Starting phenix.real_space_refine on Sat Sep 12 21:38:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xwa_67330/09_2026/9xwa_67330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xwa_67330/09_2026/9xwa_67330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xwa_67330/09_2026/9xwa_67330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xwa_67330/09_2026/9xwa_67330.map" model { file = "/net/cci-nas-00/data/ceres_data/9xwa_67330/09_2026/9xwa_67330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xwa_67330/09_2026/9xwa_67330.cif" } resolution = 3.41 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= 0.002 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 11498 2.51 5 N 3014 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18082 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7263 Classifications: {'peptide': 901} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 860} Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1568 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 7263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7263 Classifications: {'peptide': 901} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 860} Chain: "C" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1568 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.04, per 1000 atoms: 0.22 Number of scatterers: 18082 At special positions: 0 Unit cell: (105.78, 176.3, 119.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 3500 8.00 N 3014 7.00 C 11498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 754 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS A 791 " - pdb=" SG CYS A 827 " distance=2.04 Simple disulfide: pdb=" SG CYS D 372 " - pdb=" SG CYS D 396 " distance=2.03 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS D 467 " distance=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 571 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 515 " distance=2.03 Simple disulfide: pdb=" SG CYS B 754 " - pdb=" SG CYS B 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 791 " - pdb=" SG CYS B 827 " distance=2.04 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 396 " distance=2.03 Simple disulfide: pdb=" SG CYS C 414 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 426 " - pdb=" SG CYS C 571 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 515 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1001 " - " ASN A 122 " " NAG A1002 " - " ASN A 324 " " NAG A1003 " - " ASN A 732 " " NAG A1004 " - " ASN A 811 " " NAG B1001 " - " ASN B 122 " " NAG B1002 " - " ASN B 324 " " NAG B1003 " - " ASN B 732 " " NAG B1004 " - " ASN B 811 " " NAG C 601 " - " ASN C 387 " " NAG D 601 " - " ASN D 387 " " NAG E 1 " - " ASN A 100 " " NAG F 1 " - " ASN A 225 " " NAG G 1 " - " ASN A 362 " " NAG H 1 " - " ASN A 618 " " NAG I 1 " - " ASN A 595 " " NAG J 1 " - " ASN B 100 " " NAG K 1 " - " ASN B 225 " " NAG L 1 " - " ASN B 362 " " NAG M 1 " - " ASN B 618 " " NAG N 1 " - " ASN B 595 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 839.6 milliseconds 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4216 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 26 sheets defined 46.8% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.770A pdb=" N SER A 211 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.544A pdb=" N LEU A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 366 through 387 removed outlier: 4.001A pdb=" N TRP A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 397 removed outlier: 3.710A pdb=" N ASP A 397 " --> pdb=" O TRP A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 403 through 417 Processing helix chain 'A' and resid 424 through 439 Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.509A pdb=" N GLU A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'A' and resid 464 through 482 removed outlier: 3.793A pdb=" N TYR A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'A' and resid 504 through 519 removed outlier: 3.919A pdb=" N LEU A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.672A pdb=" N TRP A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.791A pdb=" N ASN A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR A 574 " --> pdb=" O PRO A 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 570 through 574' Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 647 through 664 removed outlier: 3.623A pdb=" N ALA A 652 " --> pdb=" O VAL A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 676 removed outlier: 3.697A pdb=" N ALA A 672 " --> pdb=" O PRO A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 681 removed outlier: 3.794A pdb=" N GLN A 681 " --> pdb=" O PHE A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 703 Processing helix chain 'A' and resid 707 through 731 removed outlier: 3.636A pdb=" N MET A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 756 Processing helix chain 'A' and resid 758 through 775 Processing helix chain 'A' and resid 785 through 797 removed outlier: 3.920A pdb=" N CYS A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A 792 " --> pdb=" O THR A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 removed outlier: 4.032A pdb=" N TRP A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 826 Processing helix chain 'A' and resid 830 through 841 Processing helix chain 'A' and resid 851 through 860 Processing helix chain 'A' and resid 865 through 876 removed outlier: 3.586A pdb=" N ALA A 869 " --> pdb=" O GLY A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 881 removed outlier: 3.825A pdb=" N LEU A 880 " --> pdb=" O ASN A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 891 through 899 removed outlier: 3.721A pdb=" N ILE A 895 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 897 " --> pdb=" O ASN A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 918 Processing helix chain 'A' and resid 923 through 925 No H-bonds generated for 'chain 'A' and resid 923 through 925' Processing helix chain 'A' and resid 926 through 959 Processing helix chain 'D' and resid 374 through 379 Processing helix chain 'D' and resid 399 through 407 removed outlier: 4.238A pdb=" N LEU D 403 " --> pdb=" O ASN D 399 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 406 " --> pdb=" O LYS D 402 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 424 Processing helix chain 'D' and resid 438 through 446 removed outlier: 5.019A pdb=" N SER D 443 " --> pdb=" O SER D 440 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR D 444 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 457 removed outlier: 4.762A pdb=" N SER D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 522 removed outlier: 3.699A pdb=" N ARG D 522 " --> pdb=" O GLY D 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.769A pdb=" N SER B 211 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 305 through 324 removed outlier: 3.547A pdb=" N LEU B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 314 - end of helix Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 366 through 387 removed outlier: 4.006A pdb=" N TRP B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 397 removed outlier: 3.731A pdb=" N ASP B 397 " --> pdb=" O TRP B 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 394 through 397' Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'B' and resid 464 through 482 removed outlier: 3.791A pdb=" N TYR B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'B' and resid 504 through 519 removed outlier: 3.927A pdb=" N LEU B 508 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 537 removed outlier: 3.678A pdb=" N TRP B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 574 removed outlier: 3.790A pdb=" N ASN B 573 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR B 574 " --> pdb=" O PRO B 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 570 through 574' Processing helix chain 'B' and resid 603 through 606 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.644A pdb=" N ALA B 652 " --> pdb=" O VAL B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 676 removed outlier: 3.693A pdb=" N ALA B 672 " --> pdb=" O PRO B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 removed outlier: 3.791A pdb=" N GLN B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 703 Processing helix chain 'B' and resid 707 through 731 removed outlier: 3.634A pdb=" N MET B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 756 Processing helix chain 'B' and resid 758 through 775 Processing helix chain 'B' and resid 785 through 797 removed outlier: 3.908A pdb=" N CYS B 791 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN B 792 " --> pdb=" O THR B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 812 removed outlier: 4.021A pdb=" N TRP B 802 " --> pdb=" O GLY B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 826 Processing helix chain 'B' and resid 830 through 841 Processing helix chain 'B' and resid 851 through 860 Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.587A pdb=" N ALA B 869 " --> pdb=" O GLY B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 881 removed outlier: 3.823A pdb=" N LEU B 880 " --> pdb=" O ASN B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 890 No H-bonds generated for 'chain 'B' and resid 888 through 890' Processing helix chain 'B' and resid 891 through 899 removed outlier: 3.713A pdb=" N ILE B 895 " --> pdb=" O PHE B 891 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 896 " --> pdb=" O SER B 892 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 897 " --> pdb=" O ASN B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 918 Processing helix chain 'B' and resid 923 through 925 No H-bonds generated for 'chain 'B' and resid 923 through 925' Processing helix chain 'B' and resid 926 through 959 Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 399 through 407 removed outlier: 4.244A pdb=" N LEU C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C 406 " --> pdb=" O LYS C 402 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 424 Processing helix chain 'C' and resid 438 through 446 removed outlier: 5.024A pdb=" N SER C 443 " --> pdb=" O SER C 440 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 444 " --> pdb=" O MET C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 457 removed outlier: 4.756A pdb=" N SER C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 522 removed outlier: 3.699A pdb=" N ARG C 522 " --> pdb=" O GLY C 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.685A pdb=" N GLY A 99 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU A 98 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU A 83 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A 100 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 81 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A 102 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR A 79 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A 104 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.685A pdb=" N GLY A 99 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU A 98 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU A 83 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A 100 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 81 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A 102 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR A 79 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A 104 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LYS A 221 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N HIS A 77 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET A 266 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 117 removed outlier: 3.592A pdb=" N ILE A 116 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA7, first strand: chain 'A' and resid 279 through 284 removed outlier: 6.567A pdb=" N GLN A 290 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLN A 334 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG A 292 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY A 336 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TRP A 294 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 390 through 392 removed outlier: 6.562A pdb=" N THR A 391 " --> pdb=" O THR A 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 599 through 601 removed outlier: 7.807A pdb=" N ASN A 626 " --> pdb=" O PRO A 542 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE A 544 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 587 through 588 Processing sheet with id=AB2, first strand: chain 'D' and resid 389 through 393 removed outlier: 3.870A pdb=" N SER D 389 " --> pdb=" O TRP D 434 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP D 434 " --> pdb=" O SER D 389 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 396 through 398 removed outlier: 4.016A pdb=" N CYS D 571 " --> pdb=" O CYS D 396 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR D 562 " --> pdb=" O SER D 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 490 through 494 removed outlier: 5.756A pdb=" N GLY D 541 " --> pdb=" O SER D 493 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 536 " --> pdb=" O PHE D 533 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.714A pdb=" N GLY B 99 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 97 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE B 96 " --> pdb=" O PRO B 85 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU B 98 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 83 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN B 100 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 81 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR B 102 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR B 79 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 104 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.714A pdb=" N GLY B 99 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 97 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE B 96 " --> pdb=" O PRO B 85 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU B 98 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 83 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN B 100 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 81 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR B 102 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR B 79 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 104 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LYS B 221 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N HIS B 77 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 266 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.582A pdb=" N ILE B 116 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB9, first strand: chain 'B' and resid 187 through 189 Processing sheet with id=AC1, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AC2, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.574A pdb=" N GLN B 290 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLN B 334 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 292 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLY B 336 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TRP B 294 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 390 through 392 removed outlier: 6.555A pdb=" N THR B 391 " --> pdb=" O THR B 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 599 through 601 removed outlier: 7.806A pdb=" N ASN B 626 " --> pdb=" O PRO B 542 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE B 544 " --> pdb=" O ASN B 626 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 587 through 588 Processing sheet with id=AC6, first strand: chain 'C' and resid 389 through 393 removed outlier: 3.870A pdb=" N SER C 389 " --> pdb=" O TRP C 434 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP C 434 " --> pdb=" O SER C 389 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.019A pdb=" N CYS C 571 " --> pdb=" O CYS C 396 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR C 562 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 490 through 494 removed outlier: 5.745A pdb=" N GLY C 541 " --> pdb=" O SER C 493 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 536 " --> pdb=" O PHE C 533 " (cutoff:3.500A) 827 hydrogen bonds defined for protein. 2310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.13 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: 5801 1.34 - 1.46: 4192 1.46 - 1.58: 8423 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 18528 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C1 NAG B1004 " pdb=" O5 NAG B1004 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 ... (remaining 18523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 24511 1.65 - 3.30: 640 3.30 - 4.95: 73 4.95 - 6.60: 10 6.60 - 8.26: 6 Bond angle restraints: 25240 Sorted by residual: angle pdb=" C GLN A 204 " pdb=" N ALA A 205 " pdb=" CA ALA A 205 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C GLN B 204 " pdb=" N ALA B 205 " pdb=" CA ALA B 205 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N PHE B 173 " pdb=" CA PHE B 173 " pdb=" C PHE B 173 " ideal model delta sigma weight residual 108.34 112.63 -4.29 1.31e+00 5.83e-01 1.07e+01 angle pdb=" C VAL A 566 " pdb=" N THR A 567 " pdb=" CA THR A 567 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N PHE A 173 " pdb=" CA PHE A 173 " pdb=" C PHE A 173 " ideal model delta sigma weight residual 108.34 112.50 -4.16 1.31e+00 5.83e-01 1.01e+01 ... (remaining 25235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 9691 17.33 - 34.66: 1278 34.66 - 51.99: 333 51.99 - 69.31: 88 69.31 - 86.64: 22 Dihedral angle restraints: 11412 sinusoidal: 4894 harmonic: 6518 Sorted by residual: dihedral pdb=" CA TRP B 399 " pdb=" C TRP B 399 " pdb=" N LEU B 400 " pdb=" CA LEU B 400 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA TRP A 399 " pdb=" C TRP A 399 " pdb=" N LEU A 400 " pdb=" CA LEU A 400 " ideal model delta harmonic sigma weight residual 180.00 154.92 25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ASN B 811 " pdb=" C ASN B 811 " pdb=" N ALA B 812 " pdb=" CA ALA B 812 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 11409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2762 0.098 - 0.195: 108 0.195 - 0.293: 2 0.293 - 0.390: 2 0.390 - 0.488: 2 Chirality restraints: 2876 Sorted by residual: chirality pdb=" C1 NAG A1004 " pdb=" ND2 ASN A 811 " pdb=" C2 NAG A1004 " pdb=" O5 NAG A1004 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C1 NAG B1004 " pdb=" ND2 ASN B 811 " pdb=" C2 NAG B1004 " pdb=" O5 NAG B1004 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2873 not shown) Planarity restraints: 3232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 811 " -0.001 2.00e-02 2.50e+03 2.40e-02 7.20e+00 pdb=" CG ASN B 811 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 811 " -0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 811 " 0.031 2.00e-02 2.50e+03 pdb=" C1 NAG B1004 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 811 " 0.000 2.00e-02 2.50e+03 2.36e-02 6.99e+00 pdb=" CG ASN A 811 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 811 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN A 811 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG A1004 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 944 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C VAL B 944 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL B 944 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 945 " 0.012 2.00e-02 2.50e+03 ... (remaining 3229 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1450 2.74 - 3.28: 17917 3.28 - 3.82: 29919 3.82 - 4.36: 35434 4.36 - 4.90: 63081 Nonbonded interactions: 147801 Sorted by model distance: nonbonded pdb=" O PHE B 726 " pdb=" OG1 THR B 730 " model vdw 2.198 3.040 nonbonded pdb=" O PHE A 726 " pdb=" OG1 THR A 730 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP B 703 " pdb=" NH1 ARG B 901 " model vdw 2.218 3.120 nonbonded pdb=" OD2 ASP A 703 " pdb=" NH1 ARG A 901 " model vdw 2.219 3.120 nonbonded pdb=" O SER D 428 " pdb=" OG1 THR D 569 " model vdw 2.272 3.040 ... (remaining 147796 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.090 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18570 Z= 0.172 Angle : 0.662 18.495 25354 Z= 0.332 Chirality : 0.045 0.488 2876 Planarity : 0.004 0.057 3212 Dihedral : 16.845 86.642 7160 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.79 % Favored : 93.93 % Rotamer: Outliers : 0.36 % Allowed : 24.97 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.04 (0.18), residues: 2192 helix: 0.20 (0.17), residues: 896 sheet: -0.51 (0.28), residues: 362 loop : -1.60 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 476 TYR 0.018 0.001 TYR A 592 PHE 0.022 0.001 PHE B 481 TRP 0.007 0.001 TRP B 385 HIS 0.004 0.001 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (18528) covalent geometry : angle 0.60539 / 0.32 (25240) SS BOND : bond 0.00340 / 0.17 ( 12) SS BOND : angle 1.47912 / 1.20 ( 24) hydrogen bonds : bond 0.18296 / 11.79 ( 798) hydrogen bonds : angle 6.84508 / 4.66 ( 2310) link_BETA1-4 : bond 0.01676 / 0.79 ( 10) link_BETA1-4 : angle 5.01955 / 3.48 ( 30) link_NAG-ASN : bond 0.00769 / 0.51 ( 20) link_NAG-ASN : angle 4.18141 / 2.77 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 404 LEU cc_start: 0.7203 (tp) cc_final: 0.6646 (pp) REVERT: D 461 ASP cc_start: 0.8635 (p0) cc_final: 0.8387 (p0) REVERT: B 633 ARG cc_start: 0.8248 (tmm-80) cc_final: 0.7958 (ttm-80) REVERT: C 404 LEU cc_start: 0.7226 (tp) cc_final: 0.6656 (pp) REVERT: C 459 ASN cc_start: 0.8312 (t0) cc_final: 0.8089 (t0) REVERT: C 461 ASP cc_start: 0.8626 (p0) cc_final: 0.8382 (p0) outliers start: 7 outliers final: 3 residues processed: 222 average time/residue: 0.1340 time to fit residues: 45.5927 Evaluate side-chains 170 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 832 TRP Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain B residue 832 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 ASN A 502 ASN A 829 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN B 502 ASN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105677 restraints weight = 28333.039| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.52 r_work: 0.3121 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18570 Z= 0.147 Angle : 0.643 17.180 25354 Z= 0.324 Chirality : 0.046 0.436 2876 Planarity : 0.004 0.051 3212 Dihedral : 6.442 59.354 3027 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.16 % Favored : 93.39 % Rotamer: Outliers : 3.29 % Allowed : 23.64 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.85 (0.18), residues: 2192 helix: 0.47 (0.18), residues: 908 sheet: -0.49 (0.27), residues: 362 loop : -1.62 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 901 TYR 0.013 0.001 TYR C 491 PHE 0.024 0.001 PHE B 481 TRP 0.008 0.001 TRP A 832 HIS 0.006 0.001 HIS D 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (18528) covalent geometry : angle 0.59642 / 0.31 (25240) SS BOND : bond 0.00223 / 0.12 ( 12) SS BOND : angle 0.91768 / 0.56 ( 24) hydrogen bonds : bond 0.05935 / 3.97 ( 798) hydrogen bonds : angle 5.39112 / 3.65 ( 2310) link_BETA1-4 : bond 0.01629 / 0.77 ( 10) link_BETA1-4 : angle 4.59248 / 3.19 ( 30) link_NAG-ASN : bond 0.00642 / 0.41 ( 20) link_NAG-ASN : angle 3.79920 / 2.53 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.8825 (mtm110) cc_final: 0.8623 (mtm110) REVERT: A 466 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7228 (mt) REVERT: A 944 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7998 (t) REVERT: D 404 LEU cc_start: 0.7364 (tp) cc_final: 0.6684 (pp) REVERT: D 457 ASN cc_start: 0.8803 (m-40) cc_final: 0.8602 (m-40) REVERT: D 461 ASP cc_start: 0.8658 (p0) cc_final: 0.8381 (p0) REVERT: D 525 ASP cc_start: 0.8476 (p0) cc_final: 0.8200 (p0) REVERT: B 132 ARG cc_start: 0.8847 (mtm110) cc_final: 0.8644 (mtm110) REVERT: B 466 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7215 (mt) REVERT: B 633 ARG cc_start: 0.8640 (tmm-80) cc_final: 0.7782 (ttm-80) REVERT: B 944 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7990 (t) REVERT: C 404 LEU cc_start: 0.7354 (tp) cc_final: 0.6668 (pp) REVERT: C 461 ASP cc_start: 0.8653 (p0) cc_final: 0.8369 (p0) REVERT: C 525 ASP cc_start: 0.8472 (p0) cc_final: 0.8229 (p0) outliers start: 64 outliers final: 29 residues processed: 215 average time/residue: 0.1238 time to fit residues: 42.1602 Evaluate side-chains 188 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 832 TRP Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 832 TRP Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain C residue 460 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 6 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106119 restraints weight = 28594.405| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.52 r_work: 0.3170 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18570 Z= 0.141 Angle : 0.625 17.131 25354 Z= 0.311 Chirality : 0.045 0.430 2876 Planarity : 0.004 0.057 3212 Dihedral : 6.247 57.337 3026 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.43 % Favored : 94.11 % Rotamer: Outliers : 3.60 % Allowed : 23.90 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.74 (0.18), residues: 2192 helix: 0.56 (0.17), residues: 898 sheet: -0.53 (0.27), residues: 370 loop : -1.50 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 476 TYR 0.019 0.001 TYR B 468 PHE 0.023 0.001 PHE B 481 TRP 0.010 0.001 TRP B 832 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (18528) covalent geometry : angle 0.57309 / 0.30 (25240) SS BOND : bond 0.00186 / 0.10 ( 12) SS BOND : angle 0.72748 / 0.46 ( 24) hydrogen bonds : bond 0.05753 / 3.85 ( 798) hydrogen bonds : angle 5.23035 / 3.53 ( 2310) link_BETA1-4 : bond 0.01699 / 0.79 ( 10) link_BETA1-4 : angle 4.60691 / 3.19 ( 30) link_NAG-ASN : bond 0.00543 / 0.37 ( 20) link_NAG-ASN : angle 4.02239 / 2.65 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 167 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 397 ASP cc_start: 0.8435 (p0) cc_final: 0.8175 (p0) REVERT: D 404 LEU cc_start: 0.7352 (tp) cc_final: 0.6674 (pp) REVERT: D 461 ASP cc_start: 0.8618 (p0) cc_final: 0.8363 (p0) REVERT: D 520 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8885 (mp) REVERT: D 525 ASP cc_start: 0.8505 (p0) cc_final: 0.8242 (p0) REVERT: B 309 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8396 (tt) REVERT: B 633 ARG cc_start: 0.8610 (tmm-80) cc_final: 0.7817 (ttm-80) REVERT: B 944 VAL cc_start: 0.8266 (p) cc_final: 0.8009 (t) REVERT: C 461 ASP cc_start: 0.8607 (p0) cc_final: 0.8353 (p0) REVERT: C 525 ASP cc_start: 0.8478 (p0) cc_final: 0.8238 (p0) outliers start: 70 outliers final: 39 residues processed: 228 average time/residue: 0.1199 time to fit residues: 43.2444 Evaluate side-chains 196 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 832 TRP Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 832 TRP Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 13 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 ASN D 460 GLN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102363 restraints weight = 28755.207| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.48 r_work: 0.3068 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18570 Z= 0.192 Angle : 0.653 17.315 25354 Z= 0.324 Chirality : 0.046 0.436 2876 Planarity : 0.004 0.051 3212 Dihedral : 6.192 57.840 3026 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.30 % Favored : 93.25 % Rotamer: Outliers : 4.01 % Allowed : 23.69 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.83 (0.18), residues: 2192 helix: 0.55 (0.17), residues: 900 sheet: -0.49 (0.27), residues: 364 loop : -1.66 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.018 0.002 TYR A 468 PHE 0.024 0.001 PHE A 481 TRP 0.010 0.001 TRP A 832 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (18528) covalent geometry : angle 0.60612 / 0.31 (25240) SS BOND : bond 0.00162 / 0.09 ( 12) SS BOND : angle 0.82047 / 0.60 ( 24) hydrogen bonds : bond 0.06143 / 4.13 ( 798) hydrogen bonds : angle 5.21349 / 3.53 ( 2310) link_BETA1-4 : bond 0.01678 / 0.78 ( 10) link_BETA1-4 : angle 4.65328 / 3.22 ( 30) link_NAG-ASN : bond 0.00624 / 0.41 ( 20) link_NAG-ASN : angle 3.78366 / 2.52 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 170 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7324 (mt) REVERT: A 718 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.6779 (mt0) REVERT: D 404 LEU cc_start: 0.7354 (tp) cc_final: 0.6684 (pp) REVERT: D 461 ASP cc_start: 0.8604 (p0) cc_final: 0.8325 (p0) REVERT: D 525 ASP cc_start: 0.8602 (p0) cc_final: 0.8336 (p0) REVERT: B 466 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7354 (mt) REVERT: B 633 ARG cc_start: 0.8660 (tmm-80) cc_final: 0.7809 (ttm-80) REVERT: B 718 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.6780 (mt0) REVERT: C 404 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6370 (pp) REVERT: C 461 ASP cc_start: 0.8596 (p0) cc_final: 0.8392 (p0) REVERT: C 520 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8873 (mp) REVERT: C 525 ASP cc_start: 0.8609 (p0) cc_final: 0.8359 (p0) outliers start: 78 outliers final: 53 residues processed: 232 average time/residue: 0.1214 time to fit residues: 44.8121 Evaluate side-chains 222 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 718 GLN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 791 CYS Chi-restraints excluded: chain A residue 832 TRP Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 791 CYS Chi-restraints excluded: chain B residue 832 TRP Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 ASN A 557 HIS ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN B 369 ASN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094785 restraints weight = 28705.417| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.51 r_work: 0.2961 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 18570 Z= 0.272 Angle : 0.731 17.796 25354 Z= 0.364 Chirality : 0.049 0.446 2876 Planarity : 0.005 0.054 3212 Dihedral : 6.271 58.565 3026 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.71 % Favored : 92.84 % Rotamer: Outliers : 4.98 % Allowed : 22.97 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.03 (0.17), residues: 2192 helix: 0.37 (0.17), residues: 902 sheet: -0.53 (0.29), residues: 338 loop : -1.76 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 836 TYR 0.022 0.002 TYR B 592 PHE 0.026 0.002 PHE A 481 TRP 0.013 0.001 TRP B 832 HIS 0.007 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.27 (18528) covalent geometry : angle 0.68572 / 0.35 (25240) SS BOND : bond 0.00325 / 0.17 ( 12) SS BOND : angle 0.84505 / 0.63 ( 24) hydrogen bonds : bond 0.07302 / 4.92 ( 798) hydrogen bonds : angle 5.38029 / 3.65 ( 2310) link_BETA1-4 : bond 0.01690 / 0.79 ( 10) link_BETA1-4 : angle 4.79289 / 3.32 ( 30) link_NAG-ASN : bond 0.00586 / 0.38 ( 20) link_NAG-ASN : angle 4.01720 / 2.66 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 170 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8757 (mt-10) REVERT: A 718 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7124 (mt0) REVERT: D 461 ASP cc_start: 0.8632 (p0) cc_final: 0.8360 (p0) REVERT: D 525 ASP cc_start: 0.8713 (p0) cc_final: 0.8426 (p0) REVERT: B 466 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7538 (mt) REVERT: B 718 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7113 (mt0) REVERT: C 525 ASP cc_start: 0.8715 (p0) cc_final: 0.8411 (p0) outliers start: 97 outliers final: 74 residues processed: 243 average time/residue: 0.1212 time to fit residues: 47.2959 Evaluate side-chains 232 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 154 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 718 GLN Chi-restraints excluded: chain A residue 791 CYS Chi-restraints excluded: chain A residue 832 TRP Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 791 CYS Chi-restraints excluded: chain B residue 832 TRP Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 213 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 204 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN B 369 ASN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097146 restraints weight = 28241.601| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.51 r_work: 0.3008 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18570 Z= 0.186 Angle : 0.663 17.382 25354 Z= 0.330 Chirality : 0.046 0.424 2876 Planarity : 0.005 0.068 3212 Dihedral : 6.009 56.722 3026 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.48 % Favored : 93.07 % Rotamer: Outliers : 4.42 % Allowed : 24.00 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.04 (0.17), residues: 2192 helix: 0.44 (0.17), residues: 902 sheet: -0.75 (0.27), residues: 374 loop : -1.78 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 209 TYR 0.023 0.002 TYR B 152 PHE 0.023 0.001 PHE B 481 TRP 0.010 0.001 TRP B 832 HIS 0.006 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (18528) covalent geometry : angle 0.61669 / 0.32 (25240) SS BOND : bond 0.00263 / 0.14 ( 12) SS BOND : angle 0.76572 / 0.57 ( 24) hydrogen bonds : bond 0.06655 / 4.49 ( 798) hydrogen bonds : angle 5.24494 / 3.56 ( 2310) link_BETA1-4 : bond 0.01658 / 0.78 ( 10) link_BETA1-4 : angle 4.66333 / 3.23 ( 30) link_NAG-ASN : bond 0.00600 / 0.39 ( 20) link_NAG-ASN : angle 3.83078 / 2.55 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 161 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8748 (tpt) cc_final: 0.8347 (tpt) REVERT: A 466 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7565 (mt) REVERT: A 718 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: A 840 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8261 (m-10) REVERT: D 461 ASP cc_start: 0.8560 (p0) cc_final: 0.8320 (p0) REVERT: D 525 ASP cc_start: 0.8704 (p0) cc_final: 0.8437 (p0) REVERT: B 466 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7522 (mt) REVERT: B 718 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7203 (mt0) REVERT: B 840 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8277 (m-10) REVERT: C 416 LYS cc_start: 0.7731 (mptt) cc_final: 0.7471 (mptt) REVERT: C 525 ASP cc_start: 0.8713 (p0) cc_final: 0.8454 (p0) outliers start: 86 outliers final: 65 residues processed: 234 average time/residue: 0.1231 time to fit residues: 46.2019 Evaluate side-chains 225 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 154 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 718 GLN Chi-restraints excluded: chain A residue 791 CYS Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 840 TYR Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 791 CYS Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 98 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.127202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099035 restraints weight = 28414.090| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.50 r_work: 0.3033 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18570 Z= 0.160 Angle : 0.634 17.185 25354 Z= 0.315 Chirality : 0.046 0.410 2876 Planarity : 0.004 0.066 3212 Dihedral : 5.652 56.507 3022 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.93 % Favored : 93.61 % Rotamer: Outliers : 4.73 % Allowed : 23.74 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.96 (0.18), residues: 2192 helix: 0.57 (0.18), residues: 900 sheet: -0.68 (0.27), residues: 376 loop : -1.83 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 476 TYR 0.025 0.001 TYR B 592 PHE 0.027 0.001 PHE B 481 TRP 0.007 0.001 TRP A 65 HIS 0.004 0.001 HIS B 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (18528) covalent geometry : angle 0.58745 / 0.31 (25240) SS BOND : bond 0.00230 / 0.12 ( 12) SS BOND : angle 0.72130 / 0.54 ( 24) hydrogen bonds : bond 0.06149 / 4.14 ( 798) hydrogen bonds : angle 5.15639 / 3.50 ( 2310) link_BETA1-4 : bond 0.01669 / 0.78 ( 10) link_BETA1-4 : angle 4.61404 / 3.20 ( 30) link_NAG-ASN : bond 0.00625 / 0.41 ( 20) link_NAG-ASN : angle 3.73418 / 2.48 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 160 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8833 (mt-10) REVERT: A 345 MET cc_start: 0.8650 (tpt) cc_final: 0.8367 (tpt) REVERT: A 466 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7470 (mt) REVERT: A 718 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7061 (mt0) REVERT: D 416 LYS cc_start: 0.7847 (mptt) cc_final: 0.7447 (mptt) REVERT: D 461 ASP cc_start: 0.8654 (p0) cc_final: 0.8408 (p0) REVERT: D 525 ASP cc_start: 0.8700 (p0) cc_final: 0.8456 (p0) REVERT: B 345 MET cc_start: 0.8658 (tpt) cc_final: 0.8244 (tpt) REVERT: B 466 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7385 (mt) REVERT: B 718 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.6966 (mt0) REVERT: C 404 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6240 (pp) REVERT: C 416 LYS cc_start: 0.7795 (mptt) cc_final: 0.7547 (mptt) REVERT: C 442 LYS cc_start: 0.8427 (tppt) cc_final: 0.7930 (mttm) REVERT: C 525 ASP cc_start: 0.8700 (p0) cc_final: 0.8462 (p0) outliers start: 92 outliers final: 67 residues processed: 233 average time/residue: 0.1188 time to fit residues: 44.1409 Evaluate side-chains 228 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 155 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 718 GLN Chi-restraints excluded: chain A residue 791 CYS Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 791 CYS Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 206 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 chunk 78 optimal weight: 0.2980 chunk 129 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101802 restraints weight = 28244.924| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.53 r_work: 0.3078 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18570 Z= 0.130 Angle : 0.616 16.969 25354 Z= 0.306 Chirality : 0.045 0.396 2876 Planarity : 0.004 0.062 3212 Dihedral : 5.395 55.847 3022 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.70 % Favored : 93.84 % Rotamer: Outliers : 3.39 % Allowed : 24.61 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.84 (0.18), residues: 2192 helix: 0.70 (0.18), residues: 894 sheet: -0.67 (0.27), residues: 380 loop : -1.76 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 476 TYR 0.020 0.001 TYR B 592 PHE 0.023 0.001 PHE D 439 TRP 0.008 0.001 TRP A 832 HIS 0.007 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (18528) covalent geometry : angle 0.57014 / 0.30 (25240) SS BOND : bond 0.00191 / 0.10 ( 12) SS BOND : angle 0.67461 / 0.49 ( 24) hydrogen bonds : bond 0.05630 / 3.77 ( 798) hydrogen bonds : angle 5.07135 / 3.44 ( 2310) link_BETA1-4 : bond 0.01625 / 0.76 ( 10) link_BETA1-4 : angle 4.56149 / 3.17 ( 30) link_NAG-ASN : bond 0.00679 / 0.44 ( 20) link_NAG-ASN : angle 3.62991 / 2.41 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 169 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8858 (mt-10) REVERT: A 466 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7287 (mt) REVERT: A 718 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6860 (mt0) REVERT: D 416 LYS cc_start: 0.7846 (mptt) cc_final: 0.7556 (mptt) REVERT: D 461 ASP cc_start: 0.8647 (p0) cc_final: 0.8390 (p0) REVERT: D 520 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8856 (mp) REVERT: D 525 ASP cc_start: 0.8679 (p0) cc_final: 0.8442 (p0) REVERT: B 345 MET cc_start: 0.8607 (tpt) cc_final: 0.8213 (tpt) REVERT: B 466 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7206 (mt) REVERT: B 633 ARG cc_start: 0.8673 (tmm-80) cc_final: 0.7773 (ttm-80) REVERT: B 718 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.6847 (mt0) REVERT: C 404 LEU cc_start: 0.7419 (mm) cc_final: 0.6254 (pp) REVERT: C 416 LYS cc_start: 0.7805 (mptt) cc_final: 0.7546 (mptt) REVERT: C 442 LYS cc_start: 0.8478 (tppt) cc_final: 0.7913 (mttm) REVERT: C 525 ASP cc_start: 0.8681 (p0) cc_final: 0.8449 (p0) outliers start: 66 outliers final: 49 residues processed: 224 average time/residue: 0.1254 time to fit residues: 44.3436 Evaluate side-chains 213 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 718 GLN Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 22 optimal weight: 1.9990 chunk 116 optimal weight: 0.0170 chunk 157 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 177 optimal weight: 0.1980 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 HIS ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.130966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102962 restraints weight = 28017.851| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.47 r_work: 0.3101 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18570 Z= 0.127 Angle : 0.605 17.039 25354 Z= 0.301 Chirality : 0.045 0.392 2876 Planarity : 0.004 0.062 3212 Dihedral : 5.291 55.899 3022 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.52 % Favored : 94.02 % Rotamer: Outliers : 3.75 % Allowed : 24.15 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.73 (0.18), residues: 2192 helix: 0.75 (0.18), residues: 894 sheet: -0.60 (0.27), residues: 380 loop : -1.66 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.018 0.001 TYR B 592 PHE 0.023 0.001 PHE B 481 TRP 0.008 0.001 TRP A 832 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (18528) covalent geometry : angle 0.55845 / 0.29 (25240) SS BOND : bond 0.00167 / 0.09 ( 12) SS BOND : angle 0.63776 / 0.46 ( 24) hydrogen bonds : bond 0.05495 / 3.68 ( 798) hydrogen bonds : angle 5.01367 / 3.40 ( 2310) link_BETA1-4 : bond 0.01666 / 0.78 ( 10) link_BETA1-4 : angle 4.56759 / 3.17 ( 30) link_NAG-ASN : bond 0.00671 / 0.43 ( 20) link_NAG-ASN : angle 3.57543 / 2.36 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7207 (mt) REVERT: A 718 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6876 (mt0) REVERT: D 416 LYS cc_start: 0.7856 (mptt) cc_final: 0.7557 (mptt) REVERT: D 461 ASP cc_start: 0.8618 (p0) cc_final: 0.8353 (p0) REVERT: D 520 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8858 (mp) REVERT: D 525 ASP cc_start: 0.8701 (p0) cc_final: 0.8481 (p0) REVERT: B 195 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8586 (ptmm) REVERT: B 345 MET cc_start: 0.8590 (tpt) cc_final: 0.8273 (tpt) REVERT: B 466 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7328 (mt) REVERT: B 633 ARG cc_start: 0.8677 (tmm-80) cc_final: 0.7780 (ttm-80) REVERT: B 718 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.6886 (mt0) REVERT: C 391 ARG cc_start: 0.8413 (mmt-90) cc_final: 0.7834 (mmm-85) REVERT: C 404 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6264 (pp) REVERT: C 416 LYS cc_start: 0.7848 (mptt) cc_final: 0.7582 (mptt) REVERT: C 442 LYS cc_start: 0.8449 (tppt) cc_final: 0.7897 (mttm) REVERT: C 525 ASP cc_start: 0.8702 (p0) cc_final: 0.8477 (p0) outliers start: 73 outliers final: 57 residues processed: 221 average time/residue: 0.1267 time to fit residues: 44.3229 Evaluate side-chains 220 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 718 GLN Chi-restraints excluded: chain A residue 791 CYS Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 791 CYS Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 120 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 158 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 204 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN B 591 HIS ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100535 restraints weight = 27905.364| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.43 r_work: 0.3073 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18570 Z= 0.156 Angle : 0.625 17.245 25354 Z= 0.310 Chirality : 0.046 0.394 2876 Planarity : 0.004 0.066 3212 Dihedral : 5.318 56.794 3022 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.79 % Favored : 93.75 % Rotamer: Outliers : 3.60 % Allowed : 24.25 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.74 (0.18), residues: 2192 helix: 0.70 (0.18), residues: 900 sheet: -0.57 (0.27), residues: 380 loop : -1.66 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.044 0.002 TYR B 152 PHE 0.024 0.001 PHE B 481 TRP 0.014 0.001 TRP A 593 HIS 0.007 0.001 HIS A 591 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (18528) covalent geometry : angle 0.58008 / 0.30 (25240) SS BOND : bond 0.00205 / 0.11 ( 12) SS BOND : angle 0.66727 / 0.49 ( 24) hydrogen bonds : bond 0.05712 / 3.84 ( 798) hydrogen bonds : angle 5.02032 / 3.40 ( 2310) link_BETA1-4 : bond 0.01673 / 0.78 ( 10) link_BETA1-4 : angle 4.61413 / 3.20 ( 30) link_NAG-ASN : bond 0.00626 / 0.41 ( 20) link_NAG-ASN : angle 3.59487 / 2.38 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 153 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7264 (mt) REVERT: A 593 TRP cc_start: 0.9087 (m100) cc_final: 0.8860 (m100) REVERT: A 718 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7003 (mt0) REVERT: D 416 LYS cc_start: 0.7859 (mptt) cc_final: 0.7555 (mptt) REVERT: D 461 ASP cc_start: 0.8655 (p0) cc_final: 0.8407 (p0) REVERT: D 525 ASP cc_start: 0.8699 (p0) cc_final: 0.8467 (p0) REVERT: B 345 MET cc_start: 0.8636 (tpt) cc_final: 0.8295 (tpt) REVERT: B 466 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7325 (mt) REVERT: B 718 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6989 (mt0) REVERT: C 391 ARG cc_start: 0.8420 (mmt-90) cc_final: 0.7828 (mmm-85) REVERT: C 404 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6254 (pp) REVERT: C 416 LYS cc_start: 0.7847 (mptt) cc_final: 0.7587 (mptt) REVERT: C 442 LYS cc_start: 0.8407 (tppt) cc_final: 0.7921 (mttm) REVERT: C 525 ASP cc_start: 0.8695 (p0) cc_final: 0.8475 (p0) outliers start: 70 outliers final: 62 residues processed: 211 average time/residue: 0.1213 time to fit residues: 40.8990 Evaluate side-chains 220 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 153 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 718 GLN Chi-restraints excluded: chain A residue 791 CYS Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 591 HIS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 791 CYS Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 57 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 198 optimal weight: 0.0670 chunk 81 optimal weight: 0.0970 chunk 181 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 HIS ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102606 restraints weight = 28394.616| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.52 r_work: 0.3087 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18570 Z= 0.129 Angle : 0.608 17.014 25354 Z= 0.302 Chirality : 0.045 0.390 2876 Planarity : 0.004 0.065 3212 Dihedral : 5.276 56.146 3022 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.70 % Favored : 93.84 % Rotamer: Outliers : 3.39 % Allowed : 24.41 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.68 (0.18), residues: 2192 helix: 0.79 (0.18), residues: 892 sheet: -0.60 (0.27), residues: 384 loop : -1.63 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.043 0.001 TYR B 152 PHE 0.023 0.001 PHE A 481 TRP 0.014 0.001 TRP B 593 HIS 0.013 0.001 HIS B 591 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (18528) covalent geometry : angle 0.56282 / 0.29 (25240) SS BOND : bond 0.00183 / 0.10 ( 12) SS BOND : angle 0.64242 / 0.47 ( 24) hydrogen bonds : bond 0.05541 / 3.72 ( 798) hydrogen bonds : angle 4.99207 / 3.38 ( 2310) link_BETA1-4 : bond 0.01644 / 0.77 ( 10) link_BETA1-4 : angle 4.56469 / 3.16 ( 30) link_NAG-ASN : bond 0.00655 / 0.43 ( 20) link_NAG-ASN : angle 3.54216 / 2.35 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.27 seconds wall clock time: 69 minutes 9.45 seconds (4149.45 seconds total)