Starting phenix.real_space_refine on Thu Sep 18 09:06:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9daz_46708/09_2025/9daz_46708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9daz_46708/09_2025/9daz_46708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9daz_46708/09_2025/9daz_46708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9daz_46708/09_2025/9daz_46708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9daz_46708/09_2025/9daz_46708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9daz_46708/09_2025/9daz_46708.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 52 5.16 5 C 9592 2.51 5 N 2504 2.21 5 O 2924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15074 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 887, 6761 Classifications: {'peptide': 887} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 43, 'TRANS': 843} Chain breaks: 4 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 25, 'ASN:plan1': 7, 'HIS:plan': 2, 'GLN:plan1': 11, 'ARG:plan': 4, 'ASP:plan': 12, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 237 Chain: "B" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 473 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain breaks: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 6761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 887, 6761 Classifications: {'peptide': 887} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 43, 'TRANS': 843} Chain breaks: 4 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 25, 'ASN:plan1': 7, 'HIS:plan': 2, 'GLN:plan1': 11, 'ARG:plan': 4, 'ASP:plan': 12, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 237 Chain: "D" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 473 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain breaks: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 54 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Time building chain proxies: 3.54, per 1000 atoms: 0.23 Number of scatterers: 15074 At special positions: 0 Unit cell: (166.254, 105.798, 115.874, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 52 16.00 O 2924 8.00 N 2504 7.00 C 9592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 762 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 799 " - pdb=" SG CYS A 835 " distance=2.04 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 762 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS C 799 " - pdb=" SG CYS C 835 " distance=2.04 Simple disulfide: pdb=" SG CYS D 587 " - pdb=" SG CYS D 600 " 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 3 " NAG-ASN " NAG A1301 " - " ASN A 126 " " NAG C1301 " - " ASN C 126 " " NAG E 1 " - " ASN A 682 " " NAG F 1 " - " ASN A 84 " " NAG G 1 " - " ASN A 233 " " NAG H 1 " - " ASN A 626 " " NAG I 1 " - " ASN A 740 " " NAG J 1 " - " ASN B 559 " " NAG K 1 " - " ASN C 682 " " NAG L 1 " - " ASN C 84 " " NAG M 1 " - " ASN C 233 " " NAG N 1 " - " ASN C 626 " " NAG O 1 " - " ASN C 740 " " NAG P 1 " - " ASN D 559 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 525.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 391 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 387 " pdb=" ZN C1302 " pdb="ZN ZN C1302 " - pdb=" NE2 HIS C 391 " pdb="ZN ZN C1302 " - pdb=" NE2 HIS C 387 " 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3700 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 26 sheets defined 48.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.540A pdb=" N VAL A 71 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 313 through 332 removed outlier: 4.175A pdb=" N GLY A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 374 through 391 removed outlier: 3.794A pdb=" N HIS A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 405 through 425 removed outlier: 3.813A pdb=" N ASN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TYR A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 4.254A pdb=" N ASN A 429 " --> pdb=" O PRO A 426 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 430 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS A 431 " --> pdb=" O TRP A 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 431' Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.578A pdb=" N LEU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 removed outlier: 3.912A pdb=" N ALA A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.712A pdb=" N VAL A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 490 removed outlier: 3.573A pdb=" N TYR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.802A pdb=" N LEU A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 545 removed outlier: 3.948A pdb=" N ARG A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TRP A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 614 removed outlier: 3.540A pdb=" N LYS A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 611 through 614' Processing helix chain 'A' and resid 624 through 628 removed outlier: 3.505A pdb=" N THR A 628 " --> pdb=" O LEU A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 650 Processing helix chain 'A' and resid 651 through 654 Processing helix chain 'A' and resid 655 through 672 removed outlier: 3.964A pdb=" N ILE A 663 " --> pdb=" O ARG A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 683 removed outlier: 3.681A pdb=" N ALA A 680 " --> pdb=" O PRO A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 690 removed outlier: 4.079A pdb=" N ILE A 688 " --> pdb=" O LEU A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 711 removed outlier: 4.310A pdb=" N TRP A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 738 Proline residue: A 729 - end of helix Processing helix chain 'A' and resid 747 through 764 Processing helix chain 'A' and resid 766 through 783 removed outlier: 3.507A pdb=" N ASN A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 819 Processing helix chain 'A' and resid 823 through 833 Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 856 through 870 removed outlier: 4.498A pdb=" N THR A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 870 " --> pdb=" O SER A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 884 removed outlier: 4.462A pdb=" N LEU A 876 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 893 Processing helix chain 'A' and resid 897 through 906 Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 933 through 967 removed outlier: 5.874A pdb=" N ASP A 957 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.540A pdb=" N VAL C 71 " --> pdb=" O PRO C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 304 through 311 Processing helix chain 'C' and resid 313 through 332 removed outlier: 4.174A pdb=" N GLY C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Proline residue: C 322 - end of helix Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 374 through 391 removed outlier: 3.795A pdb=" N HIS C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 405 through 425 removed outlier: 3.813A pdb=" N ASN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TYR C 418 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU C 419 " --> pdb=" O TYR C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 4.255A pdb=" N ASN C 429 " --> pdb=" O PRO C 426 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 430 " --> pdb=" O THR C 427 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS C 431 " --> pdb=" O TRP C 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 426 through 431' Processing helix chain 'C' and resid 432 through 438 removed outlier: 4.578A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 447 removed outlier: 3.912A pdb=" N ALA C 444 " --> pdb=" O TYR C 440 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 461 Processing helix chain 'C' and resid 463 through 470 removed outlier: 3.712A pdb=" N VAL C 470 " --> pdb=" O GLN C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 490 removed outlier: 3.573A pdb=" N TYR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 479 " --> pdb=" O SER C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'C' and resid 512 through 526 removed outlier: 3.802A pdb=" N LEU C 516 " --> pdb=" O ILE C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 545 removed outlier: 3.948A pdb=" N ARG C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TRP C 543 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 614 removed outlier: 3.539A pdb=" N LYS C 614 " --> pdb=" O ASP C 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 611 through 614' Processing helix chain 'C' and resid 624 through 628 removed outlier: 3.505A pdb=" N THR C 628 " --> pdb=" O LEU C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 650 Processing helix chain 'C' and resid 651 through 654 Processing helix chain 'C' and resid 655 through 672 removed outlier: 3.964A pdb=" N ILE C 663 " --> pdb=" O ARG C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 683 removed outlier: 3.681A pdb=" N ALA C 680 " --> pdb=" O PRO C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 690 removed outlier: 4.079A pdb=" N ILE C 688 " --> pdb=" O LEU C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 711 removed outlier: 4.310A pdb=" N TRP C 696 " --> pdb=" O GLU C 692 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR C 705 " --> pdb=" O SER C 701 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 738 Proline residue: C 729 - end of helix Processing helix chain 'C' and resid 747 through 764 Processing helix chain 'C' and resid 766 through 783 removed outlier: 3.508A pdb=" N ASN C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 805 Processing helix chain 'C' and resid 806 through 819 Processing helix chain 'C' and resid 823 through 833 Processing helix chain 'C' and resid 838 through 849 Processing helix chain 'C' and resid 856 through 870 removed outlier: 4.498A pdb=" N THR C 861 " --> pdb=" O LYS C 857 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER C 862 " --> pdb=" O GLN C 858 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 870 " --> pdb=" O SER C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 884 removed outlier: 4.462A pdb=" N LEU C 876 " --> pdb=" O VAL C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 893 Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 912 through 926 Processing helix chain 'C' and resid 933 through 967 removed outlier: 5.873A pdb=" N ASP C 957 " --> pdb=" O LYS C 953 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL C 958 " --> pdb=" O GLU C 954 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 127 removed outlier: 7.792A pdb=" N VAL A 100 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR A 102 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU A 87 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 104 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 85 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE A 106 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR A 83 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG A 108 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 121 removed outlier: 3.793A pdb=" N ARG A 151 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 199 Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA6, first strand: chain 'A' and resid 287 through 292 removed outlier: 8.107A pdb=" N VAL A 359 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP A 341 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR A 361 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A 343 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AA8, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AA9, first strand: chain 'A' and resid 585 through 588 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 596 Processing sheet with id=AB2, first strand: chain 'B' and resid 552 through 554 Processing sheet with id=AB3, first strand: chain 'B' and resid 552 through 554 removed outlier: 3.651A pdb=" N SER B 598 " --> pdb=" O SER B 589 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 607 through 609 removed outlier: 6.843A pdb=" N VAL B 646 " --> pdb=" O VAL B 657 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AB6, first strand: chain 'C' and resid 126 through 127 removed outlier: 7.793A pdb=" N VAL C 100 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR C 102 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU C 87 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR C 104 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL C 85 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 106 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR C 83 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG C 108 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 117 through 121 removed outlier: 3.792A pdb=" N ARG C 151 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 191 through 199 Processing sheet with id=AB9, first strand: chain 'C' and resid 243 through 245 Processing sheet with id=AC1, first strand: chain 'C' and resid 287 through 292 removed outlier: 8.107A pdb=" N VAL C 359 " --> pdb=" O LYS C 339 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP C 341 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR C 361 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 343 " --> pdb=" O TYR C 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 398 through 400 Processing sheet with id=AC3, first strand: chain 'C' and resid 607 through 609 Processing sheet with id=AC4, first strand: chain 'C' and resid 585 through 588 Processing sheet with id=AC5, first strand: chain 'C' and resid 595 through 596 Processing sheet with id=AC6, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AC7, first strand: chain 'D' and resid 552 through 554 removed outlier: 3.651A pdb=" N SER D 598 " --> pdb=" O SER D 589 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 607 through 609 removed outlier: 6.843A pdb=" N VAL D 646 " --> pdb=" O VAL D 657 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2244 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: 2.80 Time building geometry restraints manager: 1.75 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: 4683 1.34 - 1.46: 3261 1.46 - 1.58: 7194 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 15228 Sorted by residual: bond pdb=" CB TRP C 517 " pdb=" CG TRP C 517 " ideal model delta sigma weight residual 1.498 1.525 -0.027 3.10e-02 1.04e+03 7.74e-01 bond pdb=" CB TRP A 517 " pdb=" CG TRP A 517 " ideal model delta sigma weight residual 1.498 1.524 -0.026 3.10e-02 1.04e+03 7.27e-01 bond pdb=" N GLY A 183 " pdb=" CA GLY A 183 " ideal model delta sigma weight residual 1.449 1.437 0.012 1.45e-02 4.76e+03 6.87e-01 bond pdb=" N GLY C 183 " pdb=" CA GLY C 183 " ideal model delta sigma weight residual 1.449 1.437 0.012 1.45e-02 4.76e+03 6.87e-01 bond pdb=" CB PRO C 587 " pdb=" CG PRO C 587 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.14e-01 ... (remaining 15223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 20305 1.22 - 2.44: 440 2.44 - 3.66: 99 3.66 - 4.87: 17 4.87 - 6.09: 5 Bond angle restraints: 20866 Sorted by residual: angle pdb=" C ASN A 488 " pdb=" N PHE A 489 " pdb=" CA PHE A 489 " ideal model delta sigma weight residual 122.38 116.29 6.09 1.81e+00 3.05e-01 1.13e+01 angle pdb=" C ASN C 488 " pdb=" N PHE C 489 " pdb=" CA PHE C 489 " ideal model delta sigma weight residual 122.38 116.32 6.06 1.81e+00 3.05e-01 1.12e+01 angle pdb=" C ASN A 462 " pdb=" N THR A 463 " pdb=" CA THR A 463 " ideal model delta sigma weight residual 120.49 124.76 -4.27 1.42e+00 4.96e-01 9.05e+00 angle pdb=" C ASN C 462 " pdb=" N THR C 463 " pdb=" CA THR C 463 " ideal model delta sigma weight residual 120.49 124.76 -4.27 1.42e+00 4.96e-01 9.05e+00 angle pdb=" N LEU C 623 " pdb=" CA LEU C 623 " pdb=" C LEU C 623 " ideal model delta sigma weight residual 111.56 115.57 -4.01 1.53e+00 4.27e-01 6.87e+00 ... (remaining 20861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 8868 16.89 - 33.77: 308 33.77 - 50.66: 64 50.66 - 67.55: 6 67.55 - 84.44: 8 Dihedral angle restraints: 9254 sinusoidal: 3564 harmonic: 5690 Sorted by residual: dihedral pdb=" CA ILE A 585 " pdb=" C ILE A 585 " pdb=" N VAL A 586 " pdb=" CA VAL A 586 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ILE C 585 " pdb=" C ILE C 585 " pdb=" N VAL C 586 " pdb=" CA VAL C 586 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LEU A 602 " pdb=" C LEU A 602 " pdb=" N PRO A 603 " pdb=" CA PRO A 603 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 9251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1634 0.034 - 0.069: 609 0.069 - 0.103: 149 0.103 - 0.137: 80 0.137 - 0.171: 8 Chirality restraints: 2480 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 233 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 233 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA ILE A 552 " pdb=" N ILE A 552 " pdb=" C ILE A 552 " pdb=" CB ILE A 552 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 2477 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 549 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO C 550 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 550 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 550 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 549 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 550 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 550 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 550 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 489 " 0.013 2.00e-02 2.50e+03 1.19e-02 2.46e+00 pdb=" CG PHE C 489 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 489 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 489 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 489 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 489 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 489 " 0.002 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2773 2.78 - 3.31: 13626 3.31 - 3.84: 25444 3.84 - 4.37: 31035 4.37 - 4.90: 52027 Nonbonded interactions: 124905 Sorted by model distance: nonbonded pdb=" OD1 ASP C 711 " pdb=" O HOH C1401 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP A 711 " pdb=" O HOH A1401 " model vdw 2.245 3.040 nonbonded pdb=" NE2 GLN A 921 " pdb=" OD1 ASN A 925 " model vdw 2.245 3.120 nonbonded pdb=" NE2 GLN C 921 " pdb=" OD1 ASN C 925 " model vdw 2.245 3.120 nonbonded pdb=" OE1 GLU A 410 " pdb="ZN ZN A1302 " model vdw 2.261 2.230 ... (remaining 124900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'O' } 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: 8.780 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.770 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.002 0.039 15266 Z= 0.104 Angle : 0.483 6.094 20962 Z= 0.263 Chirality : 0.042 0.171 2480 Planarity : 0.004 0.043 2626 Dihedral : 9.524 84.437 5536 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.74 % Allowed : 3.60 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.19), residues: 1894 helix: 1.20 (0.18), residues: 824 sheet: 0.33 (0.27), residues: 360 loop : -0.14 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 721 TYR 0.012 0.001 TYR C 83 PHE 0.027 0.001 PHE C 489 TRP 0.010 0.001 TRP C 393 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00210 (15228) covalent geometry : angle 0.47734 (20866) SS BOND : bond 0.00322 ( 6) SS BOND : angle 0.99358 ( 12) hydrogen bonds : bond 0.14222 ( 794) hydrogen bonds : angle 5.62869 ( 2244) metal coordination : bond 0.00230 ( 4) link_BETA1-4 : bond 0.00409 ( 12) link_BETA1-4 : angle 1.23450 ( 36) link_BETA1-6 : bond 0.00352 ( 2) link_BETA1-6 : angle 1.17826 ( 6) link_NAG-ASN : bond 0.00214 ( 14) link_NAG-ASN : angle 1.17539 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.602 Fit side-chains REVERT: A 282 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.6501 (tp) REVERT: A 329 GLN cc_start: 0.7980 (mt0) cc_final: 0.7643 (mm-40) REVERT: A 422 ASP cc_start: 0.7881 (t70) cc_final: 0.7597 (t0) REVERT: A 443 MET cc_start: 0.8838 (mtt) cc_final: 0.8280 (mtt) REVERT: A 522 GLN cc_start: 0.7834 (mt0) cc_final: 0.7306 (pt0) REVERT: A 606 GLU cc_start: 0.8226 (tt0) cc_final: 0.8014 (tm-30) REVERT: A 607 LYS cc_start: 0.8663 (tttt) cc_final: 0.7994 (tttm) REVERT: C 282 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6506 (tp) REVERT: C 329 GLN cc_start: 0.7923 (mt0) cc_final: 0.7595 (mm-40) REVERT: C 422 ASP cc_start: 0.7878 (t70) cc_final: 0.7598 (t0) REVERT: C 443 MET cc_start: 0.8798 (mtt) cc_final: 0.8222 (mtt) REVERT: C 606 GLU cc_start: 0.8253 (tt0) cc_final: 0.8043 (tm-30) REVERT: C 607 LYS cc_start: 0.8651 (tttt) cc_final: 0.7994 (tttm) outliers start: 10 outliers final: 2 residues processed: 178 average time/residue: 0.6993 time to fit residues: 135.8526 Evaluate side-chains 126 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 517 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 144 HIS A 409 ASN A 597 GLN A 870 ASN C 105 ASN C 144 HIS C 409 ASN C 597 GLN C 648 GLN C 870 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120901 restraints weight = 14454.128| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.60 r_work: 0.3207 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15266 Z= 0.219 Angle : 0.671 7.632 20962 Z= 0.353 Chirality : 0.050 0.199 2480 Planarity : 0.005 0.050 2626 Dihedral : 5.674 79.199 2636 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.91 % Allowed : 6.54 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.19), residues: 1894 helix: 1.09 (0.18), residues: 856 sheet: 0.24 (0.26), residues: 356 loop : -0.51 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 441 TYR 0.023 0.002 TYR C 83 PHE 0.037 0.003 PHE C 489 TRP 0.017 0.003 TRP A 393 HIS 0.009 0.002 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00512 (15228) covalent geometry : angle 0.66481 (20866) SS BOND : bond 0.01063 ( 6) SS BOND : angle 1.90459 ( 12) hydrogen bonds : bond 0.06583 ( 794) hydrogen bonds : angle 4.36654 ( 2244) metal coordination : bond 0.00963 ( 4) link_BETA1-4 : bond 0.00396 ( 12) link_BETA1-4 : angle 1.56983 ( 36) link_BETA1-6 : bond 0.00204 ( 2) link_BETA1-6 : angle 1.80254 ( 6) link_NAG-ASN : bond 0.00332 ( 14) link_NAG-ASN : angle 1.35089 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.450 Fit side-chains REVERT: A 204 LYS cc_start: 0.7383 (mtpt) cc_final: 0.7095 (mtpp) REVERT: A 329 GLN cc_start: 0.7945 (mt0) cc_final: 0.7501 (mm-40) REVERT: A 422 ASP cc_start: 0.8184 (t70) cc_final: 0.7846 (t0) REVERT: A 607 LYS cc_start: 0.8846 (tttt) cc_final: 0.8071 (tttm) REVERT: A 648 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7728 (tp40) REVERT: A 770 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: A 901 ASN cc_start: 0.8464 (m-40) cc_final: 0.8239 (m110) REVERT: C 204 LYS cc_start: 0.7399 (mtpt) cc_final: 0.7155 (mtpp) REVERT: C 329 GLN cc_start: 0.7916 (mt0) cc_final: 0.7463 (mm-40) REVERT: C 422 ASP cc_start: 0.8182 (t70) cc_final: 0.7847 (t0) REVERT: C 607 LYS cc_start: 0.8850 (tttt) cc_final: 0.8074 (tttm) REVERT: C 739 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7832 (mtmm) REVERT: C 770 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: C 901 ASN cc_start: 0.8517 (m-40) cc_final: 0.8239 (m110) outliers start: 26 outliers final: 12 residues processed: 138 average time/residue: 0.7399 time to fit residues: 111.2141 Evaluate side-chains 136 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 517 TRP Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 770 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 179 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN A 637 ASN C 409 ASN C 637 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120801 restraints weight = 14583.960| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.61 r_work: 0.3198 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15266 Z= 0.200 Angle : 0.643 7.146 20962 Z= 0.339 Chirality : 0.049 0.196 2480 Planarity : 0.005 0.053 2626 Dihedral : 5.836 80.046 2636 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.06 % Favored : 97.84 % Rotamer: Outliers : 2.13 % Allowed : 7.79 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.18), residues: 1894 helix: 1.08 (0.18), residues: 840 sheet: 0.19 (0.26), residues: 354 loop : -0.65 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 441 TYR 0.020 0.002 TYR A 83 PHE 0.034 0.002 PHE C 489 TRP 0.020 0.002 TRP A 393 HIS 0.007 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00465 (15228) covalent geometry : angle 0.63582 (20866) SS BOND : bond 0.01427 ( 6) SS BOND : angle 2.34753 ( 12) hydrogen bonds : bond 0.06223 ( 794) hydrogen bonds : angle 4.29407 ( 2244) metal coordination : bond 0.00763 ( 4) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 1.51264 ( 36) link_BETA1-6 : bond 0.00187 ( 2) link_BETA1-6 : angle 1.79758 ( 6) link_NAG-ASN : bond 0.00309 ( 14) link_NAG-ASN : angle 1.30811 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.596 Fit side-chains REVERT: A 204 LYS cc_start: 0.7400 (mtpt) cc_final: 0.7118 (mtpp) REVERT: A 329 GLN cc_start: 0.7955 (mt0) cc_final: 0.7515 (mm-40) REVERT: A 422 ASP cc_start: 0.8169 (t70) cc_final: 0.7885 (t0) REVERT: A 522 GLN cc_start: 0.7938 (mt0) cc_final: 0.7518 (mt0) REVERT: A 607 LYS cc_start: 0.8877 (tttt) cc_final: 0.8077 (tttm) REVERT: A 648 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7840 (tp40) REVERT: A 739 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7830 (mtmm) REVERT: A 770 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: A 901 ASN cc_start: 0.8518 (m-40) cc_final: 0.8268 (m110) REVERT: A 940 GLN cc_start: 0.7941 (mt0) cc_final: 0.7662 (mt0) REVERT: C 204 LYS cc_start: 0.7402 (mtpt) cc_final: 0.7160 (mtpp) REVERT: C 329 GLN cc_start: 0.7929 (mt0) cc_final: 0.7455 (mm-40) REVERT: C 422 ASP cc_start: 0.8164 (t70) cc_final: 0.7876 (t0) REVERT: C 522 GLN cc_start: 0.7999 (mt0) cc_final: 0.7505 (mt0) REVERT: C 607 LYS cc_start: 0.8876 (tttt) cc_final: 0.8067 (tttm) REVERT: C 739 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7821 (mtmm) REVERT: C 770 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: C 901 ASN cc_start: 0.8507 (m-40) cc_final: 0.8243 (m110) REVERT: C 940 GLN cc_start: 0.7929 (mt0) cc_final: 0.7607 (mt0) outliers start: 29 outliers final: 15 residues processed: 140 average time/residue: 0.7865 time to fit residues: 119.3858 Evaluate side-chains 141 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 517 TRP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain D residue 593 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 94 optimal weight: 8.9990 chunk 169 optimal weight: 0.0670 chunk 135 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN C 409 ASN C 637 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122274 restraints weight = 14531.533| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.56 r_work: 0.3206 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15266 Z= 0.188 Angle : 0.631 6.965 20962 Z= 0.332 Chirality : 0.048 0.191 2480 Planarity : 0.005 0.054 2626 Dihedral : 5.894 80.447 2636 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 2.57 % Allowed : 8.24 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.18), residues: 1894 helix: 1.03 (0.17), residues: 840 sheet: 0.18 (0.26), residues: 354 loop : -0.69 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.019 0.002 TYR A 83 PHE 0.033 0.002 PHE A 489 TRP 0.021 0.002 TRP A 393 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00436 (15228) covalent geometry : angle 0.62378 (20866) SS BOND : bond 0.01371 ( 6) SS BOND : angle 2.22820 ( 12) hydrogen bonds : bond 0.06017 ( 794) hydrogen bonds : angle 4.26387 ( 2244) metal coordination : bond 0.00688 ( 4) link_BETA1-4 : bond 0.00440 ( 12) link_BETA1-4 : angle 1.50563 ( 36) link_BETA1-6 : bond 0.00216 ( 2) link_BETA1-6 : angle 1.71562 ( 6) link_NAG-ASN : bond 0.00301 ( 14) link_NAG-ASN : angle 1.30339 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.657 Fit side-chains REVERT: A 204 LYS cc_start: 0.7402 (mtpt) cc_final: 0.7117 (mtpp) REVERT: A 329 GLN cc_start: 0.7914 (mt0) cc_final: 0.7443 (mm-40) REVERT: A 422 ASP cc_start: 0.8214 (t70) cc_final: 0.7945 (t0) REVERT: A 522 GLN cc_start: 0.7957 (mt0) cc_final: 0.7442 (mt0) REVERT: A 607 LYS cc_start: 0.8877 (tttt) cc_final: 0.8060 (tttm) REVERT: A 648 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7771 (tp40) REVERT: A 739 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7798 (mtmm) REVERT: A 770 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 901 ASN cc_start: 0.8509 (m-40) cc_final: 0.8254 (m110) REVERT: A 940 GLN cc_start: 0.7942 (mt0) cc_final: 0.7678 (mt0) REVERT: C 204 LYS cc_start: 0.7374 (mtpt) cc_final: 0.7138 (mtpp) REVERT: C 329 GLN cc_start: 0.7907 (mt0) cc_final: 0.7443 (mm-40) REVERT: C 422 ASP cc_start: 0.8212 (t70) cc_final: 0.7942 (t0) REVERT: C 522 GLN cc_start: 0.8023 (mt0) cc_final: 0.7561 (mt0) REVERT: C 607 LYS cc_start: 0.8880 (tttt) cc_final: 0.8056 (tttm) REVERT: C 739 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7814 (mtmm) REVERT: C 770 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: C 901 ASN cc_start: 0.8507 (m-40) cc_final: 0.8251 (m110) REVERT: C 940 GLN cc_start: 0.7918 (mt0) cc_final: 0.7664 (mt0) outliers start: 35 outliers final: 18 residues processed: 141 average time/residue: 0.7703 time to fit residues: 118.3023 Evaluate side-chains 143 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 517 TRP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain D residue 593 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN C 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122992 restraints weight = 14514.578| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.56 r_work: 0.3223 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15266 Z= 0.163 Angle : 0.601 8.534 20962 Z= 0.317 Chirality : 0.046 0.186 2480 Planarity : 0.005 0.053 2626 Dihedral : 5.831 80.787 2636 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.11 % Favored : 97.78 % Rotamer: Outliers : 2.28 % Allowed : 9.04 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.18), residues: 1894 helix: 1.20 (0.17), residues: 832 sheet: 0.22 (0.26), residues: 354 loop : -0.68 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.018 0.002 TYR A 502 PHE 0.032 0.002 PHE A 489 TRP 0.020 0.002 TRP A 393 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00373 (15228) covalent geometry : angle 0.59328 (20866) SS BOND : bond 0.01255 ( 6) SS BOND : angle 2.33334 ( 12) hydrogen bonds : bond 0.05635 ( 794) hydrogen bonds : angle 4.21504 ( 2244) metal coordination : bond 0.00571 ( 4) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 1.47016 ( 36) link_BETA1-6 : bond 0.00254 ( 2) link_BETA1-6 : angle 1.56458 ( 6) link_NAG-ASN : bond 0.00290 ( 14) link_NAG-ASN : angle 1.25186 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.603 Fit side-chains REVERT: A 204 LYS cc_start: 0.7411 (mtpt) cc_final: 0.7122 (mtpp) REVERT: A 329 GLN cc_start: 0.7839 (mt0) cc_final: 0.7387 (mm-40) REVERT: A 422 ASP cc_start: 0.8153 (t70) cc_final: 0.7885 (t0) REVERT: A 522 GLN cc_start: 0.7946 (mt0) cc_final: 0.7482 (mt0) REVERT: A 607 LYS cc_start: 0.8872 (tttt) cc_final: 0.8051 (tttm) REVERT: A 648 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7608 (tp40) REVERT: A 739 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7837 (mtmm) REVERT: A 770 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 901 ASN cc_start: 0.8508 (m-40) cc_final: 0.8249 (m110) REVERT: A 940 GLN cc_start: 0.7940 (mt0) cc_final: 0.7685 (mt0) REVERT: C 204 LYS cc_start: 0.7399 (mtpt) cc_final: 0.7157 (mtpp) REVERT: C 329 GLN cc_start: 0.7836 (mt0) cc_final: 0.7389 (mm-40) REVERT: C 422 ASP cc_start: 0.8153 (t70) cc_final: 0.7884 (t0) REVERT: C 522 GLN cc_start: 0.8036 (mt0) cc_final: 0.7564 (mt0) REVERT: C 607 LYS cc_start: 0.8872 (tttt) cc_final: 0.8045 (tttm) REVERT: C 739 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7795 (mtmm) REVERT: C 770 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: C 901 ASN cc_start: 0.8488 (m-40) cc_final: 0.8237 (m110) REVERT: C 940 GLN cc_start: 0.7916 (mt0) cc_final: 0.7674 (mt0) outliers start: 31 outliers final: 22 residues processed: 140 average time/residue: 0.7649 time to fit residues: 116.5433 Evaluate side-chains 147 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 517 TRP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain D residue 593 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 124 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 148 optimal weight: 0.0050 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125050 restraints weight = 14467.739| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.54 r_work: 0.3249 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15266 Z= 0.118 Angle : 0.522 5.682 20962 Z= 0.276 Chirality : 0.043 0.177 2480 Planarity : 0.004 0.050 2626 Dihedral : 5.539 81.249 2636 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.21 % Allowed : 9.85 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.19), residues: 1894 helix: 1.51 (0.18), residues: 830 sheet: 0.34 (0.26), residues: 354 loop : -0.61 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.017 0.001 TYR A 502 PHE 0.029 0.001 PHE C 489 TRP 0.017 0.001 TRP C 393 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00255 (15228) covalent geometry : angle 0.51579 (20866) SS BOND : bond 0.00875 ( 6) SS BOND : angle 1.64673 ( 12) hydrogen bonds : bond 0.04667 ( 794) hydrogen bonds : angle 4.05493 ( 2244) metal coordination : bond 0.00310 ( 4) link_BETA1-4 : bond 0.00455 ( 12) link_BETA1-4 : angle 1.39418 ( 36) link_BETA1-6 : bond 0.00304 ( 2) link_BETA1-6 : angle 1.37975 ( 6) link_NAG-ASN : bond 0.00274 ( 14) link_NAG-ASN : angle 1.12592 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.604 Fit side-chains REVERT: A 204 LYS cc_start: 0.7387 (mtpt) cc_final: 0.7055 (mtpp) REVERT: A 329 GLN cc_start: 0.7792 (mt0) cc_final: 0.7354 (mm-40) REVERT: A 422 ASP cc_start: 0.8030 (t70) cc_final: 0.7764 (t0) REVERT: A 522 GLN cc_start: 0.7895 (mt0) cc_final: 0.7423 (mt0) REVERT: A 607 LYS cc_start: 0.8810 (tttt) cc_final: 0.8010 (tttm) REVERT: A 739 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7843 (mtmm) REVERT: A 770 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: A 901 ASN cc_start: 0.8497 (m-40) cc_final: 0.8221 (m110) REVERT: A 940 GLN cc_start: 0.7804 (mt0) cc_final: 0.7594 (mt0) REVERT: C 204 LYS cc_start: 0.7393 (mtpt) cc_final: 0.7110 (mtpp) REVERT: C 329 GLN cc_start: 0.7791 (mt0) cc_final: 0.7349 (mm-40) REVERT: C 422 ASP cc_start: 0.7966 (t70) cc_final: 0.7697 (t0) REVERT: C 522 GLN cc_start: 0.7972 (mt0) cc_final: 0.7493 (mt0) REVERT: C 607 LYS cc_start: 0.8814 (tttt) cc_final: 0.8008 (tttm) REVERT: C 770 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: C 901 ASN cc_start: 0.8492 (m-40) cc_final: 0.8224 (m110) REVERT: C 940 GLN cc_start: 0.7788 (mt0) cc_final: 0.7584 (mt0) outliers start: 30 outliers final: 20 residues processed: 137 average time/residue: 0.7029 time to fit residues: 105.3321 Evaluate side-chains 143 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 517 TRP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain D residue 593 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 36 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 637 ASN ** C 527 GLN ** 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 = 0.3715 r_free = 0.3715 target = 0.149888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121336 restraints weight = 14461.308| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.60 r_work: 0.3216 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15266 Z= 0.176 Angle : 0.603 6.619 20962 Z= 0.316 Chirality : 0.047 0.182 2480 Planarity : 0.005 0.051 2626 Dihedral : 5.788 80.303 2636 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.28 % Allowed : 9.93 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.19), residues: 1894 helix: 1.31 (0.18), residues: 832 sheet: 0.28 (0.26), residues: 354 loop : -0.67 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 441 TYR 0.018 0.002 TYR C 502 PHE 0.032 0.002 PHE A 489 TRP 0.018 0.002 TRP A 393 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00406 (15228) covalent geometry : angle 0.59656 (20866) SS BOND : bond 0.01206 ( 6) SS BOND : angle 1.74066 ( 12) hydrogen bonds : bond 0.05673 ( 794) hydrogen bonds : angle 4.14345 ( 2244) metal coordination : bond 0.00678 ( 4) link_BETA1-4 : bond 0.00443 ( 12) link_BETA1-4 : angle 1.50506 ( 36) link_BETA1-6 : bond 0.00237 ( 2) link_BETA1-6 : angle 1.60427 ( 6) link_NAG-ASN : bond 0.00288 ( 14) link_NAG-ASN : angle 1.22176 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.579 Fit side-chains REVERT: A 204 LYS cc_start: 0.7384 (mtpt) cc_final: 0.7052 (mtpp) REVERT: A 329 GLN cc_start: 0.7845 (mt0) cc_final: 0.7399 (mm-40) REVERT: A 422 ASP cc_start: 0.8102 (t70) cc_final: 0.7824 (t0) REVERT: A 522 GLN cc_start: 0.7958 (mt0) cc_final: 0.7480 (mt0) REVERT: A 607 LYS cc_start: 0.8912 (tttt) cc_final: 0.8074 (tttm) REVERT: A 648 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7638 (tp40) REVERT: A 739 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7811 (mtmm) REVERT: A 770 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: A 901 ASN cc_start: 0.8492 (m-40) cc_final: 0.8237 (m110) REVERT: A 940 GLN cc_start: 0.7940 (mt0) cc_final: 0.7723 (mt0) REVERT: C 204 LYS cc_start: 0.7388 (mtpt) cc_final: 0.7048 (mtpp) REVERT: C 329 GLN cc_start: 0.7838 (mt0) cc_final: 0.7394 (mm-40) REVERT: C 422 ASP cc_start: 0.8095 (t70) cc_final: 0.7819 (t0) REVERT: C 522 GLN cc_start: 0.8044 (mt0) cc_final: 0.7546 (mt0) REVERT: C 607 LYS cc_start: 0.8916 (tttt) cc_final: 0.8075 (tttm) REVERT: C 739 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7806 (mtmm) REVERT: C 770 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: C 901 ASN cc_start: 0.8493 (m-40) cc_final: 0.8244 (m110) REVERT: C 940 GLN cc_start: 0.7894 (mt0) cc_final: 0.7674 (mt0) outliers start: 31 outliers final: 19 residues processed: 142 average time/residue: 0.7294 time to fit residues: 113.0158 Evaluate side-chains 145 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 517 TRP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain D residue 593 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 136 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 chunk 50 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 166 optimal weight: 0.4980 chunk 180 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN A 515 ASN A 637 ASN C 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125197 restraints weight = 14535.279| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.54 r_work: 0.3254 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15266 Z= 0.119 Angle : 0.534 9.304 20962 Z= 0.282 Chirality : 0.043 0.174 2480 Planarity : 0.004 0.050 2626 Dihedral : 5.554 81.268 2636 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.69 % Allowed : 10.37 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 1894 helix: 1.59 (0.18), residues: 830 sheet: 0.38 (0.26), residues: 354 loop : -0.60 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 441 TYR 0.017 0.001 TYR A 502 PHE 0.029 0.001 PHE A 489 TRP 0.017 0.001 TRP C 393 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00260 (15228) covalent geometry : angle 0.52513 (20866) SS BOND : bond 0.01259 ( 6) SS BOND : angle 2.84535 ( 12) hydrogen bonds : bond 0.04654 ( 794) hydrogen bonds : angle 4.03438 ( 2244) metal coordination : bond 0.00252 ( 4) link_BETA1-4 : bond 0.00448 ( 12) link_BETA1-4 : angle 1.39239 ( 36) link_BETA1-6 : bond 0.00262 ( 2) link_BETA1-6 : angle 1.36768 ( 6) link_NAG-ASN : bond 0.00271 ( 14) link_NAG-ASN : angle 1.10732 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.631 Fit side-chains REVERT: A 204 LYS cc_start: 0.7374 (mtpt) cc_final: 0.7042 (mtpp) REVERT: A 329 GLN cc_start: 0.7773 (mt0) cc_final: 0.7347 (mm-40) REVERT: A 422 ASP cc_start: 0.8023 (t70) cc_final: 0.7756 (t0) REVERT: A 522 GLN cc_start: 0.7912 (mt0) cc_final: 0.7440 (mt0) REVERT: A 607 LYS cc_start: 0.8831 (tttt) cc_final: 0.8024 (tttm) REVERT: A 739 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7830 (mtmm) REVERT: A 770 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 901 ASN cc_start: 0.8486 (m-40) cc_final: 0.8219 (m110) REVERT: A 940 GLN cc_start: 0.7849 (mt0) cc_final: 0.7649 (mt0) REVERT: C 204 LYS cc_start: 0.7376 (mtpt) cc_final: 0.7037 (mtpp) REVERT: C 329 GLN cc_start: 0.7766 (mt0) cc_final: 0.7337 (mm-40) REVERT: C 422 ASP cc_start: 0.7957 (t70) cc_final: 0.7690 (t0) REVERT: C 522 GLN cc_start: 0.7983 (mt0) cc_final: 0.7424 (mt0) REVERT: C 607 LYS cc_start: 0.8837 (tttt) cc_final: 0.8023 (tttm) REVERT: C 770 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: C 901 ASN cc_start: 0.8473 (m-40) cc_final: 0.8209 (m110) outliers start: 23 outliers final: 17 residues processed: 142 average time/residue: 0.6967 time to fit residues: 108.1892 Evaluate side-chains 143 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 517 TRP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain D residue 593 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 51 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 637 ASN C 515 ASN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122862 restraints weight = 14473.249| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.56 r_work: 0.3220 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15266 Z= 0.182 Angle : 0.621 9.409 20962 Z= 0.326 Chirality : 0.047 0.178 2480 Planarity : 0.005 0.051 2626 Dihedral : 5.871 80.434 2636 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.06 % Allowed : 10.29 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.19), residues: 1894 helix: 1.31 (0.17), residues: 832 sheet: 0.30 (0.26), residues: 354 loop : -0.68 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 441 TYR 0.018 0.002 TYR A 502 PHE 0.032 0.002 PHE A 489 TRP 0.018 0.002 TRP C 393 HIS 0.005 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00422 (15228) covalent geometry : angle 0.61353 (20866) SS BOND : bond 0.01332 ( 6) SS BOND : angle 2.56717 ( 12) hydrogen bonds : bond 0.05781 ( 794) hydrogen bonds : angle 4.16550 ( 2244) metal coordination : bond 0.00706 ( 4) link_BETA1-4 : bond 0.00452 ( 12) link_BETA1-4 : angle 1.51749 ( 36) link_BETA1-6 : bond 0.00247 ( 2) link_BETA1-6 : angle 1.61771 ( 6) link_NAG-ASN : bond 0.00290 ( 14) link_NAG-ASN : angle 1.21207 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.603 Fit side-chains REVERT: A 204 LYS cc_start: 0.7393 (mtpt) cc_final: 0.7068 (mtpp) REVERT: A 329 GLN cc_start: 0.7835 (mt0) cc_final: 0.7379 (mm-40) REVERT: A 522 GLN cc_start: 0.7948 (mt0) cc_final: 0.7468 (mt0) REVERT: A 607 LYS cc_start: 0.8915 (tttt) cc_final: 0.8080 (tttm) REVERT: A 648 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7605 (tp40) REVERT: A 739 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7821 (mtmm) REVERT: A 770 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: A 901 ASN cc_start: 0.8505 (m-40) cc_final: 0.8244 (m110) REVERT: A 940 GLN cc_start: 0.7943 (mt0) cc_final: 0.7725 (mt0) REVERT: C 204 LYS cc_start: 0.7391 (mtpt) cc_final: 0.7061 (mtpp) REVERT: C 329 GLN cc_start: 0.7829 (mt0) cc_final: 0.7378 (mm-40) REVERT: C 522 GLN cc_start: 0.8022 (mt0) cc_final: 0.7532 (mt0) REVERT: C 607 LYS cc_start: 0.8920 (tttt) cc_final: 0.8075 (tttm) REVERT: C 739 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7827 (mtmm) REVERT: C 770 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: C 901 ASN cc_start: 0.8497 (m-40) cc_final: 0.8214 (m110) outliers start: 28 outliers final: 19 residues processed: 142 average time/residue: 0.7646 time to fit residues: 118.2223 Evaluate side-chains 149 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 517 TRP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain D residue 593 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123317 restraints weight = 14542.498| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.58 r_work: 0.3224 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15266 Z= 0.158 Angle : 0.594 8.829 20962 Z= 0.312 Chirality : 0.046 0.176 2480 Planarity : 0.005 0.051 2626 Dihedral : 5.847 80.799 2636 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.84 % Allowed : 10.66 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 1894 helix: 1.34 (0.18), residues: 832 sheet: 0.30 (0.26), residues: 354 loop : -0.68 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.017 0.002 TYR C 502 PHE 0.031 0.002 PHE A 489 TRP 0.018 0.002 TRP C 393 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00361 (15228) covalent geometry : angle 0.58653 (20866) SS BOND : bond 0.01189 ( 6) SS BOND : angle 2.35548 ( 12) hydrogen bonds : bond 0.05473 ( 794) hydrogen bonds : angle 4.13506 ( 2244) metal coordination : bond 0.00554 ( 4) link_BETA1-4 : bond 0.00449 ( 12) link_BETA1-4 : angle 1.48286 ( 36) link_BETA1-6 : bond 0.00257 ( 2) link_BETA1-6 : angle 1.50635 ( 6) link_NAG-ASN : bond 0.00283 ( 14) link_NAG-ASN : angle 1.20314 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.564 Fit side-chains REVERT: A 204 LYS cc_start: 0.7405 (mtpt) cc_final: 0.7071 (mtpp) REVERT: A 329 GLN cc_start: 0.7811 (mt0) cc_final: 0.7371 (mm-40) REVERT: A 422 ASP cc_start: 0.8105 (t70) cc_final: 0.7842 (t0) REVERT: A 522 GLN cc_start: 0.7951 (mt0) cc_final: 0.7470 (mt0) REVERT: A 607 LYS cc_start: 0.8897 (tttt) cc_final: 0.8068 (tttm) REVERT: A 739 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7810 (mtmm) REVERT: A 770 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: A 901 ASN cc_start: 0.8450 (m-40) cc_final: 0.8186 (m110) REVERT: C 204 LYS cc_start: 0.7407 (mtpt) cc_final: 0.7067 (mtpp) REVERT: C 329 GLN cc_start: 0.7799 (mt0) cc_final: 0.7357 (mm-40) REVERT: C 422 ASP cc_start: 0.8100 (t70) cc_final: 0.7836 (t0) REVERT: C 522 GLN cc_start: 0.8037 (mt0) cc_final: 0.7504 (mt0) REVERT: C 607 LYS cc_start: 0.8885 (tttt) cc_final: 0.8090 (tttm) REVERT: C 739 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7834 (mtmm) REVERT: C 770 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: C 901 ASN cc_start: 0.8444 (m-40) cc_final: 0.8157 (m110) outliers start: 25 outliers final: 19 residues processed: 140 average time/residue: 0.7243 time to fit residues: 111.0804 Evaluate side-chains 146 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 517 TRP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain D residue 593 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 185 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 147 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123201 restraints weight = 14423.144| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.56 r_work: 0.3224 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15266 Z= 0.166 Angle : 0.602 8.634 20962 Z= 0.316 Chirality : 0.046 0.177 2480 Planarity : 0.005 0.051 2626 Dihedral : 5.875 80.602 2636 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.84 % Allowed : 10.59 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.19), residues: 1894 helix: 1.31 (0.17), residues: 832 sheet: 0.29 (0.26), residues: 354 loop : -0.69 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.017 0.002 TYR C 502 PHE 0.032 0.002 PHE A 489 TRP 0.018 0.002 TRP A 393 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00382 (15228) covalent geometry : angle 0.59430 (20866) SS BOND : bond 0.01215 ( 6) SS BOND : angle 2.32984 ( 12) hydrogen bonds : bond 0.05543 ( 794) hydrogen bonds : angle 4.14440 ( 2244) metal coordination : bond 0.00597 ( 4) link_BETA1-4 : bond 0.00447 ( 12) link_BETA1-4 : angle 1.49619 ( 36) link_BETA1-6 : bond 0.00247 ( 2) link_BETA1-6 : angle 1.55245 ( 6) link_NAG-ASN : bond 0.00282 ( 14) link_NAG-ASN : angle 1.21635 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6193.26 seconds wall clock time: 105 minutes 59.86 seconds (6359.86 seconds total)