Sorted by residual: bond pdb=" CA PHE F 577 " pdb=" C PHE F 577 " ideal model delta sigma weight residual 1.532 1.457 0.075 9.60e-03 1.09e+04 6.09e+01 bond pdb=" C VAL B 410 " pdb=" O VAL B 410 " ideal model delta sigma weight residual 1.236 1.178 0.059 1.04e-02 9.25e+03 3.17e+01 bond pdb=" N ASN B 409 " pdb=" CA ASN B 409 " ideal model delta sigma weight residual 1.463 1.396 0.067 1.30e-02 5.92e+03 2.63e+01 bond pdb=" C MET B 408 " pdb=" O MET B 408 " ideal model delta sigma weight residual 1.234 1.181 0.053 1.07e-02 8.73e+03 2.45e+01 bond pdb=" CA MET B 408 " pdb=" C MET B 408 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.34e-02 5.57e+03 2.06e+01 ... (remaining 29703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 39433 3.05 - 6.10: 620 6.10 - 9.14: 81 9.14 - 12.19: 5 12.19 - 15.24: 1 Bond angle restraints: 40140 Sorted by residual: angle pdb=" N PHE F 577 " pdb=" CA PHE F 577 " pdb=" C PHE F 577 " ideal model delta sigma weight residual 110.91 100.67 10.24 1.17e+00 7.31e-01 7.65e+01 angle pdb=" N LEU G1118 " pdb=" CA LEU G1118 " pdb=" C LEU G1118 " ideal model delta sigma weight residual 111.14 103.34 7.80 1.08e+00 8.57e-01 5.21e+01 angle pdb=" N MET B 408 " pdb=" CA MET B 408 " pdb=" C MET B 408 " ideal model delta sigma weight residual 109.79 119.76 -9.97 1.56e+00 4.11e-01 4.08e+01 angle pdb=" N ASP F 550 " pdb=" CA ASP F 550 " pdb=" CB ASP F 550 " ideal model delta sigma weight residual 114.17 107.62 6.55 1.14e+00 7.69e-01 3.30e+01 angle pdb=" CB MET B 408 " pdb=" CG MET B 408 " pdb=" SD MET B 408 " ideal model delta sigma weight residual 112.70 97.46 15.24 3.00e+00 1.11e-01 2.58e+01 ... (remaining 40135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 17828 34.80 - 69.60: 469 69.60 - 104.39: 47 104.39 - 139.19: 3 139.19 - 173.99: 1 Dihedral angle restraints: 18348 sinusoidal: 7704 harmonic: 10644 Sorted by residual: dihedral pdb=" CA LYS D 491 " pdb=" C LYS D 491 " pdb=" N TRP D 492 " pdb=" CA TRP D 492 " ideal model delta harmonic sigma weight residual -180.00 -138.07 -41.93 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" CA LYS B 927 " pdb=" C LYS B 927 " pdb=" N ARG B 928 " pdb=" CA ARG B 928 " ideal model delta harmonic sigma weight residual 180.00 144.21 35.79 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA GLN C 511 " pdb=" C GLN C 511 " pdb=" N PRO C 512 " pdb=" CA PRO C 512 " ideal model delta harmonic sigma weight residual 180.00 144.67 35.33 0 5.00e+00 4.00e-02 4.99e+01 ... (remaining 18345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4167 0.092 - 0.184: 364 0.184 - 0.276: 14 0.276 - 0.368: 2 0.368 - 0.461: 2 Chirality restraints: 4549 Sorted by residual: chirality pdb=" CA ASP B 407 " pdb=" N ASP B 407 " pdb=" C ASP B 407 " pdb=" CB ASP B 407 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA MET B 408 " pdb=" N MET B 408 " pdb=" C MET B 408 " pdb=" CB MET B 408 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB VAL E 930 " pdb=" CA VAL E 930 " pdb=" CG1 VAL E 930 " pdb=" CG2 VAL E 930 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 4546 not shown) Planarity restraints: 5129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 511 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO C 512 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 512 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 512 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 693 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO B 694 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 407 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C ASP B 407 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP B 407 " -0.020 2.00e-02 2.50e+03 pdb=" N MET B 408 " -0.017 2.00e-02 2.50e+03 ... (remaining 5126 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6974 2.79 - 3.32: 26426 3.32 - 3.84: 48060 3.84 - 4.37: 56162 4.37 - 4.90: 94608 Nonbonded interactions: 232230 Sorted by model distance: nonbonded pdb=" O PRO B 455 " pdb=" OG1 THR B 458 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP B 407 " pdb=" CD2 PHE B 480 " model vdw 2.292 3.340 nonbonded pdb=" OG SER C 528 " pdb=" O LYS C 530 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 717 " pdb=" O GLN A 720 " model vdw 2.294 3.040 nonbonded pdb=" O LYS G1040 " pdb=" OG1 THR G1077 " model vdw 2.300 3.040 ... (remaining 232225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 410 through 487 or resid 496 through 526 or resid 539 thro \ ugh 733 or resid 752 through 1379)) selection = (chain 'B' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) selection = (chain 'C' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) selection = (chain 'D' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 1378)) selection = (chain 'E' and (resid 409 through 732 or resid 751 through 1378)) selection = (chain 'F' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) } 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: 0.010 Normalize map: mean=0, sd=1: 4.540 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.290 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29708 Z= 0.258 Angle : 0.940 15.240 40140 Z= 0.506 Chirality : 0.054 0.461 4549 Planarity : 0.008 0.107 5129 Dihedral : 16.270 173.988 11394 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 0.37 % Allowed : 7.56 % Favored : 92.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.15 % 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: -4.31 (0.11), residues: 3583 helix: -2.97 (0.08), residues: 1747 sheet: -2.05 (0.24), residues: 381 loop : -2.74 (0.14), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 553 TYR 0.021 0.002 TYR D 784 PHE 0.028 0.002 PHE B 753 TRP 0.016 0.002 TRP C 841 HIS 0.017 0.002 HIS E 453 Details of bonding type rmsd covalent geometry : bond 0.00538 (29708) covalent geometry : angle 0.93954 (40140) hydrogen bonds : bond 0.16362 ( 1209) hydrogen bonds : angle 6.77341 ( 3519) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 640 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7555 (pt0) REVERT: A 507 GLU cc_start: 0.6849 (tt0) cc_final: 0.6591 (mm-30) REVERT: A 510 LYS cc_start: 0.7754 (ptmt) cc_final: 0.7539 (ptmm) REVERT: A 550 MET cc_start: 0.7541 (mtt) cc_final: 0.7025 (mtp) REVERT: A 594 LYS cc_start: 0.7771 (mptt) cc_final: 0.7445 (tptp) REVERT: A 597 GLN cc_start: 0.7687 (mt0) cc_final: 0.7393 (mt0) REVERT: A 614 LYS cc_start: 0.6453 (ttpt) cc_final: 0.6091 (ttpp) REVERT: A 662 VAL cc_start: 0.7959 (t) cc_final: 0.7732 (t) REVERT: B 498 ARG cc_start: 0.7235 (ttp80) cc_final: 0.6995 (ttp80) REVERT: B 500 LEU cc_start: 0.7315 (mt) cc_final: 0.7112 (mp) REVERT: B 593 LYS cc_start: 0.7500 (tttp) cc_final: 0.7209 (ttmt) REVERT: B 616 PHE cc_start: 0.7257 (m-80) cc_final: 0.6610 (t80) REVERT: B 828 ARG cc_start: 0.7007 (ptp90) cc_final: 0.6803 (mtm-85) REVERT: B 878 SER cc_start: 0.8127 (p) cc_final: 0.7622 (m) REVERT: B 925 MET cc_start: 0.7156 (mtt) cc_final: 0.6923 (mtm) REVERT: B 1336 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7178 (tm-30) REVERT: B 1340 ASN cc_start: 0.7255 (m-40) cc_final: 0.7015 (t0) REVERT: C 408 MET cc_start: 0.6365 (mtp) cc_final: 0.6099 (mtt) REVERT: C 549 MET cc_start: 0.2811 (mtp) cc_final: 0.2322 (ptm) REVERT: C 573 ARG cc_start: 0.5955 (mtm-85) cc_final: 0.5701 (ttp80) REVERT: C 708 ASP cc_start: 0.7175 (m-30) cc_final: 0.6725 (m-30) REVERT: C 727 ASN cc_start: 0.6039 (m-40) cc_final: 0.5795 (m110) REVERT: C 815 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6251 (mm-30) REVERT: C 891 ASP cc_start: 0.6804 (p0) cc_final: 0.6531 (t0) REVERT: C 1325 GLU cc_start: 0.7336 (tp30) cc_final: 0.7065 (tp30) REVERT: D 447 PRO cc_start: 0.6350 (Cg_exo) cc_final: 0.6090 (Cg_endo) REVERT: D 463 MET cc_start: 0.7939 (tpp) cc_final: 0.7655 (tpt) REVERT: D 504 PHE cc_start: 0.4682 (m-80) cc_final: 0.4448 (m-80) REVERT: D 516 PHE cc_start: 0.6427 (t80) cc_final: 0.6025 (t80) REVERT: D 671 LYS cc_start: 0.7491 (mtmt) cc_final: 0.6894 (ptmm) REVERT: D 762 MET cc_start: 0.6904 (mmm) cc_final: 0.6310 (mmt) REVERT: D 821 SER cc_start: 0.7829 (p) cc_final: 0.7464 (m) REVERT: D 898 HIS cc_start: 0.7593 (p-80) cc_final: 0.7364 (p-80) REVERT: D 1365 ASP cc_start: 0.6584 (t0) cc_final: 0.6364 (t0) REVERT: E 501 ARG cc_start: 0.3091 (mmm160) cc_final: 0.2746 (mtm-85) REVERT: E 546 MET cc_start: 0.0224 (ttp) cc_final: -0.0515 (ttp) REVERT: E 549 MET cc_start: 0.0543 (mmp) cc_final: 0.0314 (pmm) REVERT: E 898 HIS cc_start: 0.7348 (p-80) cc_final: 0.6897 (p-80) REVERT: E 911 ASN cc_start: 0.7587 (t0) cc_final: 0.7337 (t0) REVERT: E 1328 LYS cc_start: 0.7702 (mtpt) cc_final: 0.7363 (mptt) REVERT: F 408 MET cc_start: 0.1411 (ptt) cc_final: 0.0689 (pmm) REVERT: F 546 MET cc_start: 0.4554 (mtt) cc_final: 0.3847 (mtt) REVERT: F 550 ASP cc_start: 0.4274 (t70) cc_final: 0.3902 (t0) REVERT: F 579 ARG cc_start: 0.4874 (mtm180) cc_final: 0.4340 (tpt90) REVERT: F 593 LYS cc_start: 0.5966 (tppt) cc_final: 0.5641 (mtpt) REVERT: F 756 TYR cc_start: 0.7019 (t80) cc_final: 0.6786 (t80) REVERT: F 820 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7429 (mm110) REVERT: G 324 ARG cc_start: 0.2259 (mmp80) cc_final: 0.1866 (tpp80) REVERT: G 325 LEU cc_start: 0.5197 (pp) cc_final: 0.4708 (mp) REVERT: G 973 MET cc_start: 0.2976 (tpt) cc_final: 0.2074 (tmm) REVERT: G 1050 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.4454 (pt0) REVERT: G 1119 GLU cc_start: 0.3265 (tm-30) cc_final: 0.2316 (tm-30) outliers start: 12 outliers final: 3 residues processed: 650 average time/residue: 0.2209 time to fit residues: 215.2367 Evaluate side-chains 375 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 371 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain G residue 1046 LEU Chi-restraints excluded: chain G residue 1048 ILE Chi-restraints excluded: chain G residue 1050 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 687 GLN A 703 ASN A 727 GLN A 781 ASN A 849 ASN A1346 GLN A1351 HIS B 420 ASN B 453 HIS B 533 GLN B 639 GLN B 702 ASN B 797 ASN B 799 GLN B 820 GLN B1350 HIS C 424 GLN C 443 ASN C 510 HIS C 531 GLN C 533 GLN C 562 ASN C 686 GLN C 712 ASN C 799 GLN C1345 GLN D 780 ASN ** D 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 ASN D1350 HIS E 443 ASN E 551 ASN E 775 ASN E 896 GLN E1340 ASN E1345 GLN E1350 HIS F 440 GLN F 443 ASN F 562 ASN F 686 GLN F 719 GLN F 829 GLN F 848 ASN F1345 GLN F1350 HIS G 977 ASN G1055 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.192271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154787 restraints weight = 35976.494| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.87 r_work: 0.3348 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29708 Z= 0.157 Angle : 0.649 9.284 40140 Z= 0.326 Chirality : 0.043 0.234 4549 Planarity : 0.006 0.084 5129 Dihedral : 7.630 164.455 3936 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.44 % Allowed : 11.63 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.03 % 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: -2.48 (0.13), residues: 3583 helix: -1.17 (0.11), residues: 1737 sheet: -1.79 (0.25), residues: 354 loop : -2.08 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 576 TYR 0.017 0.002 TYR D 756 PHE 0.029 0.002 PHE D 442 TRP 0.016 0.001 TRP F 841 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00357 (29708) covalent geometry : angle 0.64864 (40140) hydrogen bonds : bond 0.04316 ( 1209) hydrogen bonds : angle 4.54839 ( 3519) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 390 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 507 GLU cc_start: 0.7325 (tt0) cc_final: 0.7052 (mm-30) REVERT: A 510 LYS cc_start: 0.8089 (ptmt) cc_final: 0.7790 (ptmm) REVERT: A 550 MET cc_start: 0.7861 (mtt) cc_final: 0.7466 (mtp) REVERT: A 594 LYS cc_start: 0.8225 (mptt) cc_final: 0.7976 (tptp) REVERT: A 597 GLN cc_start: 0.8078 (mt0) cc_final: 0.7789 (mt0) REVERT: A 614 LYS cc_start: 0.7086 (ttpt) cc_final: 0.6725 (ttpp) REVERT: A 663 LYS cc_start: 0.7919 (pttm) cc_final: 0.7572 (pttp) REVERT: B 593 LYS cc_start: 0.8086 (tttp) cc_final: 0.7828 (ttmt) REVERT: B 600 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.5955 (ptp-170) REVERT: B 616 PHE cc_start: 0.7814 (m-80) cc_final: 0.7228 (t80) REVERT: B 925 MET cc_start: 0.7405 (mtt) cc_final: 0.7072 (mtm) REVERT: B 1336 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8015 (tm-30) REVERT: B 1340 ASN cc_start: 0.7803 (m-40) cc_final: 0.7482 (t0) REVERT: C 408 MET cc_start: 0.6520 (mtp) cc_final: 0.6069 (mtt) REVERT: C 435 TYR cc_start: 0.7088 (m-80) cc_final: 0.6658 (m-80) REVERT: C 531 GLN cc_start: 0.3809 (OUTLIER) cc_final: 0.3401 (tm-30) REVERT: C 573 ARG cc_start: 0.6566 (mtm-85) cc_final: 0.5996 (ttp80) REVERT: C 727 ASN cc_start: 0.6125 (m-40) cc_final: 0.5882 (m110) REVERT: C 731 TYR cc_start: 0.6987 (m-10) cc_final: 0.6775 (m-10) REVERT: C 878 SER cc_start: 0.7712 (p) cc_final: 0.7480 (p) REVERT: C 891 ASP cc_start: 0.7320 (p0) cc_final: 0.6873 (t0) REVERT: C 1325 GLU cc_start: 0.7342 (tp30) cc_final: 0.7029 (tp30) REVERT: D 447 PRO cc_start: 0.6354 (Cg_exo) cc_final: 0.6121 (Cg_endo) REVERT: D 463 MET cc_start: 0.7920 (tpp) cc_final: 0.7717 (tpt) REVERT: D 504 PHE cc_start: 0.4460 (m-80) cc_final: 0.4199 (m-80) REVERT: D 516 PHE cc_start: 0.6419 (t80) cc_final: 0.5703 (t80) REVERT: D 518 ASP cc_start: 0.5534 (t0) cc_final: 0.5025 (m-30) REVERT: D 554 GLN cc_start: 0.5577 (mp10) cc_final: 0.4837 (mt0) REVERT: D 601 LYS cc_start: 0.7731 (tptp) cc_final: 0.7250 (tttt) REVERT: D 671 LYS cc_start: 0.7733 (mtmt) cc_final: 0.7001 (ptmm) REVERT: D 757 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6886 (pt0) REVERT: D 759 PHE cc_start: 0.8257 (m-10) cc_final: 0.8036 (m-80) REVERT: D 821 SER cc_start: 0.7924 (p) cc_final: 0.7577 (m) REVERT: D 898 HIS cc_start: 0.7864 (p-80) cc_final: 0.7640 (p-80) REVERT: D 927 LYS cc_start: 0.4896 (ptpp) cc_final: 0.4537 (ttpp) REVERT: D 1348 ASP cc_start: 0.7847 (t70) cc_final: 0.7500 (t0) REVERT: D 1358 TRP cc_start: 0.8123 (OUTLIER) cc_final: 0.7091 (m-90) REVERT: D 1365 ASP cc_start: 0.7270 (t0) cc_final: 0.6728 (t0) REVERT: E 438 LEU cc_start: 0.2563 (OUTLIER) cc_final: 0.2287 (tp) REVERT: E 463 MET cc_start: 0.5015 (tpp) cc_final: 0.4332 (tpp) REVERT: E 501 ARG cc_start: 0.3120 (mmm160) cc_final: 0.2495 (mtm-85) REVERT: E 508 LYS cc_start: 0.4636 (mtpt) cc_final: 0.4413 (mtmt) REVERT: E 549 MET cc_start: 0.0661 (mmt) cc_final: 0.0149 (pmm) REVERT: E 898 HIS cc_start: 0.7750 (p-80) cc_final: 0.7393 (p-80) REVERT: E 1328 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7575 (mptt) REVERT: F 408 MET cc_start: 0.1894 (ptt) cc_final: 0.1063 (pmm) REVERT: F 482 MET cc_start: 0.7313 (ttm) cc_final: 0.6563 (ttt) REVERT: F 546 MET cc_start: 0.4741 (mtt) cc_final: 0.4076 (mtt) REVERT: F 554 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6809 (mp10) REVERT: F 593 LYS cc_start: 0.6042 (tppt) cc_final: 0.5588 (mtpt) REVERT: F 640 ARG cc_start: 0.2928 (ttp-170) cc_final: 0.2604 (ttt-90) REVERT: F 922 ASP cc_start: 0.7334 (m-30) cc_final: 0.6822 (t0) REVERT: G 325 LEU cc_start: 0.4040 (pp) cc_final: 0.3655 (mp) REVERT: G 972 ASP cc_start: 0.3189 (t70) cc_final: 0.2346 (t0) REVERT: G 973 MET cc_start: 0.2838 (tpt) cc_final: 0.2165 (tmm) REVERT: G 1003 ASP cc_start: 0.3466 (t0) cc_final: 0.3231 (t70) REVERT: G 1050 GLU cc_start: 0.6076 (tp30) cc_final: 0.5373 (tp30) REVERT: G 1096 MET cc_start: 0.4710 (mmt) cc_final: 0.4175 (mmt) REVERT: G 1119 GLU cc_start: 0.3673 (tm-30) cc_final: 0.2736 (tt0) REVERT: G 1131 ARG cc_start: 0.1599 (mtp180) cc_final: 0.1169 (mtt90) outliers start: 47 outliers final: 21 residues processed: 423 average time/residue: 0.2226 time to fit residues: 145.2584 Evaluate side-chains 342 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 316 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 925 MET Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 710 MET Chi-restraints excluded: chain D residue 728 PHE Chi-restraints excluded: chain D residue 887 ASP Chi-restraints excluded: chain D residue 1358 TRP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain F residue 554 GLN Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain G residue 986 LEU Chi-restraints excluded: chain G residue 1091 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 258 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS A 838 ASN B 829 GLN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 HIS C1350 HIS ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN E1340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.189268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151449 restraints weight = 36175.953| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.12 r_work: 0.3266 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 29708 Z= 0.200 Angle : 0.678 13.406 40140 Z= 0.335 Chirality : 0.045 0.161 4549 Planarity : 0.006 0.078 5129 Dihedral : 7.332 159.280 3929 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.45 % Allowed : 13.83 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.06 % 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: -1.84 (0.14), residues: 3583 helix: -0.61 (0.12), residues: 1770 sheet: -1.67 (0.26), residues: 355 loop : -1.75 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 828 TYR 0.017 0.002 TYR G1057 PHE 0.022 0.002 PHE G1124 TRP 0.016 0.002 TRP C 841 HIS 0.006 0.001 HIS F1350 Details of bonding type rmsd covalent geometry : bond 0.00485 (29708) covalent geometry : angle 0.67804 (40140) hydrogen bonds : bond 0.04441 ( 1209) hydrogen bonds : angle 4.38825 ( 3519) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 334 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 GLU cc_start: 0.6168 (tp30) cc_final: 0.5665 (tt0) REVERT: A 507 GLU cc_start: 0.7351 (tt0) cc_final: 0.7024 (mm-30) REVERT: A 550 MET cc_start: 0.8211 (mtt) cc_final: 0.8003 (mtp) REVERT: A 594 LYS cc_start: 0.8284 (mptt) cc_final: 0.7889 (tptp) REVERT: A 614 LYS cc_start: 0.7264 (ttpt) cc_final: 0.6850 (ttpp) REVERT: A 663 LYS cc_start: 0.8097 (pttm) cc_final: 0.7623 (pttp) REVERT: B 408 MET cc_start: 0.4821 (mtm) cc_final: 0.4153 (tpp) REVERT: B 508 LYS cc_start: 0.8053 (tptt) cc_final: 0.7844 (tttt) REVERT: B 593 LYS cc_start: 0.8310 (tttp) cc_final: 0.7982 (ttmt) REVERT: B 815 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6985 (mt-10) REVERT: B 1340 ASN cc_start: 0.8060 (m-40) cc_final: 0.7626 (t0) REVERT: C 408 MET cc_start: 0.6485 (mtp) cc_final: 0.5703 (mtt) REVERT: C 435 TYR cc_start: 0.7396 (m-80) cc_final: 0.6806 (m-80) REVERT: C 483 ARG cc_start: 0.6546 (mpt180) cc_final: 0.6115 (tpp-160) REVERT: C 573 ARG cc_start: 0.6397 (mtm-85) cc_final: 0.5859 (ttp-110) REVERT: C 731 TYR cc_start: 0.7259 (m-10) cc_final: 0.7012 (m-10) REVERT: C 1325 GLU cc_start: 0.7396 (tp30) cc_final: 0.7081 (tp30) REVERT: C 1372 GLU cc_start: 0.7512 (tp30) cc_final: 0.7079 (tt0) REVERT: D 465 ARG cc_start: 0.7626 (ttm110) cc_final: 0.6612 (ttm-80) REVERT: D 504 PHE cc_start: 0.4672 (m-80) cc_final: 0.4449 (m-80) REVERT: D 518 ASP cc_start: 0.5552 (OUTLIER) cc_final: 0.5094 (m-30) REVERT: D 554 GLN cc_start: 0.5311 (mp10) cc_final: 0.4513 (mt0) REVERT: D 632 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5500 (mm-30) REVERT: D 643 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7895 (Cg_endo) REVERT: D 671 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7081 (ptmm) REVERT: D 755 SER cc_start: 0.6278 (m) cc_final: 0.5780 (p) REVERT: D 757 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6877 (pt0) REVERT: D 821 SER cc_start: 0.7933 (p) cc_final: 0.7730 (m) REVERT: D 898 HIS cc_start: 0.7905 (p-80) cc_final: 0.7670 (p-80) REVERT: D 927 LYS cc_start: 0.5074 (ptpp) cc_final: 0.4704 (ttpp) REVERT: D 1348 ASP cc_start: 0.8061 (t70) cc_final: 0.7802 (t0) REVERT: D 1365 ASP cc_start: 0.7415 (t0) cc_final: 0.7135 (t0) REVERT: E 427 GLU cc_start: 0.5065 (mt-10) cc_final: 0.4285 (mm-30) REVERT: E 428 MET cc_start: 0.4045 (mtp) cc_final: 0.3575 (mtp) REVERT: E 438 LEU cc_start: 0.2561 (OUTLIER) cc_final: 0.2283 (tp) REVERT: E 501 ARG cc_start: 0.3195 (mmm160) cc_final: 0.2579 (mtm-85) REVERT: E 508 LYS cc_start: 0.5056 (mtpt) cc_final: 0.4578 (mtmt) REVERT: E 549 MET cc_start: 0.0243 (mmt) cc_final: -0.0126 (tpp) REVERT: E 646 TYR cc_start: 0.5629 (m-80) cc_final: 0.5206 (m-10) REVERT: E 647 ARG cc_start: 0.4343 (ptt-90) cc_final: 0.3916 (ttm-80) REVERT: E 679 ARG cc_start: -0.0024 (OUTLIER) cc_final: -0.0959 (mmp80) REVERT: E 898 HIS cc_start: 0.7798 (p-80) cc_final: 0.7408 (p-80) REVERT: E 1328 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7572 (mptt) REVERT: F 408 MET cc_start: 0.1764 (ptt) cc_final: 0.1254 (pmm) REVERT: F 482 MET cc_start: 0.7378 (ttm) cc_final: 0.6620 (ttt) REVERT: F 519 GLU cc_start: 0.5162 (OUTLIER) cc_final: 0.4779 (tm-30) REVERT: F 545 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5342 (mm) REVERT: F 593 LYS cc_start: 0.6199 (tppt) cc_final: 0.5750 (mtpt) REVERT: F 617 LEU cc_start: 0.0564 (OUTLIER) cc_final: 0.0212 (pp) REVERT: F 640 ARG cc_start: 0.2898 (ttp-170) cc_final: 0.2645 (ttt-90) REVERT: F 756 TYR cc_start: 0.7490 (t80) cc_final: 0.7204 (t80) REVERT: F 922 ASP cc_start: 0.7403 (m-30) cc_final: 0.6816 (t0) REVERT: F 1321 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6583 (mt) REVERT: G 325 LEU cc_start: 0.3678 (OUTLIER) cc_final: 0.3440 (pt) REVERT: G 1050 GLU cc_start: 0.5971 (tp30) cc_final: 0.4333 (pt0) REVERT: G 1068 ILE cc_start: 0.2277 (mm) cc_final: 0.1971 (tp) REVERT: G 1099 GLU cc_start: 0.4866 (OUTLIER) cc_final: 0.4205 (mt-10) REVERT: G 1119 GLU cc_start: 0.3719 (tm-30) cc_final: 0.2729 (tt0) REVERT: G 1131 ARG cc_start: 0.2007 (mtp180) cc_final: 0.1210 (mtt90) outliers start: 80 outliers final: 43 residues processed: 395 average time/residue: 0.1975 time to fit residues: 123.1281 Evaluate side-chains 357 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 925 MET Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 710 MET Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 728 PHE Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 1323 THR Chi-restraints excluded: chain E residue 1329 LYS Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 986 LEU Chi-restraints excluded: chain G residue 1091 PHE Chi-restraints excluded: chain G residue 1099 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 31 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 167 optimal weight: 0.0270 chunk 285 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 128 optimal weight: 0.0370 chunk 42 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS B 896 GLN C 510 HIS D 535 HIS D 799 GLN D 829 GLN E1337 HIS E1340 ASN F 443 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.194186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137436 restraints weight = 35287.890| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.67 r_work: 0.3420 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29708 Z= 0.111 Angle : 0.584 10.251 40140 Z= 0.286 Chirality : 0.042 0.162 4549 Planarity : 0.005 0.077 5129 Dihedral : 6.816 150.371 3929 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.90 % Allowed : 15.39 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.03 % 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: -1.23 (0.14), residues: 3583 helix: -0.01 (0.12), residues: 1763 sheet: -1.57 (0.26), residues: 350 loop : -1.53 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 828 TYR 0.014 0.001 TYR A 732 PHE 0.014 0.001 PHE A 643 TRP 0.010 0.001 TRP F 841 HIS 0.005 0.001 HIS E 453 Details of bonding type rmsd covalent geometry : bond 0.00250 (29708) covalent geometry : angle 0.58427 (40140) hydrogen bonds : bond 0.03555 ( 1209) hydrogen bonds : angle 4.07359 ( 3519) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 322 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 496 GLU cc_start: 0.6076 (tp30) cc_final: 0.5577 (tt0) REVERT: A 507 GLU cc_start: 0.7247 (tt0) cc_final: 0.6780 (mm-30) REVERT: A 594 LYS cc_start: 0.8129 (mptt) cc_final: 0.7526 (tptp) REVERT: A 614 LYS cc_start: 0.7005 (ttpt) cc_final: 0.6593 (ttpp) REVERT: A 663 LYS cc_start: 0.8010 (pttm) cc_final: 0.7434 (pttp) REVERT: A 709 ASP cc_start: 0.8298 (m-30) cc_final: 0.8069 (m-30) REVERT: A 1334 CYS cc_start: 0.7963 (p) cc_final: 0.7642 (m) REVERT: B 408 MET cc_start: 0.4723 (OUTLIER) cc_final: 0.4100 (tpp) REVERT: B 593 LYS cc_start: 0.8140 (tttp) cc_final: 0.7748 (ttmt) REVERT: B 600 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6272 (ptp-170) REVERT: B 803 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8597 (mt) REVERT: B 815 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6883 (mt-10) REVERT: C 408 MET cc_start: 0.6364 (mtp) cc_final: 0.5717 (mtt) REVERT: C 435 TYR cc_start: 0.7226 (m-80) cc_final: 0.6751 (m-80) REVERT: C 483 ARG cc_start: 0.6211 (mpt180) cc_final: 0.5295 (ttm-80) REVERT: C 511 GLN cc_start: 0.6105 (mm-40) cc_final: 0.5527 (tt0) REVERT: C 573 ARG cc_start: 0.6325 (mtm-85) cc_final: 0.5601 (ttp80) REVERT: C 1372 GLU cc_start: 0.7562 (tp30) cc_final: 0.7145 (tt0) REVERT: D 465 ARG cc_start: 0.7343 (ttm110) cc_final: 0.6302 (ttt180) REVERT: D 504 PHE cc_start: 0.4191 (m-80) cc_final: 0.3942 (m-80) REVERT: D 518 ASP cc_start: 0.5499 (OUTLIER) cc_final: 0.5015 (m-30) REVERT: D 554 GLN cc_start: 0.5032 (mp10) cc_final: 0.4503 (mt0) REVERT: D 632 GLU cc_start: 0.5790 (mm-30) cc_final: 0.5469 (mm-30) REVERT: D 643 PRO cc_start: 0.8109 (Cg_exo) cc_final: 0.7848 (Cg_endo) REVERT: D 671 LYS cc_start: 0.7828 (mtmt) cc_final: 0.7041 (ptmm) REVERT: D 755 SER cc_start: 0.6237 (m) cc_final: 0.5749 (p) REVERT: D 757 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6668 (pt0) REVERT: D 898 HIS cc_start: 0.7787 (p-80) cc_final: 0.7565 (p-80) REVERT: D 927 LYS cc_start: 0.4918 (ptpp) cc_final: 0.4608 (ttpp) REVERT: D 1348 ASP cc_start: 0.7949 (t70) cc_final: 0.7631 (t0) REVERT: D 1365 ASP cc_start: 0.7527 (t0) cc_final: 0.7244 (t0) REVERT: E 428 MET cc_start: 0.3629 (mtp) cc_final: 0.3249 (mtp) REVERT: E 435 TYR cc_start: 0.2782 (m-80) cc_final: 0.2409 (m-10) REVERT: E 501 ARG cc_start: 0.3003 (mmm160) cc_final: 0.2439 (mtm-85) REVERT: E 542 LEU cc_start: 0.0953 (OUTLIER) cc_final: 0.0691 (mp) REVERT: E 646 TYR cc_start: 0.5378 (m-80) cc_final: 0.4759 (m-80) REVERT: E 647 ARG cc_start: 0.4321 (ptt-90) cc_final: 0.3972 (ttm-80) REVERT: E 679 ARG cc_start: -0.0215 (OUTLIER) cc_final: -0.0974 (mmp80) REVERT: E 898 HIS cc_start: 0.7789 (p-80) cc_final: 0.7391 (p-80) REVERT: E 1328 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7109 (mptt) REVERT: F 408 MET cc_start: 0.1702 (ptt) cc_final: 0.1173 (pmm) REVERT: F 519 GLU cc_start: 0.4851 (OUTLIER) cc_final: 0.4526 (tm-30) REVERT: F 546 MET cc_start: 0.4785 (mtt) cc_final: 0.4541 (mtt) REVERT: F 593 LYS cc_start: 0.6068 (tppt) cc_final: 0.5600 (mtpt) REVERT: F 640 ARG cc_start: 0.2916 (ttp-170) cc_final: 0.2649 (ttt-90) REVERT: F 922 ASP cc_start: 0.7364 (m-30) cc_final: 0.6699 (t0) REVERT: F 1321 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6705 (mt) REVERT: G 991 LYS cc_start: 0.3300 (pttp) cc_final: 0.2991 (ptmm) REVERT: G 1006 PHE cc_start: 0.2411 (m-80) cc_final: 0.1964 (m-80) REVERT: G 1050 GLU cc_start: 0.5675 (tp30) cc_final: 0.4125 (pt0) REVERT: G 1068 ILE cc_start: 0.1986 (mm) cc_final: 0.1662 (tp) REVERT: G 1099 GLU cc_start: 0.4727 (OUTLIER) cc_final: 0.4054 (mt-10) REVERT: G 1119 GLU cc_start: 0.3529 (OUTLIER) cc_final: 0.2770 (tt0) REVERT: G 1131 ARG cc_start: 0.1694 (mtp180) cc_final: 0.1127 (mtt90) outliers start: 62 outliers final: 34 residues processed: 365 average time/residue: 0.2035 time to fit residues: 115.9528 Evaluate side-chains 344 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 698 ASP Chi-restraints excluded: chain D residue 710 MET Chi-restraints excluded: chain D residue 728 PHE Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 887 ASP Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1321 ILE Chi-restraints excluded: chain E residue 1329 LYS Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1335 ILE Chi-restraints excluded: chain G residue 1059 SER Chi-restraints excluded: chain G residue 1091 PHE Chi-restraints excluded: chain G residue 1099 GLU Chi-restraints excluded: chain G residue 1119 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 275 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 349 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 223 optimal weight: 0.2980 chunk 148 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 HIS ** D1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.193388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134562 restraints weight = 35259.737| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.10 r_work: 0.3391 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29708 Z= 0.120 Angle : 0.580 9.593 40140 Z= 0.281 Chirality : 0.042 0.149 4549 Planarity : 0.005 0.076 5129 Dihedral : 6.605 148.168 3929 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.48 % Allowed : 15.76 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3583 helix: 0.35 (0.13), residues: 1749 sheet: -1.39 (0.27), residues: 343 loop : -1.38 (0.17), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 828 TYR 0.017 0.001 TYR A 732 PHE 0.036 0.001 PHE D 442 TRP 0.009 0.001 TRP F 841 HIS 0.005 0.001 HIS C 510 Details of bonding type rmsd covalent geometry : bond 0.00279 (29708) covalent geometry : angle 0.57977 (40140) hydrogen bonds : bond 0.03581 ( 1209) hydrogen bonds : angle 3.96121 ( 3519) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 315 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 GLU cc_start: 0.6142 (tp30) cc_final: 0.5627 (tt0) REVERT: A 507 GLU cc_start: 0.7305 (tt0) cc_final: 0.6879 (mm-30) REVERT: A 594 LYS cc_start: 0.8245 (mptt) cc_final: 0.7630 (tptp) REVERT: A 614 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6720 (ttpp) REVERT: A 663 LYS cc_start: 0.7979 (pttm) cc_final: 0.7477 (pttt) REVERT: A 680 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7051 (tpt90) REVERT: A 729 PHE cc_start: 0.7749 (m-80) cc_final: 0.7538 (m-80) REVERT: A 915 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: A 1334 CYS cc_start: 0.7947 (p) cc_final: 0.7645 (m) REVERT: B 408 MET cc_start: 0.4733 (OUTLIER) cc_final: 0.4150 (tpp) REVERT: B 593 LYS cc_start: 0.8232 (tttp) cc_final: 0.7824 (ttmt) REVERT: B 803 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8604 (mt) REVERT: B 815 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7034 (mt-10) REVERT: C 408 MET cc_start: 0.6391 (mtp) cc_final: 0.5697 (mtt) REVERT: C 435 TYR cc_start: 0.7232 (m-80) cc_final: 0.6786 (m-80) REVERT: C 573 ARG cc_start: 0.6401 (mtm-85) cc_final: 0.5704 (ttp80) REVERT: C 1372 GLU cc_start: 0.7562 (tp30) cc_final: 0.7157 (tt0) REVERT: D 504 PHE cc_start: 0.4275 (m-80) cc_final: 0.4006 (m-80) REVERT: D 518 ASP cc_start: 0.5488 (OUTLIER) cc_final: 0.5014 (m-30) REVERT: D 554 GLN cc_start: 0.4968 (mp10) cc_final: 0.4314 (mt0) REVERT: D 671 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7032 (ptmm) REVERT: D 755 SER cc_start: 0.6329 (m) cc_final: 0.5824 (p) REVERT: D 757 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6767 (pt0) REVERT: D 898 HIS cc_start: 0.7855 (p-80) cc_final: 0.7634 (p-80) REVERT: D 927 LYS cc_start: 0.5095 (ptpp) cc_final: 0.4837 (ttpp) REVERT: D 936 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4302 (mm) REVERT: D 1348 ASP cc_start: 0.8021 (t70) cc_final: 0.7714 (t0) REVERT: D 1365 ASP cc_start: 0.7596 (t0) cc_final: 0.7351 (t0) REVERT: E 428 MET cc_start: 0.3488 (mtp) cc_final: 0.3223 (mtp) REVERT: E 435 TYR cc_start: 0.2849 (m-80) cc_final: 0.2314 (m-10) REVERT: E 501 ARG cc_start: 0.2967 (mmm160) cc_final: 0.2434 (mtm-85) REVERT: E 576 ARG cc_start: 0.2573 (tpp-160) cc_final: 0.1866 (tpp80) REVERT: E 647 ARG cc_start: 0.4366 (ptt-90) cc_final: 0.3908 (ttm-80) REVERT: E 679 ARG cc_start: -0.0153 (OUTLIER) cc_final: -0.0883 (mmp80) REVERT: E 898 HIS cc_start: 0.7827 (p-80) cc_final: 0.7395 (p-80) REVERT: E 1328 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7228 (mptt) REVERT: F 408 MET cc_start: 0.1959 (ptt) cc_final: 0.1362 (pmm) REVERT: F 482 MET cc_start: 0.7175 (ttm) cc_final: 0.6303 (ttt) REVERT: F 519 GLU cc_start: 0.4689 (OUTLIER) cc_final: 0.4349 (tm-30) REVERT: F 545 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5250 (mm) REVERT: F 593 LYS cc_start: 0.6049 (tppt) cc_final: 0.5540 (mtpt) REVERT: F 617 LEU cc_start: 0.0501 (OUTLIER) cc_final: 0.0143 (pp) REVERT: F 629 LEU cc_start: 0.4293 (OUTLIER) cc_final: 0.3966 (tt) REVERT: F 922 ASP cc_start: 0.7391 (m-30) cc_final: 0.6739 (t0) REVERT: F 1321 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6718 (mt) REVERT: G 987 MET cc_start: 0.2560 (tpt) cc_final: 0.2117 (tpt) REVERT: G 991 LYS cc_start: 0.3348 (pttp) cc_final: 0.3053 (ptmm) REVERT: G 1050 GLU cc_start: 0.5847 (tp30) cc_final: 0.4220 (pt0) REVERT: G 1099 GLU cc_start: 0.4767 (OUTLIER) cc_final: 0.4153 (mt-10) REVERT: G 1119 GLU cc_start: 0.3552 (OUTLIER) cc_final: 0.2827 (tt0) REVERT: G 1131 ARG cc_start: 0.1848 (mtp180) cc_final: 0.1292 (mtt90) outliers start: 81 outliers final: 48 residues processed: 373 average time/residue: 0.1844 time to fit residues: 108.6706 Evaluate side-chains 363 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 925 MET Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 710 MET Chi-restraints excluded: chain D residue 728 PHE Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 887 ASP Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1329 LYS Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 710 MET Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 1048 ILE Chi-restraints excluded: chain G residue 1059 SER Chi-restraints excluded: chain G residue 1091 PHE Chi-restraints excluded: chain G residue 1099 GLU Chi-restraints excluded: chain G residue 1119 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 158 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 16 optimal weight: 0.0060 chunk 186 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 350 optimal weight: 7.9990 chunk 240 optimal weight: 0.0170 chunk 88 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 510 HIS D1326 GLN ** D1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 791 ASN E1340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136187 restraints weight = 35130.603| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.30 r_work: 0.3382 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29708 Z= 0.117 Angle : 0.573 12.197 40140 Z= 0.278 Chirality : 0.042 0.157 4549 Planarity : 0.004 0.072 5129 Dihedral : 6.474 146.966 3929 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.60 % Allowed : 15.67 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.03 % 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: -0.63 (0.14), residues: 3583 helix: 0.51 (0.13), residues: 1757 sheet: -1.22 (0.27), residues: 337 loop : -1.29 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 448 TYR 0.022 0.001 TYR E 646 PHE 0.013 0.001 PHE A 643 TRP 0.009 0.001 TRP F 841 HIS 0.004 0.001 HIS E 453 Details of bonding type rmsd covalent geometry : bond 0.00274 (29708) covalent geometry : angle 0.57315 (40140) hydrogen bonds : bond 0.03478 ( 1209) hydrogen bonds : angle 3.91996 ( 3519) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 315 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 GLU cc_start: 0.6120 (tp30) cc_final: 0.5630 (tt0) REVERT: A 507 GLU cc_start: 0.7301 (tt0) cc_final: 0.6865 (mm-30) REVERT: A 594 LYS cc_start: 0.8271 (mptt) cc_final: 0.7603 (tptp) REVERT: A 613 ASP cc_start: 0.7705 (t0) cc_final: 0.7474 (t70) REVERT: A 614 LYS cc_start: 0.7146 (ttpt) cc_final: 0.6768 (ttpp) REVERT: A 663 LYS cc_start: 0.8043 (pttm) cc_final: 0.7601 (pttt) REVERT: A 680 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7044 (tpt90) REVERT: A 725 LEU cc_start: 0.7095 (pp) cc_final: 0.6333 (tp) REVERT: A 729 PHE cc_start: 0.7710 (m-80) cc_final: 0.7426 (m-80) REVERT: A 758 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5848 (pm20) REVERT: A 888 ASP cc_start: 0.7263 (p0) cc_final: 0.6999 (t0) REVERT: A 915 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: A 1334 CYS cc_start: 0.7963 (p) cc_final: 0.7662 (m) REVERT: B 408 MET cc_start: 0.4709 (OUTLIER) cc_final: 0.4136 (tpp) REVERT: B 593 LYS cc_start: 0.8206 (tttp) cc_final: 0.7801 (ttmt) REVERT: B 600 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6245 (ptp-170) REVERT: B 725 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7154 (tt) REVERT: B 803 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8618 (mt) REVERT: B 815 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6973 (mt-10) REVERT: C 408 MET cc_start: 0.6370 (mtp) cc_final: 0.5683 (mtt) REVERT: C 435 TYR cc_start: 0.7139 (m-80) cc_final: 0.6793 (m-80) REVERT: C 483 ARG cc_start: 0.6666 (mmp-170) cc_final: 0.5698 (ttm-80) REVERT: C 495 GLU cc_start: 0.5322 (OUTLIER) cc_final: 0.4832 (tt0) REVERT: C 573 ARG cc_start: 0.6392 (mtm-85) cc_final: 0.5649 (ttp80) REVERT: C 1372 GLU cc_start: 0.7581 (tp30) cc_final: 0.7181 (tt0) REVERT: D 465 ARG cc_start: 0.7240 (ttm110) cc_final: 0.6295 (ttm-80) REVERT: D 504 PHE cc_start: 0.4265 (m-80) cc_final: 0.3980 (m-80) REVERT: D 518 ASP cc_start: 0.5477 (OUTLIER) cc_final: 0.5001 (m-30) REVERT: D 554 GLN cc_start: 0.4945 (mp10) cc_final: 0.4189 (mt0) REVERT: D 578 ASP cc_start: 0.5284 (OUTLIER) cc_final: 0.5005 (t70) REVERT: D 614 LEU cc_start: 0.7013 (tt) cc_final: 0.6796 (tp) REVERT: D 643 PRO cc_start: 0.8049 (Cg_exo) cc_final: 0.7756 (Cg_endo) REVERT: D 666 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6558 (t80) REVERT: D 671 LYS cc_start: 0.7799 (mtmt) cc_final: 0.6947 (ptmm) REVERT: D 755 SER cc_start: 0.6340 (m) cc_final: 0.5834 (p) REVERT: D 757 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6744 (pt0) REVERT: D 800 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8490 (t0) REVERT: D 898 HIS cc_start: 0.7831 (p-80) cc_final: 0.7618 (p-80) REVERT: D 936 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4354 (mm) REVERT: D 1348 ASP cc_start: 0.8070 (t70) cc_final: 0.7761 (t0) REVERT: D 1365 ASP cc_start: 0.7598 (t0) cc_final: 0.7353 (t0) REVERT: D 1375 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8074 (mtmm) REVERT: E 428 MET cc_start: 0.3728 (mtp) cc_final: 0.3514 (mtp) REVERT: E 435 TYR cc_start: 0.2920 (m-80) cc_final: 0.2295 (m-10) REVERT: E 501 ARG cc_start: 0.2932 (mmm160) cc_final: 0.2395 (mtm-85) REVERT: E 576 ARG cc_start: 0.2664 (tpp-160) cc_final: 0.1853 (tpp80) REVERT: E 647 ARG cc_start: 0.4215 (ptt-90) cc_final: 0.3789 (ttm-80) REVERT: E 679 ARG cc_start: -0.0114 (OUTLIER) cc_final: -0.0872 (mmp80) REVERT: E 828 ARG cc_start: 0.6720 (mmm160) cc_final: 0.6448 (mmt-90) REVERT: E 898 HIS cc_start: 0.7819 (p-80) cc_final: 0.7385 (p-80) REVERT: E 922 ASP cc_start: 0.5486 (m-30) cc_final: 0.4854 (m-30) REVERT: E 1328 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7209 (mptt) REVERT: F 408 MET cc_start: 0.1875 (ptt) cc_final: 0.1271 (pmm) REVERT: F 519 GLU cc_start: 0.4652 (OUTLIER) cc_final: 0.4396 (tm-30) REVERT: F 593 LYS cc_start: 0.6114 (tppt) cc_final: 0.5622 (mtpt) REVERT: F 617 LEU cc_start: 0.0345 (OUTLIER) cc_final: -0.0007 (pp) REVERT: F 629 LEU cc_start: 0.4262 (OUTLIER) cc_final: 0.3930 (tt) REVERT: F 922 ASP cc_start: 0.7381 (m-30) cc_final: 0.6816 (t0) REVERT: F 1321 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6717 (mt) REVERT: G 987 MET cc_start: 0.2551 (tpt) cc_final: 0.2072 (tpt) REVERT: G 991 LYS cc_start: 0.3360 (pttp) cc_final: 0.3055 (ptmm) REVERT: G 1050 GLU cc_start: 0.5836 (tp30) cc_final: 0.4179 (pt0) REVERT: G 1099 GLU cc_start: 0.4782 (OUTLIER) cc_final: 0.4203 (mt-10) REVERT: G 1119 GLU cc_start: 0.3551 (OUTLIER) cc_final: 0.2848 (tt0) REVERT: G 1131 ARG cc_start: 0.2152 (mtp180) cc_final: 0.1557 (mtt90) outliers start: 85 outliers final: 49 residues processed: 376 average time/residue: 0.1993 time to fit residues: 117.0566 Evaluate side-chains 365 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 296 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 925 MET Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 495 GLU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 666 PHE Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 710 MET Chi-restraints excluded: chain D residue 800 ASN Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1323 THR Chi-restraints excluded: chain E residue 1329 LYS Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 692 ILE Chi-restraints excluded: chain F residue 699 GLN Chi-restraints excluded: chain F residue 710 MET Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 1048 ILE Chi-restraints excluded: chain G residue 1059 SER Chi-restraints excluded: chain G residue 1090 MET Chi-restraints excluded: chain G residue 1091 PHE Chi-restraints excluded: chain G residue 1099 GLU Chi-restraints excluded: chain G residue 1119 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 254 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 chunk 345 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 8 optimal weight: 0.0000 chunk 245 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 ASN C 510 HIS D 510 HIS ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 797 ASN E1340 ASN F 443 ASN F 727 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.191114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132816 restraints weight = 35248.924| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.39 r_work: 0.3299 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29708 Z= 0.182 Angle : 0.629 8.816 40140 Z= 0.306 Chirality : 0.044 0.147 4549 Planarity : 0.005 0.079 5129 Dihedral : 6.741 148.032 3929 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.09 % Allowed : 15.51 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.03 % 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: -0.83 (0.14), residues: 3583 helix: 0.28 (0.13), residues: 1775 sheet: -1.21 (0.27), residues: 336 loop : -1.34 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 858 TYR 0.015 0.002 TYR G1057 PHE 0.013 0.002 PHE E 610 TRP 0.012 0.001 TRP C 841 HIS 0.005 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00443 (29708) covalent geometry : angle 0.62858 (40140) hydrogen bonds : bond 0.03984 ( 1209) hydrogen bonds : angle 4.08746 ( 3519) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 302 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 GLU cc_start: 0.7263 (tt0) cc_final: 0.6792 (mm-30) REVERT: A 553 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.4972 (ptt90) REVERT: A 613 ASP cc_start: 0.7776 (t0) cc_final: 0.7426 (t0) REVERT: A 614 LYS cc_start: 0.7061 (ttpt) cc_final: 0.6631 (ttpp) REVERT: A 663 LYS cc_start: 0.7981 (pttm) cc_final: 0.7449 (pttt) REVERT: A 729 PHE cc_start: 0.7821 (m-80) cc_final: 0.7531 (m-80) REVERT: A 758 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5872 (tm-30) REVERT: A 888 ASP cc_start: 0.7540 (p0) cc_final: 0.7055 (t0) REVERT: A 915 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: A 1334 CYS cc_start: 0.7987 (p) cc_final: 0.7626 (m) REVERT: B 408 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4160 (tpp) REVERT: B 725 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7149 (tt) REVERT: B 803 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8644 (mt) REVERT: B 815 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7054 (mt-10) REVERT: B 881 LYS cc_start: 0.7459 (tppt) cc_final: 0.6959 (mmtt) REVERT: C 435 TYR cc_start: 0.7193 (m-80) cc_final: 0.6739 (m-80) REVERT: C 495 GLU cc_start: 0.5204 (OUTLIER) cc_final: 0.4783 (tt0) REVERT: C 573 ARG cc_start: 0.6328 (mtm-85) cc_final: 0.5568 (ttp-110) REVERT: C 708 ASP cc_start: 0.8233 (m-30) cc_final: 0.7894 (m-30) REVERT: C 1372 GLU cc_start: 0.7684 (tp30) cc_final: 0.7207 (tt0) REVERT: D 504 PHE cc_start: 0.4192 (m-80) cc_final: 0.3895 (m-80) REVERT: D 518 ASP cc_start: 0.5437 (OUTLIER) cc_final: 0.4922 (m-30) REVERT: D 546 MET cc_start: 0.4403 (OUTLIER) cc_final: 0.2895 (ppp) REVERT: D 554 GLN cc_start: 0.4952 (mp10) cc_final: 0.4151 (mt0) REVERT: D 643 PRO cc_start: 0.8064 (Cg_exo) cc_final: 0.7836 (Cg_endo) REVERT: D 666 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.6502 (t80) REVERT: D 671 LYS cc_start: 0.7811 (mtmt) cc_final: 0.6938 (ptmm) REVERT: D 755 SER cc_start: 0.6302 (m) cc_final: 0.5763 (p) REVERT: D 757 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6723 (pt0) REVERT: D 800 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8525 (t0) REVERT: D 898 HIS cc_start: 0.7879 (p-80) cc_final: 0.7628 (p-80) REVERT: D 936 LEU cc_start: 0.4997 (OUTLIER) cc_final: 0.4281 (mm) REVERT: D 1348 ASP cc_start: 0.8184 (t70) cc_final: 0.7865 (t0) REVERT: D 1365 ASP cc_start: 0.7610 (t0) cc_final: 0.7312 (t0) REVERT: D 1375 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7950 (mtmm) REVERT: E 428 MET cc_start: 0.3826 (mtp) cc_final: 0.3603 (mtp) REVERT: E 435 TYR cc_start: 0.2895 (m-80) cc_final: 0.2264 (m-10) REVERT: E 463 MET cc_start: 0.5097 (tpp) cc_final: 0.4804 (tpt) REVERT: E 501 ARG cc_start: 0.2948 (mmm160) cc_final: 0.2379 (mtm-85) REVERT: E 549 MET cc_start: 0.1429 (ttm) cc_final: 0.0629 (ptm) REVERT: E 576 ARG cc_start: 0.2490 (tpp-160) cc_final: 0.1903 (tpp80) REVERT: E 647 ARG cc_start: 0.4325 (ptt-90) cc_final: 0.3716 (ttm-80) REVERT: E 679 ARG cc_start: 0.0110 (OUTLIER) cc_final: -0.0860 (mmp80) REVERT: E 827 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7716 (ttmm) REVERT: E 898 HIS cc_start: 0.7733 (p-80) cc_final: 0.7307 (p-80) REVERT: E 922 ASP cc_start: 0.5573 (m-30) cc_final: 0.4909 (m-30) REVERT: E 1328 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7166 (mptt) REVERT: F 408 MET cc_start: 0.2054 (ptt) cc_final: 0.1460 (pmm) REVERT: F 593 LYS cc_start: 0.6116 (tppt) cc_final: 0.5626 (mtpt) REVERT: F 617 LEU cc_start: 0.0593 (OUTLIER) cc_final: 0.0178 (pp) REVERT: F 629 LEU cc_start: 0.4232 (OUTLIER) cc_final: 0.3913 (tt) REVERT: F 1321 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6538 (mt) REVERT: G 987 MET cc_start: 0.2637 (tpt) cc_final: 0.1949 (tpt) REVERT: G 1050 GLU cc_start: 0.5708 (tp30) cc_final: 0.4732 (tt0) REVERT: G 1068 ILE cc_start: 0.1918 (mm) cc_final: 0.1468 (tp) REVERT: G 1099 GLU cc_start: 0.4787 (OUTLIER) cc_final: 0.4215 (mt-10) REVERT: G 1119 GLU cc_start: 0.3620 (OUTLIER) cc_final: 0.2872 (tt0) REVERT: G 1131 ARG cc_start: 0.2253 (mtp180) cc_final: 0.1752 (mtt90) outliers start: 101 outliers final: 69 residues processed: 373 average time/residue: 0.1967 time to fit residues: 116.4749 Evaluate side-chains 378 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 291 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 925 MET Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 495 GLU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 510 HIS Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 666 PHE Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 698 ASP Chi-restraints excluded: chain D residue 710 MET Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 800 ASN Chi-restraints excluded: chain D residue 821 SER Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1323 THR Chi-restraints excluded: chain E residue 1329 LYS Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 692 ILE Chi-restraints excluded: chain F residue 699 GLN Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 1048 ILE Chi-restraints excluded: chain G residue 1059 SER Chi-restraints excluded: chain G residue 1090 MET Chi-restraints excluded: chain G residue 1091 PHE Chi-restraints excluded: chain G residue 1099 GLU Chi-restraints excluded: chain G residue 1119 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 18 optimal weight: 1.9990 chunk 266 optimal weight: 0.0970 chunk 65 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 24 optimal weight: 0.0070 chunk 131 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 331 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN C 511 GLN D 510 HIS ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1339 GLN E 829 GLN E1340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.194029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136371 restraints weight = 35199.902| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.35 r_work: 0.3360 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29708 Z= 0.103 Angle : 0.562 9.775 40140 Z= 0.274 Chirality : 0.041 0.146 4549 Planarity : 0.004 0.073 5129 Dihedral : 6.407 144.499 3929 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.39 % Allowed : 16.74 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.46 (0.15), residues: 3583 helix: 0.63 (0.13), residues: 1768 sheet: -1.14 (0.27), residues: 322 loop : -1.20 (0.17), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 680 TYR 0.017 0.001 TYR A 732 PHE 0.042 0.001 PHE D 442 TRP 0.010 0.001 TRP F 841 HIS 0.005 0.001 HIS D 510 Details of bonding type rmsd covalent geometry : bond 0.00230 (29708) covalent geometry : angle 0.56154 (40140) hydrogen bonds : bond 0.03330 ( 1209) hydrogen bonds : angle 3.87951 ( 3519) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 319 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 GLU cc_start: 0.6282 (tp30) cc_final: 0.5623 (tt0) REVERT: A 507 GLU cc_start: 0.7299 (tt0) cc_final: 0.6842 (mm-30) REVERT: A 548 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.5203 (p0) REVERT: A 553 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5785 (ptt180) REVERT: A 613 ASP cc_start: 0.7770 (t0) cc_final: 0.7350 (t0) REVERT: A 614 LYS cc_start: 0.6994 (ttpt) cc_final: 0.6598 (ttpp) REVERT: A 663 LYS cc_start: 0.7988 (pttm) cc_final: 0.7466 (pttt) REVERT: A 680 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7056 (tpt90) REVERT: A 725 LEU cc_start: 0.7017 (pp) cc_final: 0.6385 (tp) REVERT: A 729 PHE cc_start: 0.7612 (m-80) cc_final: 0.7358 (m-80) REVERT: A 758 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5806 (pm20) REVERT: A 888 ASP cc_start: 0.7304 (p0) cc_final: 0.6862 (t0) REVERT: A 915 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 1334 CYS cc_start: 0.7923 (p) cc_final: 0.7648 (m) REVERT: B 408 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.4102 (tpp) REVERT: B 593 LYS cc_start: 0.8135 (tttp) cc_final: 0.7688 (ttmt) REVERT: B 725 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7075 (tt) REVERT: B 803 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8594 (mt) REVERT: B 815 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7110 (mt-10) REVERT: B 878 SER cc_start: 0.7891 (p) cc_final: 0.7272 (m) REVERT: B 881 LYS cc_start: 0.7431 (tppt) cc_final: 0.6966 (mmtt) REVERT: C 435 TYR cc_start: 0.7030 (m-80) cc_final: 0.6783 (m-80) REVERT: C 481 PHE cc_start: 0.6952 (m-10) cc_final: 0.6716 (m-10) REVERT: C 483 ARG cc_start: 0.6531 (mmp-170) cc_final: 0.5542 (ttm-80) REVERT: C 495 GLU cc_start: 0.5206 (OUTLIER) cc_final: 0.4809 (tt0) REVERT: C 573 ARG cc_start: 0.6390 (mtm-85) cc_final: 0.5609 (ttp80) REVERT: C 708 ASP cc_start: 0.8195 (m-30) cc_final: 0.7854 (m-30) REVERT: C 1372 GLU cc_start: 0.7562 (tp30) cc_final: 0.7173 (tt0) REVERT: D 504 PHE cc_start: 0.4103 (m-80) cc_final: 0.3812 (m-80) REVERT: D 518 ASP cc_start: 0.5462 (OUTLIER) cc_final: 0.4970 (m-30) REVERT: D 546 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.2793 (ppp) REVERT: D 554 GLN cc_start: 0.4984 (mp10) cc_final: 0.4178 (mt0) REVERT: D 578 ASP cc_start: 0.5249 (OUTLIER) cc_final: 0.5042 (t70) REVERT: D 632 GLU cc_start: 0.5969 (mm-30) cc_final: 0.5653 (mm-30) REVERT: D 643 PRO cc_start: 0.8005 (Cg_exo) cc_final: 0.7740 (Cg_endo) REVERT: D 666 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.6515 (t80) REVERT: D 671 LYS cc_start: 0.7839 (mtmt) cc_final: 0.6945 (ptmm) REVERT: D 757 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6674 (pt0) REVERT: D 898 HIS cc_start: 0.7758 (p-80) cc_final: 0.7529 (p-80) REVERT: D 936 LEU cc_start: 0.4946 (OUTLIER) cc_final: 0.4289 (mm) REVERT: D 1348 ASP cc_start: 0.8123 (t70) cc_final: 0.7793 (t0) REVERT: D 1365 ASP cc_start: 0.7631 (t0) cc_final: 0.7321 (t0) REVERT: D 1375 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7974 (mtmm) REVERT: E 435 TYR cc_start: 0.2885 (m-80) cc_final: 0.2272 (m-10) REVERT: E 463 MET cc_start: 0.4999 (tpp) cc_final: 0.4537 (tpt) REVERT: E 501 ARG cc_start: 0.2908 (mmm160) cc_final: 0.2387 (mtm-85) REVERT: E 549 MET cc_start: 0.1310 (ttm) cc_final: 0.0478 (ttp) REVERT: E 627 ARG cc_start: 0.4668 (ptm160) cc_final: 0.4098 (ptt180) REVERT: E 647 ARG cc_start: 0.4270 (ptt-90) cc_final: 0.3693 (ttm-80) REVERT: E 679 ARG cc_start: -0.0034 (OUTLIER) cc_final: -0.0858 (mmp80) REVERT: E 828 ARG cc_start: 0.6697 (mmm160) cc_final: 0.6145 (mmt-90) REVERT: E 898 HIS cc_start: 0.7730 (p-80) cc_final: 0.7275 (p-80) REVERT: E 922 ASP cc_start: 0.5483 (m-30) cc_final: 0.4839 (m-30) REVERT: E 1328 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7181 (mptt) REVERT: F 408 MET cc_start: 0.2048 (ptt) cc_final: 0.1415 (pmm) REVERT: F 482 MET cc_start: 0.7010 (ttm) cc_final: 0.5768 (tpt) REVERT: F 593 LYS cc_start: 0.6103 (tppt) cc_final: 0.5600 (mtpt) REVERT: F 617 LEU cc_start: 0.0561 (OUTLIER) cc_final: 0.0134 (pp) REVERT: F 627 ARG cc_start: 0.2940 (mtt180) cc_final: 0.2733 (mtt-85) REVERT: F 629 LEU cc_start: 0.4161 (OUTLIER) cc_final: 0.3837 (tt) REVERT: F 891 ASP cc_start: 0.6209 (p0) cc_final: 0.6003 (t0) REVERT: F 922 ASP cc_start: 0.7366 (m-30) cc_final: 0.6836 (t0) REVERT: F 1321 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6538 (mt) REVERT: G 1050 GLU cc_start: 0.5665 (tp30) cc_final: 0.4860 (tt0) REVERT: G 1099 GLU cc_start: 0.4818 (OUTLIER) cc_final: 0.4312 (mt-10) REVERT: G 1119 GLU cc_start: 0.3532 (OUTLIER) cc_final: 0.2831 (tt0) REVERT: G 1131 ARG cc_start: 0.2093 (mtp180) cc_final: 0.1659 (mtt90) outliers start: 78 outliers final: 48 residues processed: 376 average time/residue: 0.2080 time to fit residues: 122.8849 Evaluate side-chains 375 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 307 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 925 MET Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 495 GLU Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 666 PHE Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 692 ILE Chi-restraints excluded: chain F residue 699 GLN Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 1048 ILE Chi-restraints excluded: chain G residue 1059 SER Chi-restraints excluded: chain G residue 1090 MET Chi-restraints excluded: chain G residue 1091 PHE Chi-restraints excluded: chain G residue 1099 GLU Chi-restraints excluded: chain G residue 1119 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 317 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 314 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 167 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 781 ASN B 562 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 511 GLN E 799 GLN E1340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.193046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134470 restraints weight = 35229.973| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.03 r_work: 0.3322 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29708 Z= 0.126 Angle : 0.576 10.146 40140 Z= 0.279 Chirality : 0.042 0.148 4549 Planarity : 0.004 0.077 5129 Dihedral : 6.408 144.191 3929 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.75 % Allowed : 16.77 % Favored : 80.48 % 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: -0.41 (0.15), residues: 3583 helix: 0.65 (0.13), residues: 1769 sheet: -1.07 (0.27), residues: 337 loop : -1.14 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 680 TYR 0.012 0.001 TYR G1057 PHE 0.033 0.001 PHE D 442 TRP 0.009 0.001 TRP G1054 HIS 0.004 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00297 (29708) covalent geometry : angle 0.57627 (40140) hydrogen bonds : bond 0.03506 ( 1209) hydrogen bonds : angle 3.89740 ( 3519) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 307 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 GLU cc_start: 0.7152 (tt0) cc_final: 0.6771 (mm-30) REVERT: A 548 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.5210 (p0) REVERT: A 553 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5924 (ptt180) REVERT: A 614 LYS cc_start: 0.6975 (ttpt) cc_final: 0.6515 (ttpp) REVERT: A 663 LYS cc_start: 0.7928 (pttm) cc_final: 0.7541 (pttt) REVERT: A 680 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6949 (tpt90) REVERT: A 725 LEU cc_start: 0.6996 (pp) cc_final: 0.6371 (tp) REVERT: A 729 PHE cc_start: 0.7668 (m-80) cc_final: 0.7346 (m-80) REVERT: A 758 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5946 (tm-30) REVERT: A 888 ASP cc_start: 0.7271 (p0) cc_final: 0.6855 (t0) REVERT: A 915 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 1334 CYS cc_start: 0.7756 (p) cc_final: 0.7540 (m) REVERT: B 408 MET cc_start: 0.4621 (OUTLIER) cc_final: 0.4245 (tpp) REVERT: B 725 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7238 (tt) REVERT: B 803 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8584 (mt) REVERT: B 815 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6802 (mt-10) REVERT: B 878 SER cc_start: 0.8002 (p) cc_final: 0.7392 (m) REVERT: B 881 LYS cc_start: 0.7360 (tppt) cc_final: 0.6848 (mmtt) REVERT: C 495 GLU cc_start: 0.5274 (OUTLIER) cc_final: 0.4857 (tt0) REVERT: C 573 ARG cc_start: 0.6448 (mtm-85) cc_final: 0.5726 (ttp80) REVERT: C 708 ASP cc_start: 0.7968 (m-30) cc_final: 0.7614 (m-30) REVERT: C 1372 GLU cc_start: 0.7420 (tp30) cc_final: 0.7059 (tt0) REVERT: D 504 PHE cc_start: 0.4168 (m-80) cc_final: 0.3816 (m-80) REVERT: D 518 ASP cc_start: 0.5444 (OUTLIER) cc_final: 0.4970 (m-30) REVERT: D 546 MET cc_start: 0.4355 (OUTLIER) cc_final: 0.2833 (ppp) REVERT: D 554 GLN cc_start: 0.4923 (mp10) cc_final: 0.4102 (mt0) REVERT: D 578 ASP cc_start: 0.5263 (OUTLIER) cc_final: 0.5027 (t70) REVERT: D 643 PRO cc_start: 0.8027 (Cg_exo) cc_final: 0.7799 (Cg_endo) REVERT: D 666 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.6395 (t80) REVERT: D 671 LYS cc_start: 0.7779 (mtmt) cc_final: 0.6921 (ptmm) REVERT: D 757 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6706 (pt0) REVERT: D 800 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8499 (t0) REVERT: D 898 HIS cc_start: 0.7689 (p-80) cc_final: 0.7456 (p-80) REVERT: D 936 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4263 (mm) REVERT: D 1348 ASP cc_start: 0.7844 (t70) cc_final: 0.7491 (t0) REVERT: D 1365 ASP cc_start: 0.7489 (t0) cc_final: 0.7225 (t0) REVERT: D 1375 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7892 (mtmm) REVERT: E 435 TYR cc_start: 0.2922 (m-80) cc_final: 0.2289 (m-10) REVERT: E 463 MET cc_start: 0.5021 (tpp) cc_final: 0.4589 (tpt) REVERT: E 501 ARG cc_start: 0.2908 (mmm160) cc_final: 0.2400 (mtm-85) REVERT: E 549 MET cc_start: 0.1382 (ttm) cc_final: 0.0539 (ptm) REVERT: E 576 ARG cc_start: 0.2467 (tpp-160) cc_final: 0.1764 (tpp80) REVERT: E 647 ARG cc_start: 0.4185 (ptt-90) cc_final: 0.3640 (ttm-80) REVERT: E 679 ARG cc_start: 0.0146 (OUTLIER) cc_final: -0.0862 (mmp80) REVERT: E 898 HIS cc_start: 0.7639 (p-80) cc_final: 0.7187 (p-80) REVERT: E 922 ASP cc_start: 0.5247 (m-30) cc_final: 0.4665 (m-30) REVERT: E 1328 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7252 (mptt) REVERT: F 408 MET cc_start: 0.2082 (ptt) cc_final: 0.1445 (pmm) REVERT: F 482 MET cc_start: 0.6904 (ttm) cc_final: 0.5871 (tpt) REVERT: F 593 LYS cc_start: 0.6058 (tppt) cc_final: 0.5577 (mtpt) REVERT: F 617 LEU cc_start: 0.0370 (OUTLIER) cc_final: -0.0016 (pp) REVERT: F 627 ARG cc_start: 0.2952 (mtt180) cc_final: 0.2751 (mtt-85) REVERT: F 629 LEU cc_start: 0.4175 (OUTLIER) cc_final: 0.3846 (tt) REVERT: F 922 ASP cc_start: 0.7204 (m-30) cc_final: 0.6814 (t0) REVERT: F 1321 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6522 (mt) REVERT: G 1050 GLU cc_start: 0.5733 (tp30) cc_final: 0.4803 (tt0) REVERT: G 1099 GLU cc_start: 0.4891 (OUTLIER) cc_final: 0.4397 (mt-10) REVERT: G 1119 GLU cc_start: 0.3442 (OUTLIER) cc_final: 0.2683 (tt0) REVERT: G 1131 ARG cc_start: 0.2178 (mtp180) cc_final: 0.1734 (mtt90) outliers start: 90 outliers final: 58 residues processed: 375 average time/residue: 0.2003 time to fit residues: 119.0475 Evaluate side-chains 376 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 925 MET Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 495 GLU Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 666 PHE Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 710 MET Chi-restraints excluded: chain D residue 800 ASN Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 887 ASP Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1323 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 692 ILE Chi-restraints excluded: chain F residue 699 GLN Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 1048 ILE Chi-restraints excluded: chain G residue 1059 SER Chi-restraints excluded: chain G residue 1090 MET Chi-restraints excluded: chain G residue 1091 PHE Chi-restraints excluded: chain G residue 1099 GLU Chi-restraints excluded: chain G residue 1119 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 253 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 82 optimal weight: 0.0370 chunk 321 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 355 optimal weight: 0.0070 chunk 330 optimal weight: 3.9990 chunk 245 optimal weight: 0.0010 chunk 156 optimal weight: 0.2980 overall best weight: 0.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN C 510 HIS C 820 GLN E1340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.194941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138465 restraints weight = 35112.468| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.38 r_work: 0.3423 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29708 Z= 0.098 Angle : 0.555 10.479 40140 Z= 0.270 Chirality : 0.041 0.145 4549 Planarity : 0.004 0.074 5129 Dihedral : 6.163 140.217 3929 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.14 % Allowed : 17.41 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.16 (0.15), residues: 3583 helix: 0.91 (0.13), residues: 1750 sheet: -0.99 (0.28), residues: 320 loop : -1.08 (0.17), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 501 TYR 0.013 0.001 TYR F 908 PHE 0.036 0.001 PHE D 442 TRP 0.009 0.001 TRP B 841 HIS 0.005 0.001 HIS C 510 Details of bonding type rmsd covalent geometry : bond 0.00215 (29708) covalent geometry : angle 0.55458 (40140) hydrogen bonds : bond 0.03195 ( 1209) hydrogen bonds : angle 3.80437 ( 3519) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 318 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 GLU cc_start: 0.6338 (tp30) cc_final: 0.5702 (tt0) REVERT: A 507 GLU cc_start: 0.7311 (tt0) cc_final: 0.6871 (mm-30) REVERT: A 553 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5595 (ptt180) REVERT: A 614 LYS cc_start: 0.6993 (ttpt) cc_final: 0.6587 (ttpp) REVERT: A 663 LYS cc_start: 0.7933 (pttm) cc_final: 0.7583 (pttt) REVERT: A 680 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6821 (tpt90) REVERT: A 725 LEU cc_start: 0.6994 (pp) cc_final: 0.6426 (tp) REVERT: A 729 PHE cc_start: 0.7576 (m-80) cc_final: 0.7240 (m-80) REVERT: A 758 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5846 (pm20) REVERT: A 888 ASP cc_start: 0.7299 (p0) cc_final: 0.6760 (t0) REVERT: A 915 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: A 1334 CYS cc_start: 0.7953 (p) cc_final: 0.7704 (m) REVERT: B 408 MET cc_start: 0.4582 (OUTLIER) cc_final: 0.4157 (tpp) REVERT: B 593 LYS cc_start: 0.8127 (tttp) cc_final: 0.7738 (ttmt) REVERT: B 725 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7147 (tt) REVERT: B 803 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8544 (mt) REVERT: B 815 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7123 (mt-10) REVERT: B 878 SER cc_start: 0.7836 (p) cc_final: 0.7219 (m) REVERT: B 881 LYS cc_start: 0.7441 (tppt) cc_final: 0.6976 (mmtt) REVERT: C 481 PHE cc_start: 0.7069 (m-10) cc_final: 0.6845 (m-10) REVERT: C 483 ARG cc_start: 0.6649 (mmp-170) cc_final: 0.5674 (ttm-80) REVERT: C 495 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.4934 (tt0) REVERT: C 573 ARG cc_start: 0.6577 (mtm-85) cc_final: 0.5869 (ttp-110) REVERT: C 708 ASP cc_start: 0.8188 (m-30) cc_final: 0.7792 (m-30) REVERT: C 1372 GLU cc_start: 0.7555 (tp30) cc_final: 0.7201 (tt0) REVERT: D 504 PHE cc_start: 0.4103 (m-80) cc_final: 0.3761 (m-80) REVERT: D 518 ASP cc_start: 0.5518 (OUTLIER) cc_final: 0.5068 (m-30) REVERT: D 546 MET cc_start: 0.4412 (OUTLIER) cc_final: 0.2939 (ppp) REVERT: D 554 GLN cc_start: 0.4971 (mp10) cc_final: 0.4108 (mt0) REVERT: D 578 ASP cc_start: 0.5320 (OUTLIER) cc_final: 0.5035 (t70) REVERT: D 601 LYS cc_start: 0.7503 (tptp) cc_final: 0.6841 (tttt) REVERT: D 632 GLU cc_start: 0.6002 (mm-30) cc_final: 0.5694 (mm-30) REVERT: D 643 PRO cc_start: 0.8015 (Cg_exo) cc_final: 0.7747 (Cg_endo) REVERT: D 658 LYS cc_start: 0.4985 (ptpp) cc_final: 0.4117 (mmtm) REVERT: D 666 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.6444 (t80) REVERT: D 671 LYS cc_start: 0.7804 (mtmt) cc_final: 0.6936 (ptmm) REVERT: D 756 TYR cc_start: 0.6399 (t80) cc_final: 0.6166 (t80) REVERT: D 757 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6615 (pt0) REVERT: D 936 LEU cc_start: 0.4792 (OUTLIER) cc_final: 0.4454 (mt) REVERT: D 1348 ASP cc_start: 0.8122 (t70) cc_final: 0.7809 (t0) REVERT: D 1365 ASP cc_start: 0.7565 (t0) cc_final: 0.7179 (t0) REVERT: D 1375 LYS cc_start: 0.8243 (ttmt) cc_final: 0.8012 (mtmm) REVERT: E 435 TYR cc_start: 0.2835 (m-80) cc_final: 0.2268 (m-10) REVERT: E 463 MET cc_start: 0.4986 (tpp) cc_final: 0.4733 (tpt) REVERT: E 501 ARG cc_start: 0.2901 (mmm160) cc_final: 0.2349 (mtm-85) REVERT: E 508 LYS cc_start: 0.5200 (mtpt) cc_final: 0.4758 (mtmt) REVERT: E 549 MET cc_start: 0.1224 (ttm) cc_final: 0.0441 (ptm) REVERT: E 627 ARG cc_start: 0.4589 (ptm160) cc_final: 0.4025 (ptt180) REVERT: E 647 ARG cc_start: 0.4146 (ptt-90) cc_final: 0.3649 (ttm-80) REVERT: E 679 ARG cc_start: 0.0012 (OUTLIER) cc_final: -0.0821 (mmp80) REVERT: E 827 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7858 (ttmm) REVERT: E 898 HIS cc_start: 0.7790 (p-80) cc_final: 0.7358 (p-80) REVERT: E 922 ASP cc_start: 0.5393 (m-30) cc_final: 0.4816 (m-30) REVERT: E 1328 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7275 (mptt) REVERT: F 408 MET cc_start: 0.1999 (ptt) cc_final: 0.1332 (pmm) REVERT: F 482 MET cc_start: 0.6902 (ttm) cc_final: 0.5876 (tpt) REVERT: F 593 LYS cc_start: 0.6041 (tppt) cc_final: 0.5561 (mtpt) REVERT: F 617 LEU cc_start: 0.0601 (OUTLIER) cc_final: 0.0194 (pp) REVERT: F 629 LEU cc_start: 0.4147 (OUTLIER) cc_final: 0.3800 (tt) REVERT: F 922 ASP cc_start: 0.7302 (m-30) cc_final: 0.6867 (t0) REVERT: F 1321 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6557 (mt) REVERT: G 1050 GLU cc_start: 0.5783 (tp30) cc_final: 0.5219 (mm-30) REVERT: G 1099 GLU cc_start: 0.5005 (OUTLIER) cc_final: 0.4446 (mt-10) REVERT: G 1119 GLU cc_start: 0.3392 (OUTLIER) cc_final: 0.2695 (tt0) REVERT: G 1131 ARG cc_start: 0.2289 (mtp180) cc_final: 0.1838 (mtt90) outliers start: 70 outliers final: 42 residues processed: 368 average time/residue: 0.2111 time to fit residues: 121.0988 Evaluate side-chains 355 residues out of total 3268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 495 GLU Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 666 PHE Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 699 GLN Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 1048 ILE Chi-restraints excluded: chain G residue 1059 SER Chi-restraints excluded: chain G residue 1091 PHE Chi-restraints excluded: chain G residue 1099 GLU Chi-restraints excluded: chain G residue 1119 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 349 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 256 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 302 optimal weight: 0.0000 chunk 89 optimal weight: 8.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 HIS ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.193282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135436 restraints weight = 35228.520| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.05 r_work: 0.3364 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29708 Z= 0.135 Angle : 0.587 10.691 40140 Z= 0.285 Chirality : 0.042 0.210 4549 Planarity : 0.005 0.074 5129 Dihedral : 6.285 137.902 3929 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.45 % Allowed : 17.32 % Favored : 80.23 % 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: -0.25 (0.15), residues: 3583 helix: 0.76 (0.13), residues: 1771 sheet: -0.98 (0.27), residues: 337 loop : -1.05 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 501 TYR 0.012 0.001 TYR G1057 PHE 0.032 0.001 PHE D 442 TRP 0.009 0.001 TRP G1054 HIS 0.005 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00323 (29708) covalent geometry : angle 0.58691 (40140) hydrogen bonds : bond 0.03558 ( 1209) hydrogen bonds : angle 3.89775 ( 3519) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9543.44 seconds wall clock time: 163 minutes 28.69 seconds (9808.69 seconds total)