Starting phenix.real_space_refine on Sun Aug 24 00:04:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cao_45398/08_2025/9cao_45398.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cao_45398/08_2025/9cao_45398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cao_45398/08_2025/9cao_45398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cao_45398/08_2025/9cao_45398.map" model { file = "/net/cci-nas-00/data/ceres_data/9cao_45398/08_2025/9cao_45398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cao_45398/08_2025/9cao_45398.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 58 atoms to isotropic. 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 48 5.16 5 C 9511 2.51 5 N 2476 2.21 5 O 2928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14965 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 7257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7257 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 856} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 7273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7273 Classifications: {'peptide': 901} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 857} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "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: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.51, per 1000 atoms: 0.23 Number of scatterers: 14965 At special positions: 0 Unit cell: (95.23, 100.58, 161.57, 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 48 16.00 O 2928 8.00 N 2476 7.00 C 9511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 761 " - pdb=" SG CYS B 768 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 834 " distance=2.03 Simple disulfide: pdb=" SG CYS A 761 " - pdb=" SG CYS A 768 " distance=2.04 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 834 " 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 C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " 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 L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A1001 " - " ASN A 265 " " NAG A1002 " - " ASN A 527 " " NAG A1003 " - " ASN A 818 " " NAG B1001 " - " ASN B 527 " " NAG B1002 " - " ASN B 818 " " NAG C 1 " - " ASN B 625 " " NAG D 1 " - " ASN B 234 " " NAG E 1 " - " ASN B 265 " " NAG F 1 " - " ASN B 681 " " NAG G 1 " - " ASN B 319 " " NAG H 1 " - " ASN B 128 " " NAG I 1 " - " ASN A 128 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 681 " " NAG L 1 " - " ASN A 625 " " NAG M 1 " - " ASN A 319 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 575.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 392 " 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3434 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 19 sheets defined 53.1% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.696A pdb=" N LEU B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 314 through 332 removed outlier: 4.038A pdb=" N GLY B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 375 through 395 removed outlier: 4.048A pdb=" N TRP B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 426 removed outlier: 3.721A pdb=" N ASN B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 420 " --> pdb=" O TYR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 439 removed outlier: 4.014A pdb=" N LEU B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.876A pdb=" N VAL B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.681A pdb=" N PHE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 492 removed outlier: 3.865A pdb=" N GLY B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 507 Processing helix chain 'B' and resid 513 through 529 removed outlier: 3.939A pdb=" N LEU B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 545 removed outlier: 4.620A pdb=" N TRP B 543 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 removed outlier: 3.787A pdb=" N TYR B 582 " --> pdb=" O GLU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 613 Processing helix chain 'B' and resid 624 through 627 Processing helix chain 'B' and resid 635 through 649 Processing helix chain 'B' and resid 650 through 653 Processing helix chain 'B' and resid 654 through 671 Processing helix chain 'B' and resid 675 through 682 removed outlier: 3.690A pdb=" N ALA B 679 " --> pdb=" O PRO B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.605A pdb=" N ILE B 687 " --> pdb=" O LEU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 710 removed outlier: 4.332A pdb=" N TYR B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 737 Proline residue: B 728 - end of helix Processing helix chain 'B' and resid 746 through 764 Processing helix chain 'B' and resid 765 through 782 Processing helix chain 'B' and resid 789 through 804 removed outlier: 4.652A pdb=" N SER B 794 " --> pdb=" O PRO B 790 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N THR B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 818 Processing helix chain 'B' and resid 821 through 833 removed outlier: 3.563A pdb=" N ALA B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 850 removed outlier: 3.559A pdb=" N LEU B 849 " --> pdb=" O LEU B 845 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 850 " --> pdb=" O SER B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 869 removed outlier: 4.185A pdb=" N THR B 860 " --> pdb=" O LYS B 856 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER B 861 " --> pdb=" O GLN B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 891 removed outlier: 4.469A pdb=" N GLY B 874 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 875 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS B 885 " --> pdb=" O GLN B 881 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LYS B 886 " --> pdb=" O SER B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 906 Processing helix chain 'B' and resid 911 through 925 Processing helix chain 'B' and resid 930 through 934 Processing helix chain 'B' and resid 936 through 966 removed outlier: 6.079A pdb=" N GLU B 956 " --> pdb=" O LYS B 952 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL B 957 " --> pdb=" O GLU B 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 314 through 332 removed outlier: 4.001A pdb=" N GLY A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 375 through 395 removed outlier: 3.745A pdb=" N TRP A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 407 through 426 removed outlier: 4.150A pdb=" N PHE A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 420 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 439 removed outlier: 3.971A pdb=" N LEU A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 removed outlier: 3.684A pdb=" N ALA A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 473 through 492 removed outlier: 4.261A pdb=" N GLY A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 507 Processing helix chain 'A' and resid 513 through 528 removed outlier: 3.594A pdb=" N LEU A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 545 removed outlier: 3.949A pdb=" N TRP A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 627 Processing helix chain 'A' and resid 635 through 650 Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 654 through 671 Processing helix chain 'A' and resid 675 through 682 removed outlier: 3.735A pdb=" N ALA A 679 " --> pdb=" O PRO A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 710 removed outlier: 4.007A pdb=" N TRP A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 737 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 746 through 764 Processing helix chain 'A' and resid 765 through 782 Processing helix chain 'A' and resid 789 through 804 removed outlier: 4.580A pdb=" N SER A 794 " --> pdb=" O PRO A 790 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N THR A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 818 Processing helix chain 'A' and resid 821 through 833 removed outlier: 3.643A pdb=" N ALA A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 850 removed outlier: 3.506A pdb=" N LEU A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 869 Processing helix chain 'A' and resid 869 through 883 removed outlier: 4.458A pdb=" N GLY A 874 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 875 " --> pdb=" O ILE A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 891 Processing helix chain 'A' and resid 892 through 896 removed outlier: 3.677A pdb=" N SER A 895 " --> pdb=" O GLY A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 906 Processing helix chain 'A' and resid 911 through 926 Processing helix chain 'A' and resid 932 through 967 removed outlier: 4.618A pdb=" N ALA A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL A 957 " --> pdb=" O GLU A 953 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 137 through 141 removed outlier: 3.854A pdb=" N SER B 84 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR B 112 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N GLU B 232 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP B 83 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASN B 234 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR B 85 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N THR B 236 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 87 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE B 238 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 89 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 117 through 120 removed outlier: 6.157A pdb=" N ASP B 118 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS B 167 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE B 150 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 192 through 200 Processing sheet with id=AA4, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AA5, first strand: chain 'B' and resid 288 through 293 removed outlier: 7.749A pdb=" N VAL B 360 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 342 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TYR B 362 " --> pdb=" O ASP B 342 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE B 344 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 606 through 608 removed outlier: 5.988A pdb=" N ILE B 552 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 586 through 588 Processing sheet with id=AA8, first strand: chain 'B' and resid 595 through 596 Processing sheet with id=AA9, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.760A pdb=" N GLU A 181 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.760A pdb=" N GLU A 181 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 109 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 106 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N THR A 112 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N GLU A 232 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP A 83 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N ASN A 234 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR A 85 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR A 236 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 87 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE A 238 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU A 89 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AB3, first strand: chain 'A' and resid 192 through 200 Processing sheet with id=AB4, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AB5, first strand: chain 'A' and resid 288 through 293 removed outlier: 6.884A pdb=" N GLN A 343 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG A 301 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLY A 345 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP A 303 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP A 342 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N TYR A 362 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 344 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 399 through 401 removed outlier: 6.858A pdb=" N THR A 400 " --> pdb=" O THR A 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.989A pdb=" N ILE A 552 " --> pdb=" O ASN A 633 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AB9, first strand: chain 'A' and resid 586 through 588 removed outlier: 3.513A pdb=" N VAL A 586 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 595 through 596 750 hydrogen bonds defined for protein. 2139 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: 2.98 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2988 1.33 - 1.45: 3892 1.45 - 1.57: 8375 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15339 Sorted by residual: bond pdb=" N HIS A 239 " pdb=" CA HIS A 239 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.74e+01 bond pdb=" N VAL A 674 " pdb=" CA VAL A 674 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.70e-03 1.32e+04 1.43e+01 bond pdb=" N VAL B 674 " pdb=" CA VAL B 674 " ideal model delta sigma weight residual 1.462 1.493 -0.031 8.70e-03 1.32e+04 1.29e+01 bond pdb=" N VAL B 320 " pdb=" CA VAL B 320 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.08e-02 8.57e+03 1.27e+01 bond pdb=" N VAL A 320 " pdb=" CA VAL A 320 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.14e+01 ... (remaining 15334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 19619 2.61 - 5.22: 1262 5.22 - 7.83: 10 7.83 - 10.44: 1 10.44 - 13.05: 2 Bond angle restraints: 20894 Sorted by residual: angle pdb=" N ALA B 936 " pdb=" CA ALA B 936 " pdb=" C ALA B 936 " ideal model delta sigma weight residual 114.04 107.83 6.21 1.24e+00 6.50e-01 2.51e+01 angle pdb=" CA GLY A 929 " pdb=" C GLY A 929 " pdb=" O GLY A 929 " ideal model delta sigma weight residual 122.24 118.25 3.99 8.70e-01 1.32e+00 2.10e+01 angle pdb=" CA GLY B 548 " pdb=" C GLY B 548 " pdb=" O GLY B 548 " ideal model delta sigma weight residual 122.57 118.42 4.15 9.20e-01 1.18e+00 2.04e+01 angle pdb=" C2 NAG G 2 " pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 110.06 123.11 -13.05 3.00e+00 1.11e-01 1.89e+01 angle pdb=" CA PHE B 490 " pdb=" CB PHE B 490 " pdb=" CG PHE B 490 " ideal model delta sigma weight residual 113.80 117.93 -4.13 1.00e+00 1.00e+00 1.70e+01 ... (remaining 20889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.01: 8810 24.01 - 48.03: 465 48.03 - 72.04: 156 72.04 - 96.06: 45 96.06 - 120.07: 39 Dihedral angle restraints: 9515 sinusoidal: 4206 harmonic: 5309 Sorted by residual: dihedral pdb=" CD ARG B 908 " pdb=" NE ARG B 908 " pdb=" CZ ARG B 908 " pdb=" NH1 ARG B 908 " ideal model delta sinusoidal sigma weight residual 0.00 46.57 -46.57 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CD ARG A 110 " pdb=" NE ARG A 110 " pdb=" CZ ARG A 110 " pdb=" NH1 ARG A 110 " ideal model delta sinusoidal sigma weight residual 0.00 -39.39 39.39 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" CD ARG B 542 " pdb=" NE ARG B 542 " pdb=" CZ ARG B 542 " pdb=" NH1 ARG B 542 " ideal model delta sinusoidal sigma weight residual 0.00 36.48 -36.48 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 9512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 2367 0.285 - 0.569: 5 0.569 - 0.854: 1 0.854 - 1.139: 1 1.139 - 1.423: 1 Chirality restraints: 2375 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.45e+03 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.35e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.85e+02 ... (remaining 2372 not shown) Planarity restraints: 2676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.281 2.00e-02 2.50e+03 2.41e-01 7.24e+02 pdb=" C7 NAG L 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.422 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1003 " 0.256 2.00e-02 2.50e+03 2.18e-01 5.93e+02 pdb=" C7 NAG A1003 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A1003 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG A1003 " -0.374 2.00e-02 2.50e+03 pdb=" O7 NAG A1003 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.217 2.00e-02 2.50e+03 1.85e-01 4.30e+02 pdb=" C7 NAG I 1 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.307 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.166 2.00e-02 2.50e+03 ... (remaining 2673 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 6220 2.89 - 3.40: 15606 3.40 - 3.90: 27978 3.90 - 4.40: 31746 4.40 - 4.90: 50749 Nonbonded interactions: 132299 Sorted by model distance: nonbonded pdb=" O THR B 277 " pdb=" N LEU B 279 " model vdw 2.392 3.120 nonbonded pdb=" O THR B 159 " pdb=" N TYR B 161 " model vdw 2.406 3.120 nonbonded pdb=" OD1 ASP B 370 " pdb=" OG SER B 374 " model vdw 2.426 3.040 nonbonded pdb=" O LEU B 845 " pdb=" OG1 THR B 848 " model vdw 2.429 3.040 nonbonded pdb=" O ARG B 843 " pdb=" OG SER B 846 " model vdw 2.434 3.040 ... (remaining 132294 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 67 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 966 or resid 1002 through 1004)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' } 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.310 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.013 0.668 15376 Z= 0.930 Angle : 1.421 15.904 20998 Z= 1.100 Chirality : 0.105 1.423 2375 Planarity : 0.024 0.354 2660 Dihedral : 18.391 120.074 6069 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.56 % Favored : 95.16 % Rotamer: Outliers : 3.95 % Allowed : 6.95 % Favored : 89.10 % 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: -0.72 (0.19), residues: 1797 helix: 0.24 (0.17), residues: 822 sheet: -0.96 (0.34), residues: 244 loop : -1.00 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 110 TYR 0.012 0.001 TYR A 85 PHE 0.016 0.002 PHE B 327 TRP 0.020 0.002 TRP A 584 HIS 0.007 0.002 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.01200 (15339) covalent geometry : angle 1.40383 (20894) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.73176 ( 8) hydrogen bonds : bond 0.17787 ( 747) hydrogen bonds : angle 7.50594 ( 2139) metal coordination : bond 0.66790 ( 1) link_BETA1-4 : bond 0.00885 ( 16) link_BETA1-4 : angle 3.32023 ( 48) link_NAG-ASN : bond 0.00717 ( 16) link_NAG-ASN : angle 3.73046 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 237 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 282 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8378 (p90) REVERT: B 435 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8846 (ttm) REVERT: B 547 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7361 (ppp) REVERT: B 924 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8310 (m-30) REVERT: A 163 VAL cc_start: 0.8627 (t) cc_final: 0.8375 (t) REVERT: A 212 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6752 (mtm) REVERT: A 229 MET cc_start: 0.8621 (mmt) cc_final: 0.8069 (mmt) REVERT: A 606 ARG cc_start: 0.7760 (ttt-90) cc_final: 0.7505 (ttm110) REVERT: A 763 ASN cc_start: 0.8330 (m-40) cc_final: 0.7753 (m110) outliers start: 63 outliers final: 15 residues processed: 274 average time/residue: 0.1298 time to fit residues: 51.4679 Evaluate side-chains 134 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 924 ASP Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 350 ASN B 378 ASN B 392 HIS B 453 HIS B 565 HIS B 581 ASN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 ASN ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 213 GLN A 270 HIS ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 732 HIS A 739 ASN A 763 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.088981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074500 restraints weight = 38385.534| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.02 r_work: 0.3042 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 15376 Z= 0.149 Angle : 0.669 10.764 20998 Z= 0.327 Chirality : 0.043 0.202 2375 Planarity : 0.005 0.059 2660 Dihedral : 14.633 115.871 2654 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.05 % Rotamer: Outliers : 2.82 % Allowed : 9.27 % Favored : 87.91 % 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: 1797 helix: 1.40 (0.17), residues: 841 sheet: -0.39 (0.32), residues: 258 loop : -0.55 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 86 TYR 0.024 0.002 TYR B 629 PHE 0.025 0.002 PHE B 490 TRP 0.017 0.001 TRP A 601 HIS 0.025 0.002 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00312 (15339) covalent geometry : angle 0.63445 (20894) SS BOND : bond 0.00484 ( 4) SS BOND : angle 1.60205 ( 8) hydrogen bonds : bond 0.04955 ( 747) hydrogen bonds : angle 5.34184 ( 2139) metal coordination : bond 0.08781 ( 1) link_BETA1-4 : bond 0.00950 ( 16) link_BETA1-4 : angle 3.20607 ( 48) link_NAG-ASN : bond 0.00738 ( 16) link_NAG-ASN : angle 3.13320 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6765 (ttp80) cc_final: 0.6407 (ttp80) REVERT: B 199 MET cc_start: 0.8744 (mmm) cc_final: 0.8520 (mmm) REVERT: B 213 GLN cc_start: 0.8863 (tp40) cc_final: 0.8660 (mm-40) REVERT: B 282 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8874 (p90) REVERT: B 418 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8534 (pt0) REVERT: B 435 MET cc_start: 0.9197 (ttm) cc_final: 0.8982 (ttm) REVERT: B 540 MET cc_start: 0.9326 (mmm) cc_final: 0.8915 (mmm) REVERT: B 555 ASP cc_start: 0.8037 (t0) cc_final: 0.7728 (t0) REVERT: A 100 LEU cc_start: 0.7431 (mt) cc_final: 0.7175 (pt) REVERT: A 163 VAL cc_start: 0.8580 (t) cc_final: 0.8368 (t) REVERT: A 212 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6510 (mtm) REVERT: A 223 CYS cc_start: 0.7655 (p) cc_final: 0.7320 (p) REVERT: A 763 ASN cc_start: 0.8125 (m110) cc_final: 0.7731 (m110) REVERT: A 897 SER cc_start: 0.7620 (m) cc_final: 0.7375 (p) outliers start: 45 outliers final: 19 residues processed: 175 average time/residue: 0.1003 time to fit residues: 27.4933 Evaluate side-chains 137 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 626 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN B 72 ASN ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 343 GLN B 393 GLN B 516 ASN A 72 ASN A 331 HIS ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.070211 restraints weight = 38078.792| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.35 r_work: 0.2953 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15376 Z= 0.166 Angle : 0.638 10.681 20998 Z= 0.307 Chirality : 0.044 0.263 2375 Planarity : 0.005 0.046 2660 Dihedral : 11.622 118.411 2642 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 2.82 % Allowed : 10.28 % Favored : 86.90 % 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 (0.20), residues: 1797 helix: 1.56 (0.17), residues: 848 sheet: -0.09 (0.32), residues: 254 loop : -0.45 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 195 TYR 0.019 0.002 TYR B 278 PHE 0.020 0.002 PHE B 490 TRP 0.021 0.001 TRP A 543 HIS 0.006 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00372 (15339) covalent geometry : angle 0.60415 (20894) SS BOND : bond 0.00686 ( 4) SS BOND : angle 1.29036 ( 8) hydrogen bonds : bond 0.04675 ( 747) hydrogen bonds : angle 5.01569 ( 2139) metal coordination : bond 0.00847 ( 1) link_BETA1-4 : bond 0.01002 ( 16) link_BETA1-4 : angle 3.34569 ( 48) link_NAG-ASN : bond 0.00414 ( 16) link_NAG-ASN : angle 2.82377 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 VAL cc_start: 0.8666 (t) cc_final: 0.8393 (p) REVERT: B 199 MET cc_start: 0.8593 (mmm) cc_final: 0.8328 (mmm) REVERT: B 282 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8225 (p90) REVERT: B 354 MET cc_start: 0.8777 (tpt) cc_final: 0.8416 (tpp) REVERT: B 362 TYR cc_start: 0.8649 (m-80) cc_final: 0.8436 (m-10) REVERT: B 418 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8667 (pt0) REVERT: B 473 ASP cc_start: 0.7286 (m-30) cc_final: 0.6763 (m-30) REVERT: B 555 ASP cc_start: 0.8308 (t0) cc_final: 0.7958 (t0) REVERT: B 919 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 331 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8330 (t70) REVERT: A 471 LEU cc_start: 0.7638 (mt) cc_final: 0.7420 (mt) REVERT: A 763 ASN cc_start: 0.7854 (m110) cc_final: 0.7187 (m110) REVERT: A 848 THR cc_start: 0.9276 (p) cc_final: 0.9074 (p) outliers start: 45 outliers final: 26 residues processed: 155 average time/residue: 0.1029 time to fit residues: 24.5192 Evaluate side-chains 131 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 626 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** 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 = 0.3347 r_free = 0.3347 target = 0.082922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067953 restraints weight = 39117.914| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.15 r_work: 0.2924 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15376 Z= 0.208 Angle : 0.643 10.036 20998 Z= 0.309 Chirality : 0.043 0.197 2375 Planarity : 0.004 0.040 2660 Dihedral : 10.519 115.379 2642 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 2.44 % Allowed : 12.22 % Favored : 85.34 % 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: 0.78 (0.20), residues: 1797 helix: 1.48 (0.17), residues: 849 sheet: -0.02 (0.33), residues: 254 loop : -0.39 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 576 TYR 0.020 0.001 TYR B 278 PHE 0.022 0.002 PHE B 490 TRP 0.008 0.001 TRP B 601 HIS 0.024 0.002 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00476 (15339) covalent geometry : angle 0.60520 (20894) SS BOND : bond 0.00350 ( 4) SS BOND : angle 1.30108 ( 8) hydrogen bonds : bond 0.04590 ( 747) hydrogen bonds : angle 4.97065 ( 2139) metal coordination : bond 0.00218 ( 1) link_BETA1-4 : bond 0.00937 ( 16) link_BETA1-4 : angle 3.59717 ( 48) link_NAG-ASN : bond 0.00371 ( 16) link_NAG-ASN : angle 2.84194 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7031 (ttp80) cc_final: 0.6794 (ttp80) REVERT: B 171 VAL cc_start: 0.8791 (t) cc_final: 0.8482 (p) REVERT: B 199 MET cc_start: 0.8679 (mmm) cc_final: 0.8425 (mmm) REVERT: B 282 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8439 (p90) REVERT: B 362 TYR cc_start: 0.8858 (m-80) cc_final: 0.8635 (m-10) REVERT: B 418 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8666 (pt0) REVERT: B 473 ASP cc_start: 0.7622 (m-30) cc_final: 0.7099 (m-30) REVERT: B 555 ASP cc_start: 0.8278 (t0) cc_final: 0.8054 (t0) REVERT: B 919 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 161 TYR cc_start: 0.7534 (m-10) cc_final: 0.7092 (m-10) REVERT: A 212 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6640 (mtm) REVERT: A 264 TRP cc_start: 0.6319 (m100) cc_final: 0.5340 (m100) REVERT: A 606 ARG cc_start: 0.7841 (ttt-90) cc_final: 0.7322 (ttm110) REVERT: A 693 MET cc_start: 0.9044 (tpp) cc_final: 0.8752 (tpp) outliers start: 39 outliers final: 29 residues processed: 140 average time/residue: 0.1062 time to fit residues: 22.7201 Evaluate side-chains 133 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 928 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** 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 = 0.3293 r_free = 0.3293 target = 0.080457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.065526 restraints weight = 39960.871| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.15 r_work: 0.2866 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 15376 Z= 0.296 Angle : 0.709 8.961 20998 Z= 0.345 Chirality : 0.045 0.205 2375 Planarity : 0.005 0.043 2660 Dihedral : 10.125 113.617 2640 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 2.88 % Allowed : 12.22 % Favored : 84.90 % 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 (0.20), residues: 1797 helix: 1.20 (0.17), residues: 855 sheet: -0.08 (0.32), residues: 257 loop : -0.55 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 595 TYR 0.023 0.002 TYR A 332 PHE 0.021 0.002 PHE B 490 TRP 0.010 0.001 TRP B 543 HIS 0.016 0.002 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00681 (15339) covalent geometry : angle 0.67364 (20894) SS BOND : bond 0.00339 ( 4) SS BOND : angle 1.22018 ( 8) hydrogen bonds : bond 0.05204 ( 747) hydrogen bonds : angle 5.13086 ( 2139) metal coordination : bond 0.00369 ( 1) link_BETA1-4 : bond 0.00898 ( 16) link_BETA1-4 : angle 3.77008 ( 48) link_NAG-ASN : bond 0.00590 ( 16) link_NAG-ASN : angle 2.84052 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7291 (ttp80) cc_final: 0.6996 (ttp80) REVERT: B 146 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8152 (tm-30) REVERT: B 171 VAL cc_start: 0.8836 (t) cc_final: 0.8577 (p) REVERT: B 282 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8406 (p90) REVERT: B 473 ASP cc_start: 0.7762 (m-30) cc_final: 0.7207 (m-30) REVERT: B 555 ASP cc_start: 0.8378 (t0) cc_final: 0.8174 (t0) REVERT: B 919 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 606 ARG cc_start: 0.7934 (ttt-90) cc_final: 0.7288 (ttm110) outliers start: 46 outliers final: 38 residues processed: 140 average time/residue: 0.1067 time to fit residues: 22.8792 Evaluate side-chains 130 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 928 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 110 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 126 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 GLN A 331 HIS ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN ** A 667 ASN ** 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 = 0.3365 r_free = 0.3365 target = 0.084229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.069383 restraints weight = 39209.242| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.15 r_work: 0.2946 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15376 Z= 0.115 Angle : 0.591 9.216 20998 Z= 0.282 Chirality : 0.041 0.207 2375 Planarity : 0.004 0.038 2660 Dihedral : 9.600 114.069 2636 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.01 % Favored : 96.88 % Rotamer: Outliers : 2.13 % Allowed : 13.35 % Favored : 84.52 % 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: 0.70 (0.20), residues: 1797 helix: 1.36 (0.18), residues: 858 sheet: 0.06 (0.33), residues: 255 loop : -0.44 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 86 TYR 0.017 0.001 TYR B 278 PHE 0.018 0.001 PHE B 490 TRP 0.013 0.001 TRP A 543 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00243 (15339) covalent geometry : angle 0.55240 (20894) SS BOND : bond 0.00316 ( 4) SS BOND : angle 1.08806 ( 8) hydrogen bonds : bond 0.03951 ( 747) hydrogen bonds : angle 4.81675 ( 2139) metal coordination : bond 0.00031 ( 1) link_BETA1-4 : bond 0.00952 ( 16) link_BETA1-4 : angle 3.74089 ( 48) link_NAG-ASN : bond 0.00282 ( 16) link_NAG-ASN : angle 2.42976 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7383 (ttp80) cc_final: 0.7121 (ttp80) REVERT: B 171 VAL cc_start: 0.8826 (t) cc_final: 0.8545 (p) REVERT: B 350 ASN cc_start: 0.8742 (m110) cc_final: 0.8542 (m110) REVERT: B 362 TYR cc_start: 0.8967 (m-80) cc_final: 0.8716 (m-10) REVERT: B 473 ASP cc_start: 0.7611 (m-30) cc_final: 0.7134 (m-30) REVERT: B 540 MET cc_start: 0.9427 (mmm) cc_final: 0.9090 (mmm) REVERT: B 555 ASP cc_start: 0.8380 (t0) cc_final: 0.8164 (t0) REVERT: B 924 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8618 (m-30) REVERT: A 212 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6534 (mtm) REVERT: A 260 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7813 (mp0) REVERT: A 435 MET cc_start: 0.8938 (tmm) cc_final: 0.8727 (tmm) REVERT: A 486 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (ttp) REVERT: A 606 ARG cc_start: 0.7925 (ttt-90) cc_final: 0.7286 (ttm110) outliers start: 34 outliers final: 21 residues processed: 139 average time/residue: 0.0992 time to fit residues: 21.2863 Evaluate side-chains 126 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 924 ASP Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 849 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 111 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069306 restraints weight = 39047.874| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.14 r_work: 0.2947 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15376 Z= 0.122 Angle : 0.586 8.862 20998 Z= 0.279 Chirality : 0.041 0.176 2375 Planarity : 0.004 0.038 2660 Dihedral : 9.358 113.306 2633 Min Nonbonded Distance : 1.630 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 2.01 % Allowed : 13.41 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.20), residues: 1797 helix: 1.46 (0.18), residues: 858 sheet: 0.16 (0.34), residues: 250 loop : -0.38 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.018 0.001 TYR B 278 PHE 0.018 0.001 PHE B 490 TRP 0.009 0.001 TRP A 543 HIS 0.004 0.001 HIS B 520 Details of bonding type rmsd covalent geometry : bond 0.00266 (15339) covalent geometry : angle 0.54821 (20894) SS BOND : bond 0.00365 ( 4) SS BOND : angle 0.93864 ( 8) hydrogen bonds : bond 0.03900 ( 747) hydrogen bonds : angle 4.72349 ( 2139) metal coordination : bond 0.00150 ( 1) link_BETA1-4 : bond 0.00927 ( 16) link_BETA1-4 : angle 3.67851 ( 48) link_NAG-ASN : bond 0.00267 ( 16) link_NAG-ASN : angle 2.38834 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7356 (ttp80) cc_final: 0.7087 (ttp80) REVERT: B 282 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8311 (p90) REVERT: B 362 TYR cc_start: 0.8984 (m-80) cc_final: 0.8742 (m-10) REVERT: B 473 ASP cc_start: 0.7600 (m-30) cc_final: 0.7098 (m-30) REVERT: B 540 MET cc_start: 0.9379 (mmm) cc_final: 0.9108 (mmm) REVERT: B 547 MET cc_start: 0.8754 (ptm) cc_final: 0.7874 (ptm) REVERT: B 555 ASP cc_start: 0.8383 (t0) cc_final: 0.8163 (t0) REVERT: B 924 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: A 212 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.6619 (mtm) REVERT: A 213 GLN cc_start: 0.8332 (tp40) cc_final: 0.7995 (tp-100) REVERT: A 435 MET cc_start: 0.8978 (tmm) cc_final: 0.8727 (tmm) REVERT: A 571 ASP cc_start: 0.8451 (t0) cc_final: 0.8143 (p0) REVERT: A 606 ARG cc_start: 0.7907 (ttt-90) cc_final: 0.7285 (ttm110) outliers start: 32 outliers final: 22 residues processed: 130 average time/residue: 0.0969 time to fit residues: 19.6250 Evaluate side-chains 121 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 924 ASP Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 656 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067619 restraints weight = 39957.661| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.18 r_work: 0.2911 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15376 Z= 0.195 Angle : 0.624 11.014 20998 Z= 0.299 Chirality : 0.042 0.190 2375 Planarity : 0.004 0.043 2660 Dihedral : 9.244 112.237 2633 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 2.01 % Allowed : 13.03 % Favored : 84.96 % 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 (0.20), residues: 1797 helix: 1.39 (0.18), residues: 856 sheet: 0.01 (0.33), residues: 258 loop : -0.38 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 908 TYR 0.018 0.001 TYR B 278 PHE 0.020 0.001 PHE B 490 TRP 0.010 0.001 TRP B 394 HIS 0.005 0.001 HIS B 520 Details of bonding type rmsd covalent geometry : bond 0.00445 (15339) covalent geometry : angle 0.58897 (20894) SS BOND : bond 0.00344 ( 4) SS BOND : angle 0.96325 ( 8) hydrogen bonds : bond 0.04313 ( 747) hydrogen bonds : angle 4.81435 ( 2139) metal coordination : bond 0.00280 ( 1) link_BETA1-4 : bond 0.00884 ( 16) link_BETA1-4 : angle 3.69163 ( 48) link_NAG-ASN : bond 0.00332 ( 16) link_NAG-ASN : angle 2.40944 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7340 (ttp80) cc_final: 0.7051 (ttp80) REVERT: B 362 TYR cc_start: 0.9049 (m-80) cc_final: 0.8794 (m-10) REVERT: B 473 ASP cc_start: 0.7635 (m-30) cc_final: 0.7127 (m-30) REVERT: B 555 ASP cc_start: 0.8382 (t0) cc_final: 0.8170 (t0) REVERT: A 212 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7175 (mtm) REVERT: A 435 MET cc_start: 0.9035 (tmm) cc_final: 0.8778 (tmm) REVERT: A 606 ARG cc_start: 0.7888 (ttt-90) cc_final: 0.7274 (ttm110) outliers start: 32 outliers final: 26 residues processed: 126 average time/residue: 0.1026 time to fit residues: 19.8091 Evaluate side-chains 119 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 849 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 78 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 176 optimal weight: 0.0770 chunk 81 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** 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 = 0.3353 r_free = 0.3353 target = 0.083595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.068790 restraints weight = 39137.991| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.13 r_work: 0.2937 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15376 Z= 0.132 Angle : 0.593 12.669 20998 Z= 0.281 Chirality : 0.041 0.197 2375 Planarity : 0.004 0.038 2660 Dihedral : 9.015 111.680 2633 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.72 % Rotamer: Outliers : 1.88 % Allowed : 13.66 % Favored : 84.46 % 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 (0.20), residues: 1797 helix: 1.41 (0.18), residues: 858 sheet: 0.13 (0.34), residues: 251 loop : -0.34 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.017 0.001 TYR B 278 PHE 0.018 0.001 PHE B 490 TRP 0.009 0.001 TRP B 394 HIS 0.004 0.001 HIS B 520 Details of bonding type rmsd covalent geometry : bond 0.00295 (15339) covalent geometry : angle 0.55658 (20894) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.97088 ( 8) hydrogen bonds : bond 0.03958 ( 747) hydrogen bonds : angle 4.71737 ( 2139) metal coordination : bond 0.00133 ( 1) link_BETA1-4 : bond 0.00915 ( 16) link_BETA1-4 : angle 3.68918 ( 48) link_NAG-ASN : bond 0.00215 ( 16) link_NAG-ASN : angle 2.28992 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7347 (ttp80) cc_final: 0.7036 (ttp80) REVERT: B 362 TYR cc_start: 0.9004 (m-80) cc_final: 0.8777 (m-10) REVERT: B 473 ASP cc_start: 0.7565 (m-30) cc_final: 0.7073 (m-30) REVERT: A 161 TYR cc_start: 0.7574 (m-10) cc_final: 0.6971 (m-10) REVERT: A 260 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7857 (mp0) REVERT: A 435 MET cc_start: 0.8991 (tmm) cc_final: 0.8727 (tmm) REVERT: A 606 ARG cc_start: 0.7874 (ttt-90) cc_final: 0.7236 (ttm110) REVERT: A 807 GLU cc_start: 0.8517 (tt0) cc_final: 0.8263 (tp30) outliers start: 30 outliers final: 27 residues processed: 123 average time/residue: 0.1125 time to fit residues: 20.8885 Evaluate side-chains 120 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 849 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 148 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 143 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069756 restraints weight = 39178.111| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.16 r_work: 0.2959 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15376 Z= 0.116 Angle : 0.597 13.452 20998 Z= 0.283 Chirality : 0.041 0.236 2375 Planarity : 0.004 0.037 2660 Dihedral : 8.698 110.605 2630 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 1.75 % Allowed : 13.66 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1797 helix: 1.45 (0.18), residues: 857 sheet: 0.20 (0.34), residues: 251 loop : -0.34 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.016 0.001 TYR B 278 PHE 0.017 0.001 PHE B 490 TRP 0.008 0.001 TRP B 394 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00255 (15339) covalent geometry : angle 0.56156 (20894) SS BOND : bond 0.00297 ( 4) SS BOND : angle 0.94847 ( 8) hydrogen bonds : bond 0.03736 ( 747) hydrogen bonds : angle 4.62473 ( 2139) metal coordination : bond 0.00012 ( 1) link_BETA1-4 : bond 0.00918 ( 16) link_BETA1-4 : angle 3.63245 ( 48) link_NAG-ASN : bond 0.00237 ( 16) link_NAG-ASN : angle 2.24527 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7387 (ttp80) cc_final: 0.7056 (ttp80) REVERT: B 362 TYR cc_start: 0.8991 (m-80) cc_final: 0.8780 (m-10) REVERT: A 161 TYR cc_start: 0.7514 (m-10) cc_final: 0.6922 (m-10) REVERT: A 212 MET cc_start: 0.7210 (mtm) cc_final: 0.6904 (mtt) REVERT: A 435 MET cc_start: 0.8880 (tmm) cc_final: 0.8610 (tmm) REVERT: A 606 ARG cc_start: 0.7881 (ttt-90) cc_final: 0.7234 (ttm110) REVERT: A 763 ASN cc_start: 0.7956 (m110) cc_final: 0.7375 (m-40) REVERT: A 897 SER cc_start: 0.6852 (m) cc_final: 0.6635 (p) outliers start: 28 outliers final: 27 residues processed: 126 average time/residue: 0.1062 time to fit residues: 20.4579 Evaluate side-chains 120 residues out of total 1597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 849 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069893 restraints weight = 39328.876| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.08 r_work: 0.2954 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15376 Z= 0.127 Angle : 0.589 13.305 20998 Z= 0.278 Chirality : 0.041 0.210 2375 Planarity : 0.004 0.037 2660 Dihedral : 8.574 109.649 2630 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 1.69 % Allowed : 14.04 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1797 helix: 1.48 (0.18), residues: 857 sheet: 0.13 (0.34), residues: 253 loop : -0.32 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.016 0.001 TYR B 278 PHE 0.017 0.001 PHE B 490 TRP 0.009 0.001 TRP B 394 HIS 0.003 0.001 HIS B 520 Details of bonding type rmsd covalent geometry : bond 0.00284 (15339) covalent geometry : angle 0.55384 (20894) SS BOND : bond 0.00292 ( 4) SS BOND : angle 0.90332 ( 8) hydrogen bonds : bond 0.03796 ( 747) hydrogen bonds : angle 4.61179 ( 2139) metal coordination : bond 0.00020 ( 1) link_BETA1-4 : bond 0.00900 ( 16) link_BETA1-4 : angle 3.60656 ( 48) link_NAG-ASN : bond 0.00235 ( 16) link_NAG-ASN : angle 2.24282 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.58 seconds wall clock time: 45 minutes 15.80 seconds (2715.80 seconds total)