Starting phenix.real_space_refine on Sat Aug 8 05:48:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31ib_58426/08_2026/31ib_58426.cif Found real_map, /net/cci-nas-00/data/ceres_data/31ib_58426/08_2026/31ib_58426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/31ib_58426/08_2026/31ib_58426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31ib_58426/08_2026/31ib_58426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/31ib_58426/08_2026/31ib_58426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31ib_58426/08_2026/31ib_58426.map" } resolution = 2.83 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= 0.012 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: 8 Type Number sf(0) Gaussians Al 4 5.89 5 P 12 5.49 5 Mg 4 5.21 5 S 120 5.16 5 C 16056 2.51 5 N 4364 2.21 5 O 4850 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25422 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "B" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "C" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "D" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "E" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "F" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "G" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 26 residue: pdb=" N UNK G 74 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 74 " occ=0.50 residue: pdb=" N UNK G 75 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 75 " occ=0.50 residue: pdb=" N UNK G 76 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 76 " occ=0.50 residue: pdb=" N UNK G 77 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 77 " occ=0.50 residue: pdb=" N UNK G 78 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 78 " occ=0.50 residue: pdb=" N UNK G 79 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 79 " occ=0.50 residue: pdb=" N UNK G 80 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 80 " occ=0.50 residue: pdb=" N UNK G 81 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 81 " occ=0.50 residue: pdb=" N UNK G 82 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 82 " occ=0.50 residue: pdb=" N UNK G 83 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 83 " occ=0.50 residue: pdb=" N UNK G 84 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 84 " occ=0.50 residue: pdb=" N UNK G 85 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 85 " occ=0.50 ... (remaining 14 not shown) Time building chain proxies: 5.79, per 1000 atoms: 0.23 Number of scatterers: 25422 At special positions: 0 Unit cell: (135.78, 132.13, 139.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 120 16.00 P 12 15.00 Al 4 13.00 Mg 4 11.99 F 12 9.00 O 4850 8.00 N 4364 7.00 C 16056 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=1, symmetry=0 Links applied TRANS " UNK H 75 " - " UNK G 85 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6028 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 32 sheets defined 52.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 412 through 424 removed outlier: 3.563A pdb=" N ALA A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.596A pdb=" N GLU A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 530 through 541 removed outlier: 4.517A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 591 through 595 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.770A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 4.109A pdb=" N ALA A 617 " --> pdb=" O PRO A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.755A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 653 " --> pdb=" O LEU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 834 through 837 Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 924 through 929 removed outlier: 3.578A pdb=" N THR A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.903A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.303A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.547A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.551A pdb=" N GLU B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'B' and resid 530 through 541 removed outlier: 4.471A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 580 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.590A pdb=" N ILE B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 611 removed outlier: 4.335A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.923A pdb=" N ALA B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 618 " --> pdb=" O GLN B 615 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 614 through 619' Processing helix chain 'B' and resid 641 through 645 removed outlier: 3.724A pdb=" N THR B 644 " --> pdb=" O VAL B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.735A pdb=" N MET B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 741 through 747 removed outlier: 4.021A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 Processing helix chain 'B' and resid 853 through 855 No H-bonds generated for 'chain 'B' and resid 853 through 855' Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 924 through 929 removed outlier: 3.578A pdb=" N THR B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.936A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.730A pdb=" N LEU C 425 " --> pdb=" O PHE C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 448 removed outlier: 3.815A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 494 through 512 removed outlier: 3.586A pdb=" N LYS C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 541 removed outlier: 4.217A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 580 Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 602 through 611 removed outlier: 4.000A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 618 removed outlier: 3.756A pdb=" N ALA C 617 " --> pdb=" O GLU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 645 removed outlier: 3.784A pdb=" N THR C 644 " --> pdb=" O VAL C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.713A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 730 removed outlier: 3.604A pdb=" N GLY C 730 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 747 Processing helix chain 'C' and resid 808 through 829 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 924 through 929 Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.958A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 423 removed outlier: 3.612A pdb=" N GLU D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.561A pdb=" N ASN D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 489 Processing helix chain 'D' and resid 494 through 512 removed outlier: 3.531A pdb=" N LYS D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 541 removed outlier: 4.000A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 535 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.509A pdb=" N ILE D 595 " --> pdb=" O VAL D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 611 removed outlier: 3.696A pdb=" N ALA D 606 " --> pdb=" O ASP D 602 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 618 removed outlier: 3.765A pdb=" N ALA D 617 " --> pdb=" O GLU D 614 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN D 618 " --> pdb=" O GLN D 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 614 through 618' Processing helix chain 'D' and resid 641 through 645 removed outlier: 4.060A pdb=" N THR D 644 " --> pdb=" O VAL D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.697A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 685 through 687 No H-bonds generated for 'chain 'D' and resid 685 through 687' Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 742 through 747 Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 833 through 838 removed outlier: 3.510A pdb=" N THR D 837 " --> pdb=" O ASP D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 855 No H-bonds generated for 'chain 'D' and resid 853 through 855' Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 924 through 929 Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.898A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 425 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.861A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 467 Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'E' and resid 494 through 511 Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 571 through 580 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.623A pdb=" N ILE E 595 " --> pdb=" O VAL E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 611 removed outlier: 3.928A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 617 removed outlier: 4.220A pdb=" N ALA E 617 " --> pdb=" O PRO E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 652 removed outlier: 3.592A pdb=" N ARG E 652 " --> pdb=" O PRO E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 692 through 703 Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 741 through 745 Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 833 through 837 Processing helix chain 'E' and resid 853 through 855 No H-bonds generated for 'chain 'E' and resid 853 through 855' Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 922 Processing helix chain 'E' and resid 924 through 929 Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.946A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 425 Processing helix chain 'F' and resid 431 through 447 removed outlier: 4.064A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 468 removed outlier: 3.609A pdb=" N ILE F 468 " --> pdb=" O TRP F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 489 Processing helix chain 'F' and resid 494 through 511 Processing helix chain 'F' and resid 528 through 540 Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.926A pdb=" N LYS F 594 " --> pdb=" O GLU F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 612 removed outlier: 3.760A pdb=" N LEU F 607 " --> pdb=" O PRO F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 662 through 673 removed outlier: 3.617A pdb=" N ILE F 669 " --> pdb=" O GLU F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.511A pdb=" N SER F 729 " --> pdb=" O TYR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 741 Processing helix chain 'F' and resid 742 through 747 Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 853 through 855 No H-bonds generated for 'chain 'F' and resid 853 through 855' Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 924 through 929 Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.838A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.650A pdb=" N ILE A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR A 638 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 589 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 519 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA A 639 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE A 521 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE A 518 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE A 656 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 620 Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690 removed outlier: 3.697A pdb=" N LYS A 690 " --> pdb=" O VAL A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 799 through 803 removed outlier: 6.047A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N MET A 766 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 910 " --> pdb=" O HIS A 934 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL A 936 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 912 " --> pdb=" O VAL A 936 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.530A pdb=" N ILE B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR B 638 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 589 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS B 517 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N CYS B 637 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 519 " --> pdb=" O CYS B 637 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ALA B 639 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE B 521 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 689 through 690 removed outlier: 3.925A pdb=" N LYS B 690 " --> pdb=" O VAL B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 764 through 770 removed outlier: 6.214A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.893A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 910 " --> pdb=" O HIS B 934 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL B 936 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 912 " --> pdb=" O VAL B 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB1, first strand: chain 'C' and resid 544 through 546 removed outlier: 5.780A pdb=" N LYS C 517 " --> pdb=" O PHE C 635 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N CYS C 637 " --> pdb=" O LYS C 517 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 519 " --> pdb=" O CYS C 637 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA C 639 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE C 521 " --> pdb=" O ALA C 639 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 619 through 620 Processing sheet with id=AB3, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.994A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 764 through 769 removed outlier: 5.917A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 805 through 806 removed outlier: 6.078A pdb=" N GLN C 805 " --> pdb=" O LYS C 851 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AB7, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB8, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.855A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 587 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR D 638 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE D 589 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS D 517 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N CYS D 637 " --> pdb=" O LYS D 517 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 519 " --> pdb=" O CYS D 637 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA D 639 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE D 521 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 619 through 620 Processing sheet with id=AC1, first strand: chain 'D' and resid 689 through 691 removed outlier: 3.544A pdb=" N LYS D 690 " --> pdb=" O VAL D 735 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 737 " --> pdb=" O LYS D 690 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 765 through 771 removed outlier: 6.076A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 878 through 879 Processing sheet with id=AC4, first strand: chain 'D' and resid 882 through 884 removed outlier: 4.065A pdb=" N LYS D 888 " --> pdb=" O SER D 884 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.524A pdb=" N ILE E 587 " --> pdb=" O ILE E 636 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N THR E 638 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE E 589 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS E 517 " --> pdb=" O PHE E 635 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N CYS E 637 " --> pdb=" O LYS E 517 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU E 519 " --> pdb=" O CYS E 637 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ALA E 639 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE E 521 " --> pdb=" O ALA E 639 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.832A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 764 through 771 removed outlier: 7.037A pdb=" N HIS E 839 " --> pdb=" O ARG E 785 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 878 through 879 removed outlier: 3.518A pdb=" N ILE E 910 " --> pdb=" O GLU E 932 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 544 through 546 removed outlier: 7.009A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 689 through 691 removed outlier: 3.501A pdb=" N LYS F 690 " --> pdb=" O VAL F 735 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 765 through 769 removed outlier: 5.906A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 877 through 879 Processing sheet with id=AD4, first strand: chain 'F' and resid 882 through 883 Processing sheet with id=AD5, first strand: chain 'G' and resid 80 through 83 removed outlier: 3.617A pdb=" N UNK G 81 " --> pdb=" O UNK H 80 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N UNK G 83 " --> pdb=" O UNK H 78 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3321 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: 5.36 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8445 1.34 - 1.46: 4374 1.46 - 1.58: 12833 1.58 - 1.69: 30 1.69 - 1.81: 198 Bond restraints: 25880 Sorted by residual: bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.455 0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.456 0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C4 ADP C1001 " pdb=" C5 ADP C1001 " ideal model delta sigma weight residual 1.490 1.458 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" C4 ADP D1001 " pdb=" C5 ADP D1001 " ideal model delta sigma weight residual 1.490 1.459 0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C4 ADP E1001 " pdb=" C5 ADP E1001 " ideal model delta sigma weight residual 1.490 1.459 0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 25875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 34609 2.19 - 4.37: 389 4.37 - 6.56: 37 6.56 - 8.74: 6 8.74 - 10.93: 1 Bond angle restraints: 35042 Sorted by residual: angle pdb=" O2B ADP E1001 " pdb=" PB ADP E1001 " pdb=" O3A ADP E1001 " ideal model delta sigma weight residual 108.20 97.27 10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" CA VAL D 626 " pdb=" C VAL D 626 " pdb=" N PRO D 627 " ideal model delta sigma weight residual 116.57 119.25 -2.68 9.80e-01 1.04e+00 7.46e+00 angle pdb=" N LYS F 432 " pdb=" CA LYS F 432 " pdb=" C LYS F 432 " ideal model delta sigma weight residual 111.28 114.23 -2.95 1.09e+00 8.42e-01 7.30e+00 angle pdb=" N GLU E 846 " pdb=" CA GLU E 846 " pdb=" C GLU E 846 " ideal model delta sigma weight residual 110.91 107.88 3.03 1.17e+00 7.31e-01 6.70e+00 angle pdb=" C GLN F 515 " pdb=" CA GLN F 515 " pdb=" CB GLN F 515 " ideal model delta sigma weight residual 110.42 115.23 -4.81 1.99e+00 2.53e-01 5.83e+00 ... (remaining 35037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 15549 35.68 - 71.36: 213 71.36 - 107.04: 12 107.04 - 142.72: 6 142.72 - 178.41: 1 Dihedral angle restraints: 15781 sinusoidal: 6410 harmonic: 9371 Sorted by residual: dihedral pdb=" CA UNK G 85 " pdb=" N UNK G 85 " pdb=" C UNK H 75 " pdb=" CA UNK H 75 " ideal model delta harmonic sigma weight residual 180.00 1.59 178.41 0 5.00e+00 4.00e-02 1.27e+03 dihedral pdb=" O2A ADP C1001 " pdb=" O3A ADP C1001 " pdb=" PA ADP C1001 " pdb=" PB ADP C1001 " ideal model delta sinusoidal sigma weight residual -60.00 69.74 -129.74 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual 300.00 176.68 123.32 1 2.00e+01 2.50e-03 3.72e+01 ... (remaining 15778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2318 0.030 - 0.061: 1118 0.061 - 0.091: 359 0.091 - 0.121: 178 0.121 - 0.151: 25 Chirality restraints: 3998 Sorted by residual: chirality pdb=" CA ILE F 645 " pdb=" N ILE F 645 " pdb=" C ILE F 645 " pdb=" CB ILE F 645 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA PRO C 603 " pdb=" N PRO C 603 " pdb=" C PRO C 603 " pdb=" CB PRO C 603 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA PRO D 845 " pdb=" N PRO D 845 " pdb=" C PRO D 845 " pdb=" CB PRO D 845 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 3995 not shown) Planarity restraints: 4507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N UNK G 85 " 0.071 2.00e-02 2.50e+03 6.30e-02 3.97e+01 pdb=" CA UNK H 75 " 0.001 2.00e-02 2.50e+03 pdb=" C UNK H 75 " -0.100 2.00e-02 2.50e+03 pdb=" O UNK H 75 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 947 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO D 948 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 948 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 948 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 430 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 431 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " -0.026 5.00e-02 4.00e+02 ... (remaining 4504 not shown) Histogram of nonbonded interaction distances: 0.23 - 1.16: 72 1.16 - 2.10: 185 2.10 - 3.03: 16508 3.03 - 3.97: 66902 3.97 - 4.90: 130338 Warning: very small nonbonded interaction distances. Nonbonded interactions: 214005 Sorted by model distance: nonbonded pdb=" CA UNK G 86 " pdb=" CA UNK H 74 " model vdw 0.229 3.900 nonbonded pdb=" CB UNK G 74 " pdb=" CB UNK H 86 " model vdw 0.291 3.840 nonbonded pdb=" C UNK G 85 " pdb=" N UNK H 75 " model vdw 0.317 3.350 nonbonded pdb=" CB UNK G 85 " pdb=" CB UNK H 75 " model vdw 0.318 3.840 nonbonded pdb=" CB UNK G 80 " pdb=" CB UNK H 80 " model vdw 0.352 3.840 ... (remaining 214000 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 412 through 1001) selection = (chain 'B' and resid 412 through 1001) selection = (chain 'C' and resid 412 through 1001) selection = (chain 'D' and resid 412 through 1001) selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.930 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.040 Process input model: 24.190 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 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 : 0.008 0.838 25882 Z= 0.444 Angle : 0.759 54.317 35045 Z= 0.408 Chirality : 0.042 0.151 3998 Planarity : 0.005 0.054 4506 Dihedral : 12.604 129.738 9750 Min Nonbonded Distance : 0.229 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.45 % Favored : 94.98 % Rotamer: Outliers : 1.68 % Allowed : 6.51 % Favored : 91.81 % 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: -1.26 (0.14), residues: 3210 helix: -1.47 (0.10), residues: 1432 sheet: -1.95 (0.23), residues: 403 loop : 0.63 (0.18), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 904 TYR 0.017 0.002 TYR E 939 PHE 0.017 0.001 PHE C 547 TRP 0.004 0.001 TRP F 464 HIS 0.005 0.001 HIS B 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (25880) covalent geometry : angle 0.62954 / 0.34 (35042) hydrogen bonds : bond 0.14453 / 9.64 ( 1149) hydrogen bonds : angle 6.63487 / 4.61 ( 3321) Misc. bond : bond 0.07157 / 3.77 ( 1) link_TRANS : bond 0.83826 / 44.12 ( 1) link_TRANS : angle 45.89594 / 35.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 358 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 652 ARG cc_start: 0.8658 (mmt-90) cc_final: 0.8433 (mpt180) REVERT: A 685 ASP cc_start: 0.8034 (t70) cc_final: 0.7705 (t70) REVERT: A 690 LYS cc_start: 0.8853 (mttp) cc_final: 0.8577 (mttt) REVERT: A 706 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: A 753 VAL cc_start: 0.8809 (t) cc_final: 0.8478 (t) REVERT: A 799 SER cc_start: 0.9021 (m) cc_final: 0.8750 (p) REVERT: B 423 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 450 ASN cc_start: 0.8327 (m-40) cc_final: 0.8011 (t0) REVERT: B 686 GLU cc_start: 0.7947 (mp0) cc_final: 0.7666 (mm-30) REVERT: B 826 MET cc_start: 0.8209 (ptp) cc_final: 0.7919 (tmm) REVERT: C 417 ILE cc_start: 0.8391 (mt) cc_final: 0.8190 (tt) REVERT: C 419 GLU cc_start: 0.8729 (tp30) cc_final: 0.8427 (tt0) REVERT: C 435 MET cc_start: 0.8627 (tpt) cc_final: 0.8356 (mmm) REVERT: C 454 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7850 (mm-30) REVERT: C 489 GLU cc_start: 0.8439 (pt0) cc_final: 0.8091 (mm-30) REVERT: C 579 LYS cc_start: 0.8674 (tptt) cc_final: 0.8428 (ttmm) REVERT: C 691 LEU cc_start: 0.8735 (pp) cc_final: 0.8491 (pp) REVERT: C 785 ARG cc_start: 0.8539 (ttp80) cc_final: 0.7848 (ttp80) REVERT: C 937 GLU cc_start: 0.8948 (pt0) cc_final: 0.8196 (pm20) REVERT: D 417 ILE cc_start: 0.8462 (mm) cc_final: 0.8111 (mp) REVERT: D 420 LYS cc_start: 0.8607 (ptmm) cc_final: 0.8406 (ptmm) REVERT: D 482 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8044 (ttt180) REVERT: D 490 ASP cc_start: 0.8518 (m-30) cc_final: 0.8254 (m-30) REVERT: D 647 GLU cc_start: 0.8484 (tp30) cc_final: 0.8052 (tp30) REVERT: D 736 GLU cc_start: 0.8193 (pm20) cc_final: 0.7980 (mm-30) REVERT: D 773 MET cc_start: 0.7610 (pp-130) cc_final: 0.7164 (pp-130) REVERT: D 919 ASP cc_start: 0.7604 (t0) cc_final: 0.7343 (m-30) REVERT: D 937 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8595 (mt-10) REVERT: E 417 ILE cc_start: 0.6885 (mm) cc_final: 0.6505 (tt) REVERT: E 435 MET cc_start: 0.8657 (tpt) cc_final: 0.8242 (tpp) REVERT: E 460 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7865 (m110) REVERT: E 554 ASP cc_start: 0.7633 (t70) cc_final: 0.7106 (t0) REVERT: E 557 GLU cc_start: 0.7999 (mp0) cc_final: 0.7486 (mp0) REVERT: E 625 ASP cc_start: 0.8470 (m-30) cc_final: 0.7733 (t0) REVERT: E 826 MET cc_start: 0.8496 (ttm) cc_final: 0.8155 (tmm) REVERT: E 922 ASP cc_start: 0.8410 (t70) cc_final: 0.8183 (m-30) REVERT: F 424 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7424 (ttm170) REVERT: F 432 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8252 (tmtt) REVERT: F 436 ASP cc_start: 0.8278 (p0) cc_final: 0.7588 (m-30) REVERT: F 441 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7233 (tp30) REVERT: F 751 PHE cc_start: 0.7952 (m-80) cc_final: 0.7669 (m-80) REVERT: F 808 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7863 (mm-30) REVERT: F 810 MET cc_start: 0.8391 (ttt) cc_final: 0.8124 (ttt) REVERT: F 846 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8310 (tt0) outliers start: 46 outliers final: 13 residues processed: 397 average time/residue: 0.7312 time to fit residues: 327.3621 Evaluate side-chains 241 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 225 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain F residue 432 LYS Chi-restraints excluded: chain F residue 515 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 GLN ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN D 477 ASN E 515 GLN F 477 ASN F 622 HIS F 934 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.072662 restraints weight = 41188.262| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.42 r_work: 0.2701 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25882 Z= 0.182 Angle : 0.723 14.530 35045 Z= 0.356 Chirality : 0.044 0.291 3998 Planarity : 0.005 0.125 4506 Dihedral : 9.079 134.197 3615 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 2.41 % Allowed : 10.89 % Favored : 86.70 % 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: 0.01 (0.14), residues: 3210 helix: 0.52 (0.12), residues: 1453 sheet: -1.21 (0.24), residues: 403 loop : 0.04 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.038 0.002 TYR E 565 PHE 0.020 0.001 PHE C 547 TRP 0.012 0.001 TRP F 770 HIS 0.008 0.001 HIS F 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (25880) covalent geometry : angle 0.71885 / 0.35 (35042) hydrogen bonds : bond 0.04591 / 3.01 ( 1149) hydrogen bonds : angle 5.10971 / 3.51 ( 3321) Misc. bond : bond 0.00313 / 0.16 ( 1) link_TRANS : bond 0.08693 / 4.58 ( 1) link_TRANS : angle 8.55573 / 7.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 249 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 LYS cc_start: 0.8943 (mttp) cc_final: 0.8658 (mttt) REVERT: A 706 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: B 415 ASP cc_start: 0.7695 (m-30) cc_final: 0.7456 (m-30) REVERT: B 419 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 450 ASN cc_start: 0.8355 (m-40) cc_final: 0.8089 (t0) REVERT: B 563 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8709 (ptt-90) REVERT: B 686 GLU cc_start: 0.8100 (mp0) cc_final: 0.7837 (mm-30) REVERT: C 419 GLU cc_start: 0.8815 (tp30) cc_final: 0.8549 (tt0) REVERT: C 435 MET cc_start: 0.8779 (tpt) cc_final: 0.8492 (mmm) REVERT: C 454 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7943 (mm-30) REVERT: C 690 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8212 (mmmt) REVERT: C 785 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8149 (ttp80) REVERT: C 937 GLU cc_start: 0.8973 (pt0) cc_final: 0.8424 (pm20) REVERT: D 417 ILE cc_start: 0.8397 (mm) cc_final: 0.8082 (mp) REVERT: D 490 ASP cc_start: 0.8740 (m-30) cc_final: 0.8463 (m-30) REVERT: D 647 GLU cc_start: 0.8684 (tp30) cc_final: 0.8232 (tp30) REVERT: D 773 MET cc_start: 0.7788 (pp-130) cc_final: 0.7459 (pp-130) REVERT: D 929 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8087 (pp20) REVERT: E 417 ILE cc_start: 0.7224 (mm) cc_final: 0.6890 (tt) REVERT: E 435 MET cc_start: 0.8633 (tpt) cc_final: 0.8275 (tpp) REVERT: E 554 ASP cc_start: 0.7762 (t70) cc_final: 0.7176 (t0) REVERT: E 557 GLU cc_start: 0.8155 (mp0) cc_final: 0.7601 (mp0) REVERT: E 625 ASP cc_start: 0.8371 (m-30) cc_final: 0.7673 (t0) REVERT: E 826 MET cc_start: 0.8706 (ttm) cc_final: 0.8407 (tmm) REVERT: E 922 ASP cc_start: 0.8533 (t70) cc_final: 0.8046 (m-30) REVERT: F 432 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8314 (pptt) REVERT: F 436 ASP cc_start: 0.8223 (p0) cc_final: 0.7490 (m-30) REVERT: F 440 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7351 (pp20) REVERT: F 441 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7343 (tp30) REVERT: F 651 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: F 846 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8409 (mt-10) REVERT: F 915 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8785 (mt-10) outliers start: 66 outliers final: 18 residues processed: 297 average time/residue: 0.6916 time to fit residues: 233.3001 Evaluate side-chains 234 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 788 GLN Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 515 GLN Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 432 LYS Chi-restraints excluded: chain F residue 651 ASP Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 269 optimal weight: 10.0000 chunk 184 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 233 optimal weight: 0.2980 chunk 181 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 255 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 HIS C 456 ASN E 460 ASN ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 677 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.102335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.075942 restraints weight = 40923.410| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.33 r_work: 0.2800 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25882 Z= 0.145 Angle : 0.627 13.362 35045 Z= 0.308 Chirality : 0.041 0.187 3998 Planarity : 0.005 0.096 4506 Dihedral : 8.335 132.499 3598 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 2.52 % Allowed : 12.21 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3210 helix: 1.32 (0.13), residues: 1461 sheet: -0.82 (0.24), residues: 404 loop : -0.08 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 422 TYR 0.017 0.002 TYR C 565 PHE 0.015 0.001 PHE C 547 TRP 0.020 0.001 TRP F 770 HIS 0.006 0.001 HIS F 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (25880) covalent geometry : angle 0.62293 / 0.31 (35042) hydrogen bonds : bond 0.03683 / 2.38 ( 1149) hydrogen bonds : angle 4.64245 / 3.19 ( 3321) Misc. bond : bond 0.00071 / 0.04 ( 1) link_TRANS : bond 0.06256 / 3.29 ( 1) link_TRANS : angle 7.90418 / 5.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 241 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 LYS cc_start: 0.8949 (mttp) cc_final: 0.8742 (mttt) REVERT: A 706 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: A 717 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 415 ASP cc_start: 0.7661 (m-30) cc_final: 0.7403 (m-30) REVERT: B 690 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7792 (ptmm) REVERT: C 419 GLU cc_start: 0.8829 (tp30) cc_final: 0.8603 (tt0) REVERT: C 435 MET cc_start: 0.8864 (tpt) cc_final: 0.8656 (mmm) REVERT: C 454 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7965 (mm-30) REVERT: C 579 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8561 (ttpp) REVERT: C 690 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8238 (tppp) REVERT: C 691 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8627 (pp) REVERT: C 785 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8397 (ttp80) REVERT: C 937 GLU cc_start: 0.8937 (pt0) cc_final: 0.8585 (pm20) REVERT: D 647 GLU cc_start: 0.8738 (tp30) cc_final: 0.8275 (tp30) REVERT: D 686 GLU cc_start: 0.8332 (mp0) cc_final: 0.8054 (tm-30) REVERT: D 773 MET cc_start: 0.7865 (pp-130) cc_final: 0.7416 (pp-130) REVERT: D 929 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8165 (pp20) REVERT: E 417 ILE cc_start: 0.7396 (mm) cc_final: 0.7060 (tt) REVERT: E 435 MET cc_start: 0.8651 (tpt) cc_final: 0.8341 (tpp) REVERT: E 515 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: E 554 ASP cc_start: 0.7745 (t70) cc_final: 0.7243 (t0) REVERT: E 557 GLU cc_start: 0.8282 (mp0) cc_final: 0.7657 (mp0) REVERT: E 625 ASP cc_start: 0.8347 (m-30) cc_final: 0.7657 (OUTLIER) REVERT: E 915 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: E 922 ASP cc_start: 0.8586 (t70) cc_final: 0.8184 (m-30) REVERT: F 436 ASP cc_start: 0.8137 (p0) cc_final: 0.7311 (m-30) REVERT: F 440 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7347 (pp20) REVERT: F 546 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8809 (tmt90) REVERT: F 647 GLU cc_start: 0.7346 (tp30) cc_final: 0.7125 (tp30) REVERT: F 908 THR cc_start: 0.8946 (m) cc_final: 0.8615 (p) REVERT: F 915 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8725 (mt-10) outliers start: 69 outliers final: 25 residues processed: 290 average time/residue: 0.7439 time to fit residues: 246.1737 Evaluate side-chains 234 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 515 GLN Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 547 PHE Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 751 PHE Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 68 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 316 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 HIS A 600 GLN B 433 HIS C 456 ASN ** E 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.072336 restraints weight = 40979.761| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.39 r_work: 0.2717 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25882 Z= 0.175 Angle : 0.629 12.060 35045 Z= 0.307 Chirality : 0.042 0.204 3998 Planarity : 0.004 0.082 4506 Dihedral : 8.245 134.764 3593 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 2.96 % Allowed : 12.61 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3210 helix: 1.58 (0.13), residues: 1464 sheet: -0.51 (0.25), residues: 402 loop : -0.23 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 459 TYR 0.045 0.002 TYR B 599 PHE 0.021 0.001 PHE C 547 TRP 0.025 0.001 TRP F 770 HIS 0.006 0.001 HIS F 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (25880) covalent geometry : angle 0.62671 / 0.31 (35042) hydrogen bonds : bond 0.03926 / 2.54 ( 1149) hydrogen bonds : angle 4.58339 / 3.15 ( 3321) Misc. bond : bond 0.00111 / 0.06 ( 1) link_TRANS : bond 0.05424 / 2.85 ( 1) link_TRANS : angle 5.77407 / 3.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 229 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 LYS cc_start: 0.8935 (mttp) cc_final: 0.8733 (mttt) REVERT: B 690 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7843 (ptmm) REVERT: C 419 GLU cc_start: 0.8823 (tp30) cc_final: 0.8598 (tt0) REVERT: C 435 MET cc_start: 0.8856 (tpt) cc_final: 0.8636 (mmm) REVERT: C 454 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7961 (mm-30) REVERT: C 579 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8535 (ttpp) REVERT: C 690 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8061 (tppp) REVERT: C 785 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8420 (ttm170) REVERT: C 937 GLU cc_start: 0.8969 (pt0) cc_final: 0.8515 (pm20) REVERT: D 417 ILE cc_start: 0.8384 (mt) cc_final: 0.8145 (mp) REVERT: D 647 GLU cc_start: 0.8756 (tp30) cc_final: 0.8291 (tp30) REVERT: D 686 GLU cc_start: 0.8338 (mp0) cc_final: 0.8023 (tm-30) REVERT: D 773 MET cc_start: 0.7894 (pp-130) cc_final: 0.7528 (pp-130) REVERT: D 874 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7964 (ptt90) REVERT: D 929 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8194 (pp20) REVERT: E 417 ILE cc_start: 0.7362 (mm) cc_final: 0.7033 (tt) REVERT: E 435 MET cc_start: 0.8668 (tpt) cc_final: 0.8345 (tpp) REVERT: E 554 ASP cc_start: 0.7780 (t70) cc_final: 0.7204 (t0) REVERT: E 557 GLU cc_start: 0.8329 (mp0) cc_final: 0.7704 (mp0) REVERT: E 625 ASP cc_start: 0.8426 (m-30) cc_final: 0.7682 (OUTLIER) REVERT: E 915 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: E 922 ASP cc_start: 0.8576 (t70) cc_final: 0.8173 (m-30) REVERT: F 436 ASP cc_start: 0.8104 (p0) cc_final: 0.7291 (m-30) REVERT: F 440 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7409 (pp20) REVERT: F 546 ARG cc_start: 0.9021 (tmt90) cc_final: 0.8781 (tmt90) REVERT: F 647 GLU cc_start: 0.7591 (tp30) cc_final: 0.7080 (tp30) REVERT: F 651 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: F 908 THR cc_start: 0.8906 (m) cc_final: 0.8471 (p) REVERT: F 915 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8707 (mt-10) outliers start: 81 outliers final: 35 residues processed: 286 average time/residue: 0.7458 time to fit residues: 243.4612 Evaluate side-chains 243 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 874 ARG Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 651 ASP Chi-restraints excluded: chain F residue 751 PHE Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 94 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 315 optimal weight: 0.2980 chunk 124 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 HIS C 456 ASN E 451 HIS E 515 GLN F 477 ASN F 491 HIS F 622 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.073442 restraints weight = 40874.853| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.39 r_work: 0.2738 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25882 Z= 0.138 Angle : 0.602 12.655 35045 Z= 0.292 Chirality : 0.041 0.148 3998 Planarity : 0.004 0.087 4506 Dihedral : 7.855 141.533 3589 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.51 % Rotamer: Outliers : 2.60 % Allowed : 13.82 % Favored : 83.59 % 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: 1.00 (0.15), residues: 3210 helix: 1.80 (0.13), residues: 1456 sheet: -0.28 (0.25), residues: 425 loop : -0.22 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 459 TYR 0.035 0.002 TYR B 599 PHE 0.015 0.001 PHE A 455 TRP 0.024 0.001 TRP F 770 HIS 0.007 0.001 HIS F 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (25880) covalent geometry : angle 0.60035 / 0.29 (35042) hydrogen bonds : bond 0.03557 / 2.29 ( 1149) hydrogen bonds : angle 4.46852 / 3.08 ( 3321) Misc. bond : bond 0.00075 / 0.04 ( 1) link_TRANS : bond 0.04868 / 2.56 ( 1) link_TRANS : angle 4.73695 / 3.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 225 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 717 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8069 (tm-30) REVERT: B 415 ASP cc_start: 0.7439 (m-30) cc_final: 0.7213 (m-30) REVERT: B 577 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8568 (mp) REVERT: B 690 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7826 (ptmm) REVERT: C 419 GLU cc_start: 0.8880 (tp30) cc_final: 0.8675 (tt0) REVERT: C 435 MET cc_start: 0.8842 (tpt) cc_final: 0.8635 (mmm) REVERT: C 454 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7940 (mm-30) REVERT: C 579 LYS cc_start: 0.8842 (ttmm) cc_final: 0.8577 (ttpp) REVERT: C 690 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8148 (tppt) REVERT: C 785 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8442 (ttm170) REVERT: C 937 GLU cc_start: 0.8947 (pt0) cc_final: 0.8514 (pm20) REVERT: D 417 ILE cc_start: 0.8390 (mt) cc_final: 0.8100 (mp) REVERT: D 647 GLU cc_start: 0.8769 (tp30) cc_final: 0.8295 (tp30) REVERT: D 686 GLU cc_start: 0.8345 (mp0) cc_final: 0.7988 (tm-30) REVERT: D 773 MET cc_start: 0.7915 (pp-130) cc_final: 0.7522 (pp-130) REVERT: D 929 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8208 (pp20) REVERT: E 417 ILE cc_start: 0.7410 (mm) cc_final: 0.7082 (tt) REVERT: E 435 MET cc_start: 0.8686 (tpt) cc_final: 0.8366 (tpp) REVERT: E 456 ASN cc_start: 0.8402 (t0) cc_final: 0.8193 (m-40) REVERT: E 494 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8392 (mtt) REVERT: E 554 ASP cc_start: 0.7777 (t70) cc_final: 0.7207 (t0) REVERT: E 557 GLU cc_start: 0.8364 (mp0) cc_final: 0.7719 (mp0) REVERT: E 625 ASP cc_start: 0.8480 (m-30) cc_final: 0.7680 (t0) REVERT: E 915 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: E 922 ASP cc_start: 0.8547 (t70) cc_final: 0.8137 (m-30) REVERT: F 440 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7413 (pp20) REVERT: F 546 ARG cc_start: 0.9000 (tmt90) cc_final: 0.8775 (tmt90) REVERT: F 647 GLU cc_start: 0.7578 (tp30) cc_final: 0.7116 (tp30) REVERT: F 651 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: F 908 THR cc_start: 0.8877 (m) cc_final: 0.8438 (p) REVERT: F 915 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8717 (mt-10) outliers start: 71 outliers final: 33 residues processed: 277 average time/residue: 0.7000 time to fit residues: 221.8006 Evaluate side-chains 248 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain E residue 494 MET Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 515 GLN Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 651 ASP Chi-restraints excluded: chain F residue 751 PHE Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 243 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 260 optimal weight: 0.7980 chunk 301 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 138 optimal weight: 0.0000 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 HIS C 456 ASN E 477 ASN F 477 ASN F 622 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.074210 restraints weight = 41013.763| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.39 r_work: 0.2735 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25882 Z= 0.127 Angle : 0.591 12.206 35045 Z= 0.286 Chirality : 0.041 0.213 3998 Planarity : 0.004 0.087 4506 Dihedral : 7.699 150.413 3587 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.51 % Rotamer: Outliers : 2.34 % Allowed : 14.00 % Favored : 83.66 % 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: 1.12 (0.15), residues: 3210 helix: 1.91 (0.13), residues: 1458 sheet: -0.01 (0.26), residues: 413 loop : -0.25 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 459 TYR 0.028 0.001 TYR B 599 PHE 0.015 0.001 PHE A 455 TRP 0.025 0.001 TRP F 770 HIS 0.005 0.001 HIS F 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (25880) covalent geometry : angle 0.58953 / 0.29 (35042) hydrogen bonds : bond 0.03395 / 2.18 ( 1149) hydrogen bonds : angle 4.39517 / 3.03 ( 3321) Misc. bond : bond 0.00088 / 0.05 ( 1) link_TRANS : bond 0.04645 / 2.44 ( 1) link_TRANS : angle 4.72519 / 3.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 0.974 Fit side-chains REVERT: A 440 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: A 717 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 415 ASP cc_start: 0.7410 (m-30) cc_final: 0.7208 (m-30) REVERT: B 577 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8520 (mp) REVERT: B 579 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8621 (mptt) REVERT: B 690 LYS cc_start: 0.8477 (ptpt) cc_final: 0.7864 (ptmm) REVERT: B 789 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6099 (t0) REVERT: C 435 MET cc_start: 0.8841 (tpt) cc_final: 0.8630 (mmm) REVERT: C 454 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7910 (mm-30) REVERT: C 579 LYS cc_start: 0.8851 (ttmm) cc_final: 0.8598 (ttpp) REVERT: C 690 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8137 (tppt) REVERT: C 785 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8442 (ttm170) REVERT: C 937 GLU cc_start: 0.8956 (pt0) cc_final: 0.8510 (pm20) REVERT: D 417 ILE cc_start: 0.8364 (mt) cc_final: 0.8070 (mp) REVERT: D 647 GLU cc_start: 0.8756 (tp30) cc_final: 0.8280 (tp30) REVERT: D 686 GLU cc_start: 0.8370 (mp0) cc_final: 0.7984 (tm-30) REVERT: D 773 MET cc_start: 0.7930 (pp-130) cc_final: 0.7529 (pp-130) REVERT: D 874 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8013 (ptt90) REVERT: D 929 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8231 (pp20) REVERT: E 417 ILE cc_start: 0.7404 (mm) cc_final: 0.7070 (tt) REVERT: E 435 MET cc_start: 0.8702 (tpt) cc_final: 0.8387 (tpp) REVERT: E 456 ASN cc_start: 0.8395 (t0) cc_final: 0.8194 (m-40) REVERT: E 515 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: E 554 ASP cc_start: 0.7780 (t70) cc_final: 0.7172 (t0) REVERT: E 557 GLU cc_start: 0.8407 (mp0) cc_final: 0.7706 (mp0) REVERT: E 625 ASP cc_start: 0.8489 (m-30) cc_final: 0.7687 (t0) REVERT: E 915 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8471 (mt-10) REVERT: E 922 ASP cc_start: 0.8579 (t70) cc_final: 0.8184 (m-30) REVERT: F 424 ARG cc_start: 0.7567 (ttp-170) cc_final: 0.7058 (ttp-170) REVERT: F 546 ARG cc_start: 0.8959 (tmt90) cc_final: 0.8729 (tmt90) REVERT: F 647 GLU cc_start: 0.7597 (tp30) cc_final: 0.7295 (tp30) REVERT: F 908 THR cc_start: 0.8864 (m) cc_final: 0.8443 (p) REVERT: F 915 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8703 (mt-10) outliers start: 64 outliers final: 27 residues processed: 271 average time/residue: 0.7234 time to fit residues: 225.5002 Evaluate side-chains 240 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 874 ARG Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 515 GLN Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 751 PHE Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 225 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 317 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 HIS C 456 ASN E 515 GLN F 477 ASN F 622 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.073878 restraints weight = 40688.081| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.39 r_work: 0.2732 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25882 Z= 0.133 Angle : 0.590 11.938 35045 Z= 0.285 Chirality : 0.041 0.197 3998 Planarity : 0.004 0.103 4506 Dihedral : 7.610 158.622 3583 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 2.38 % Allowed : 14.77 % Favored : 82.86 % 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: 1.19 (0.15), residues: 3210 helix: 1.96 (0.13), residues: 1458 sheet: 0.15 (0.26), residues: 413 loop : -0.27 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 786 TYR 0.039 0.001 TYR F 461 PHE 0.015 0.001 PHE A 455 TRP 0.026 0.001 TRP F 770 HIS 0.005 0.001 HIS F 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (25880) covalent geometry : angle 0.58830 / 0.28 (35042) hydrogen bonds : bond 0.03409 / 2.19 ( 1149) hydrogen bonds : angle 4.33275 / 2.99 ( 3321) Misc. bond : bond 0.00098 / 0.05 ( 1) link_TRANS : bond 0.04452 / 2.34 ( 1) link_TRANS : angle 4.74084 / 3.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 220 time to evaluate : 0.964 Fit side-chains REVERT: A 717 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 415 ASP cc_start: 0.7439 (m-30) cc_final: 0.7232 (m-30) REVERT: B 577 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8473 (mp) REVERT: B 579 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8596 (mptt) REVERT: B 690 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7892 (ptmm) REVERT: B 789 ASP cc_start: 0.6446 (OUTLIER) cc_final: 0.6046 (t0) REVERT: B 846 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8125 (mp0) REVERT: C 435 MET cc_start: 0.8838 (tpt) cc_final: 0.8630 (mmm) REVERT: C 454 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7906 (mm-30) REVERT: C 579 LYS cc_start: 0.8851 (ttmm) cc_final: 0.8599 (ttpp) REVERT: C 785 ARG cc_start: 0.8836 (ttp80) cc_final: 0.8373 (ttp80) REVERT: C 937 GLU cc_start: 0.8957 (pt0) cc_final: 0.8497 (pm20) REVERT: D 417 ILE cc_start: 0.8371 (mt) cc_final: 0.8078 (mp) REVERT: D 647 GLU cc_start: 0.8732 (tp30) cc_final: 0.8252 (tp30) REVERT: D 773 MET cc_start: 0.7926 (pp-130) cc_final: 0.7504 (pp-130) REVERT: D 874 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8036 (ptt90) REVERT: D 929 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8264 (pp20) REVERT: E 417 ILE cc_start: 0.7384 (mm) cc_final: 0.7063 (tt) REVERT: E 435 MET cc_start: 0.8719 (tpt) cc_final: 0.8402 (tpp) REVERT: E 456 ASN cc_start: 0.8391 (t0) cc_final: 0.8175 (m-40) REVERT: E 554 ASP cc_start: 0.7805 (t70) cc_final: 0.7231 (t0) REVERT: E 557 GLU cc_start: 0.8462 (mp0) cc_final: 0.7745 (mp0) REVERT: E 620 LEU cc_start: 0.9436 (tp) cc_final: 0.9228 (tm) REVERT: E 625 ASP cc_start: 0.8480 (m-30) cc_final: 0.7689 (t0) REVERT: E 915 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: E 922 ASP cc_start: 0.8491 (t70) cc_final: 0.8101 (m-30) REVERT: F 424 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.7082 (ttp-170) REVERT: F 440 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7458 (pp20) REVERT: F 546 ARG cc_start: 0.8931 (tmt90) cc_final: 0.8700 (tmt90) REVERT: F 908 THR cc_start: 0.8854 (m) cc_final: 0.8414 (p) REVERT: F 915 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8689 (mt-10) outliers start: 65 outliers final: 33 residues processed: 272 average time/residue: 0.7284 time to fit residues: 228.0196 Evaluate side-chains 243 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 874 ARG Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 751 PHE Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 295 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 257 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 129 optimal weight: 0.0170 chunk 54 optimal weight: 0.0970 chunk 123 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 HIS C 433 HIS C 456 ASN D 561 HIS F 477 ASN F 622 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.075912 restraints weight = 40709.743| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.38 r_work: 0.2767 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 25882 Z= 0.111 Angle : 0.578 12.158 35045 Z= 0.279 Chirality : 0.040 0.225 3998 Planarity : 0.004 0.088 4506 Dihedral : 7.431 159.108 3583 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.51 % Rotamer: Outliers : 1.68 % Allowed : 15.61 % Favored : 82.71 % 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: 1.33 (0.15), residues: 3210 helix: 2.06 (0.14), residues: 1464 sheet: 0.32 (0.26), residues: 408 loop : -0.22 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 459 TYR 0.032 0.001 TYR B 599 PHE 0.017 0.001 PHE A 455 TRP 0.023 0.001 TRP F 770 HIS 0.004 0.001 HIS F 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (25880) covalent geometry : angle 0.57690 / 0.28 (35042) hydrogen bonds : bond 0.03082 / 1.97 ( 1149) hydrogen bonds : angle 4.23056 / 2.93 ( 3321) Misc. bond : bond 0.00052 / 0.03 ( 1) link_TRANS : bond 0.04372 / 2.30 ( 1) link_TRANS : angle 4.67391 / 3.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 1.045 Fit side-chains REVERT: A 717 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 690 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7791 (ptmm) REVERT: B 789 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6086 (t0) REVERT: C 454 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7885 (mm-30) REVERT: C 579 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8601 (ttpp) REVERT: C 691 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8622 (pp) REVERT: C 785 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8375 (ttp80) REVERT: C 937 GLU cc_start: 0.8920 (pt0) cc_final: 0.8492 (pm20) REVERT: D 417 ILE cc_start: 0.8382 (mt) cc_final: 0.8092 (mp) REVERT: D 579 LYS cc_start: 0.9024 (tttp) cc_final: 0.8800 (ttmm) REVERT: D 647 GLU cc_start: 0.8717 (tp30) cc_final: 0.8227 (tp30) REVERT: D 773 MET cc_start: 0.7927 (pp-130) cc_final: 0.7419 (pp-130) REVERT: D 874 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8042 (ptt90) REVERT: D 929 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8261 (pp20) REVERT: E 417 ILE cc_start: 0.7413 (mm) cc_final: 0.7098 (tt) REVERT: E 435 MET cc_start: 0.8706 (tpt) cc_final: 0.8410 (tpp) REVERT: E 456 ASN cc_start: 0.8387 (t0) cc_final: 0.8178 (m-40) REVERT: E 554 ASP cc_start: 0.7776 (t70) cc_final: 0.7243 (t0) REVERT: E 557 GLU cc_start: 0.8454 (mp0) cc_final: 0.7809 (mp0) REVERT: E 625 ASP cc_start: 0.8438 (m-30) cc_final: 0.7670 (t0) REVERT: E 922 ASP cc_start: 0.8469 (t70) cc_final: 0.8070 (m-30) REVERT: F 424 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7169 (ttp-170) REVERT: F 440 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7343 (pp20) REVERT: F 546 ARG cc_start: 0.8927 (tmt90) cc_final: 0.8711 (tmt90) REVERT: F 908 THR cc_start: 0.8847 (m) cc_final: 0.8431 (p) REVERT: F 915 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8656 (mt-10) outliers start: 46 outliers final: 21 residues processed: 262 average time/residue: 0.6869 time to fit residues: 206.9557 Evaluate side-chains 229 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 874 ARG Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 751 PHE Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 303 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 266 optimal weight: 0.0870 chunk 276 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 HIS F 477 ASN F 622 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.074591 restraints weight = 40918.032| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.40 r_work: 0.2745 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25882 Z= 0.126 Angle : 0.589 12.164 35045 Z= 0.283 Chirality : 0.040 0.221 3998 Planarity : 0.004 0.089 4506 Dihedral : 7.469 160.529 3583 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 1.43 % Allowed : 16.01 % Favored : 82.57 % 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: 1.36 (0.15), residues: 3210 helix: 2.10 (0.14), residues: 1460 sheet: 0.35 (0.26), residues: 398 loop : -0.22 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 705 TYR 0.040 0.001 TYR F 461 PHE 0.016 0.001 PHE A 455 TRP 0.025 0.001 TRP F 770 HIS 0.005 0.001 HIS F 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (25880) covalent geometry : angle 0.58706 / 0.28 (35042) hydrogen bonds : bond 0.03239 / 2.08 ( 1149) hydrogen bonds : angle 4.21704 / 2.92 ( 3321) Misc. bond : bond 0.00091 / 0.05 ( 1) link_TRANS : bond 0.04318 / 2.27 ( 1) link_TRANS : angle 4.68147 / 3.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.051 Fit side-chains REVERT: A 652 ARG cc_start: 0.8681 (mmt-90) cc_final: 0.8370 (mmt-90) REVERT: A 717 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 690 LYS cc_start: 0.8435 (ptpt) cc_final: 0.7786 (ptmm) REVERT: B 789 ASP cc_start: 0.6461 (OUTLIER) cc_final: 0.6076 (t0) REVERT: C 454 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7934 (mm-30) REVERT: C 579 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8623 (ttpp) REVERT: C 691 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8654 (pp) REVERT: C 785 ARG cc_start: 0.8857 (ttp80) cc_final: 0.8349 (ttp80) REVERT: C 937 GLU cc_start: 0.8960 (pt0) cc_final: 0.8493 (pm20) REVERT: D 417 ILE cc_start: 0.8373 (mt) cc_final: 0.8082 (mp) REVERT: D 579 LYS cc_start: 0.9034 (tttp) cc_final: 0.8810 (ttmm) REVERT: D 647 GLU cc_start: 0.8729 (tp30) cc_final: 0.8235 (tp30) REVERT: D 773 MET cc_start: 0.7916 (pp-130) cc_final: 0.7482 (pp-130) REVERT: D 874 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8017 (ptt90) REVERT: D 929 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8271 (pp20) REVERT: E 417 ILE cc_start: 0.7374 (mm) cc_final: 0.7042 (tt) REVERT: E 435 MET cc_start: 0.8725 (tpt) cc_final: 0.8408 (tpp) REVERT: E 456 ASN cc_start: 0.8370 (t0) cc_final: 0.8141 (m-40) REVERT: E 554 ASP cc_start: 0.7827 (t70) cc_final: 0.7180 (t0) REVERT: E 557 GLU cc_start: 0.8458 (mp0) cc_final: 0.7816 (mp0) REVERT: E 625 ASP cc_start: 0.8511 (m-30) cc_final: 0.7688 (t0) REVERT: E 846 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8068 (mm-30) REVERT: E 922 ASP cc_start: 0.8460 (t70) cc_final: 0.8045 (m-30) REVERT: F 424 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7184 (ttp-170) REVERT: F 440 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7375 (pp20) REVERT: F 546 ARG cc_start: 0.8910 (tmt90) cc_final: 0.8683 (tmt90) REVERT: F 908 THR cc_start: 0.8840 (m) cc_final: 0.8410 (p) REVERT: F 915 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8674 (mt-10) outliers start: 39 outliers final: 20 residues processed: 237 average time/residue: 0.6691 time to fit residues: 181.3187 Evaluate side-chains 226 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 874 ARG Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 751 PHE Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 122 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 302 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 HIS F 477 ASN F 622 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.073468 restraints weight = 40815.331| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.40 r_work: 0.2738 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (24 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25882 Z= 0.147 Angle : 0.597 12.441 35045 Z= 0.288 Chirality : 0.041 0.258 3998 Planarity : 0.004 0.089 4506 Dihedral : 7.598 164.905 3583 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 1.32 % Allowed : 16.15 % Favored : 82.53 % 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: 1.34 (0.15), residues: 3210 helix: 2.10 (0.14), residues: 1454 sheet: 0.34 (0.26), residues: 403 loop : -0.25 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 786 TYR 0.025 0.001 TYR B 599 PHE 0.015 0.001 PHE A 455 TRP 0.027 0.001 TRP F 770 HIS 0.005 0.001 HIS F 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (25880) covalent geometry : angle 0.59494 / 0.29 (35042) hydrogen bonds : bond 0.03433 / 2.20 ( 1149) hydrogen bonds : angle 4.24416 / 2.94 ( 3321) Misc. bond : bond 0.00106 / 0.06 ( 1) link_TRANS : bond 0.04272 / 2.25 ( 1) link_TRANS : angle 4.73212 / 3.65 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 1.048 Fit side-chains REVERT: A 652 ARG cc_start: 0.8726 (mmt-90) cc_final: 0.8431 (mmt-90) REVERT: B 690 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7840 (ptmm) REVERT: B 789 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.6062 (t0) REVERT: C 454 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7976 (mm-30) REVERT: C 579 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8648 (ttpp) REVERT: C 785 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8377 (ttp80) REVERT: C 937 GLU cc_start: 0.8965 (pt0) cc_final: 0.8500 (pm20) REVERT: D 417 ILE cc_start: 0.8434 (mt) cc_final: 0.8152 (mp) REVERT: D 579 LYS cc_start: 0.9045 (tttp) cc_final: 0.8810 (ttmm) REVERT: D 647 GLU cc_start: 0.8734 (tp30) cc_final: 0.8248 (tp30) REVERT: D 686 GLU cc_start: 0.8306 (mp0) cc_final: 0.7869 (tm-30) REVERT: D 773 MET cc_start: 0.8029 (pp-130) cc_final: 0.7585 (pp-130) REVERT: D 874 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8040 (ptt90) REVERT: D 929 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8271 (pp20) REVERT: E 417 ILE cc_start: 0.7436 (mm) cc_final: 0.7106 (tt) REVERT: E 435 MET cc_start: 0.8733 (tpt) cc_final: 0.8451 (tpp) REVERT: E 456 ASN cc_start: 0.8422 (t0) cc_final: 0.8169 (m-40) REVERT: E 554 ASP cc_start: 0.7857 (t70) cc_final: 0.7260 (t0) REVERT: E 557 GLU cc_start: 0.8482 (mp0) cc_final: 0.7861 (mp0) REVERT: E 846 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8051 (mm-30) REVERT: E 922 ASP cc_start: 0.8478 (t70) cc_final: 0.8060 (m-30) REVERT: F 421 PHE cc_start: 0.5468 (m-10) cc_final: 0.5241 (m-10) REVERT: F 440 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7385 (pp20) REVERT: F 546 ARG cc_start: 0.8964 (tmt90) cc_final: 0.8738 (tmt90) REVERT: F 908 THR cc_start: 0.8858 (m) cc_final: 0.8401 (p) REVERT: F 915 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8714 (mt-10) outliers start: 36 outliers final: 21 residues processed: 233 average time/residue: 0.7010 time to fit residues: 186.5154 Evaluate side-chains 226 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 874 ARG Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 124 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 281 optimal weight: 8.9990 chunk 138 optimal weight: 0.0370 chunk 251 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 271 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 HIS F 477 ASN F 622 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.074639 restraints weight = 40695.627| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.39 r_work: 0.2761 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25882 Z= 0.121 Angle : 0.589 16.055 35045 Z= 0.283 Chirality : 0.040 0.246 3998 Planarity : 0.004 0.089 4506 Dihedral : 7.502 165.440 3583 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 16.34 % Favored : 82.27 % 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: 1.38 (0.15), residues: 3210 helix: 2.11 (0.14), residues: 1460 sheet: 0.45 (0.26), residues: 405 loop : -0.24 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 705 TYR 0.040 0.001 TYR F 461 PHE 0.014 0.001 PHE A 455 TRP 0.026 0.001 TRP F 770 HIS 0.004 0.001 HIS F 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (25880) covalent geometry : angle 0.58754 / 0.28 (35042) hydrogen bonds : bond 0.03181 / 2.04 ( 1149) hydrogen bonds : angle 4.19107 / 2.90 ( 3321) Misc. bond : bond 0.00076 / 0.04 ( 1) link_TRANS : bond 0.04265 / 2.24 ( 1) link_TRANS : angle 4.72100 / 3.66 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8940.71 seconds wall clock time: 153 minutes 0.99 seconds (9180.99 seconds total)