Starting phenix.real_space_refine on Thu Sep 18 08:59:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cam_45396/09_2025/9cam_45396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cam_45396/09_2025/9cam_45396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cam_45396/09_2025/9cam_45396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cam_45396/09_2025/9cam_45396.map" model { file = "/net/cci-nas-00/data/ceres_data/9cam_45396/09_2025/9cam_45396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cam_45396/09_2025/9cam_45396.cif" } resolution = 2.96 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= 0.033 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 75 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 9501 2.51 5 N 2481 2.21 5 O 2913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14945 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7281 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 901, 7269 Classifications: {'peptide': 901} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 857} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 901, 7269 Classifications: {'peptide': 901} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 857} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 7443 Chain: "A" Number of atoms: 7296 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 901, 7273 Classifications: {'peptide': 901} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 857} Conformer: "B" Number of residues, atoms: 901, 7273 Classifications: {'peptide': 901} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 857} bond proxies already assigned to first conformer: 7434 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "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: "B" 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 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASER B 700 " occ=0.21 ... (10 atoms not shown) pdb=" OG BSER B 700 " occ=0.79 residue: pdb=" N ASER B 758 " occ=0.98 ... (10 atoms not shown) pdb=" OG BSER B 758 " occ=0.02 residue: pdb=" N ASER A 700 " occ=0.71 ... (10 atoms not shown) pdb=" OG BSER A 700 " occ=0.29 residue: pdb=" N ASER A 758 " occ=0.02 ... (10 atoms not shown) pdb=" OG BSER A 758 " occ=0.98 Time building chain proxies: 5.96, per 1000 atoms: 0.40 Number of scatterers: 14945 At special positions: 0 Unit cell: (96.3, 101.65, 147.66, 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 2913 8.00 N 2481 7.00 C 9501 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1001 " - " ASN A 128 " " NAG A1003 " - " ASN A 527 " " NAG A1004 " - " ASN A 681 " " NAG A1005 " - " ASN A 818 " " NAG B1001 " - " ASN B 128 " " NAG B1003 " - " ASN B 527 " " NAG B1004 " - " ASN B 681 " " NAG C 1 " - " ASN B 234 " " NAG D 1 " - " ASN B 319 " " NAG E 1 " - " ASN B 625 " " NAG F 1 " - " ASN B 265 " " NAG G 1 " - " ASN A 319 " " NAG H 1 " - " ASN A 625 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 265 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" NE2 HIS B 392 " pdb="ZN ZN B1002 " - pdb=" NE2 HIS B 388 " 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3448 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 20 sheets defined 53.7% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.618A pdb=" N LEU B 280 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 314 through 333 removed outlier: 4.300A 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: 4.068A pdb=" N TRP B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 Processing helix chain 'B' and resid 407 through 426 removed outlier: 4.029A pdb=" N PHE B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 420 " --> pdb=" O TYR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.846A pdb=" N ASN B 430 " --> pdb=" O PRO B 427 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 431 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 432 " --> pdb=" O TRP B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 427 through 432' Processing helix chain 'B' and resid 433 through 439 removed outlier: 4.222A pdb=" N LEU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 448 removed outlier: 4.000A pdb=" N ALA B 445 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 removed outlier: 3.631A pdb=" N ILE B 462 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.584A pdb=" N PHE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 492 removed outlier: 3.677A pdb=" N TYR B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 507 Processing helix chain 'B' and resid 513 through 529 removed outlier: 3.708A pdb=" N LEU B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 546 removed outlier: 3.974A pdb=" N ARG B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP B 543 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 546 " --> pdb=" O ARG B 542 " (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: 3.682A pdb=" N ALA B 679 " --> pdb=" O PRO B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 689 removed outlier: 3.731A pdb=" N ILE B 687 " --> pdb=" O LEU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 710 removed outlier: 3.848A pdb=" N TRP B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR B 704 " --> pdb=" O ASER B 700 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 737 removed outlier: 3.533A pdb=" N THR B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Proline residue: B 728 - end of helix Processing helix chain 'B' and resid 746 through 763 Processing helix chain 'B' and resid 765 through 782 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 804 Processing helix chain 'B' and resid 805 through 818 Processing helix chain 'B' and resid 821 through 833 removed outlier: 3.972A pdb=" N ALA B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 849 removed outlier: 3.907A pdb=" N LEU B 849 " --> pdb=" O LEU B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 869 Processing helix chain 'B' and resid 871 through 891 removed outlier: 4.430A pdb=" N LEU B 875 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS B 885 " --> pdb=" O GLN B 881 " (cutoff:3.500A) removed outlier: 6.024A 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 932 No H-bonds generated for 'chain 'B' and resid 930 through 932' Processing helix chain 'B' and resid 933 through 967 removed outlier: 5.371A pdb=" N GLU B 956 " --> pdb=" O LYS B 952 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL B 957 " --> pdb=" O GLU B 953 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 967 " --> pdb=" O THR B 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.618A pdb=" N SER A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.893A pdb=" N LEU A 280 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 314 through 333 removed outlier: 4.332A 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 392 Processing helix chain 'A' and resid 403 through 409 removed outlier: 5.129A pdb=" N TRP A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 426 removed outlier: 4.896A pdb=" N TYR A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 420 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 439 removed outlier: 4.124A pdb=" N LEU A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.882A pdb=" N ALA A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 448 " --> pdb=" O MET A 444 " (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: 3.666A pdb=" N TYR A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 507 Processing helix chain 'A' and resid 513 through 529 removed outlier: 3.633A pdb=" N LEU A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 545 removed outlier: 3.910A pdb=" N ARG A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 613 removed outlier: 3.522A pdb=" N SER A 613 " --> pdb=" O ASP A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 610 through 613' Processing helix chain 'A' and resid 624 through 627 removed outlier: 3.673A pdb=" N THR A 627 " --> pdb=" O LEU A 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 624 through 627' Processing helix chain 'A' and resid 635 through 650 removed outlier: 3.518A pdb=" N HIS A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) 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: 3.590A pdb=" N ALA A 679 " --> pdb=" O PRO A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 689 removed outlier: 4.124A pdb=" N ILE A 687 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 710 removed outlier: 3.862A pdb=" N TRP A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR A 704 " --> pdb=" O ASER A 700 " (cutoff:3.500A) removed outlier: 4.098A 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 763 Processing helix chain 'A' and resid 765 through 782 Processing helix chain 'A' and resid 789 through 804 removed outlier: 4.366A pdb=" N SER A 794 " --> pdb=" O PRO A 790 " (cutoff:3.500A) removed outlier: 5.548A 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 832 Processing helix chain 'A' and resid 833 through 835 No H-bonds generated for 'chain 'A' and resid 833 through 835' Processing helix chain 'A' and resid 837 through 849 removed outlier: 3.910A 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 871 through 890 removed outlier: 4.486A pdb=" N LEU A 875 " --> pdb=" O ILE A 871 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYS A 885 " --> pdb=" O GLN A 881 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 Processing helix chain 'A' and resid 911 through 925 Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 933 through 967 removed outlier: 3.781A pdb=" N LYS A 952 " --> pdb=" O ILE A 948 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 953 " --> pdb=" O LYS A 949 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL A 957 " --> pdb=" O GLU A 953 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 127 through 129 removed outlier: 4.451A pdb=" N GLN B 175 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 127 through 129 removed outlier: 7.484A pdb=" N VAL B 102 " --> pdb=" O PRO B 91 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS B 104 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU B 89 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL B 87 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR B 108 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TYR B 85 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG B 110 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N GLU B 232 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP B 83 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASN B 234 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR B 85 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR B 236 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 87 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE B 238 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 89 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.526A pdb=" N TYR B 161 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU B 155 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 163 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR B 153 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS B 165 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 192 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AA6, first strand: chain 'B' and resid 288 through 293 removed outlier: 6.023A pdb=" N LEU B 299 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLN B 343 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG B 301 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLY B 345 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP B 303 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 399 through 401 removed outlier: 6.763A pdb=" N THR B 400 " --> pdb=" O THR B 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 606 through 608 removed outlier: 7.912A pdb=" N ASN B 633 " --> pdb=" O PRO B 550 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 552 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 586 through 588 Processing sheet with id=AB1, first strand: chain 'B' and resid 595 through 596 Processing sheet with id=AB2, first strand: chain 'A' and resid 128 through 129 removed outlier: 4.679A pdb=" N GLN A 175 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.562A pdb=" N SER A 84 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR A 112 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N GLU A 232 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 83 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN A 234 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR A 85 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR A 236 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 87 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE A 238 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 89 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 119 through 123 Processing sheet with id=AB5, first strand: chain 'A' and resid 192 through 200 Processing sheet with id=AB6, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AB7, first strand: chain 'A' and resid 288 through 293 removed outlier: 6.130A pdb=" N LEU A 299 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLN A 343 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 301 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY A 345 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TRP A 303 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 399 through 401 Processing sheet with id=AB9, first strand: chain 'A' and resid 606 through 608 removed outlier: 7.716A pdb=" N ASN A 633 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE A 552 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 586 through 588 Processing sheet with id=AC2, first strand: chain 'A' and resid 595 through 596 755 hydrogen bonds defined for protein. 2135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.85 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: 4287 1.33 - 1.46: 3374 1.46 - 1.58: 7580 1.58 - 1.70: 0 1.70 - 1.83: 84 Bond restraints: 15325 Sorted by residual: bond pdb=" N ILE A 122 " pdb=" CA ILE A 122 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N ILE A 235 " pdb=" CA ILE A 235 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.20e-02 6.94e+03 9.39e+00 bond pdb=" N VAL B 626 " pdb=" CA VAL B 626 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.99e+00 bond pdb=" N VAL B 383 " pdb=" CA VAL B 383 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.94e+00 bond pdb=" N VAL B 171 " pdb=" CA VAL B 171 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.21e-02 6.83e+03 7.83e+00 ... (remaining 15320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 19679 1.54 - 3.08: 1048 3.08 - 4.63: 127 4.63 - 6.17: 26 6.17 - 7.71: 3 Bond angle restraints: 20883 Sorted by residual: angle pdb=" N LYS B 673 " pdb=" CA LYS B 673 " pdb=" C LYS B 673 " ideal model delta sigma weight residual 113.88 108.45 5.43 1.23e+00 6.61e-01 1.95e+01 angle pdb=" N ARG B 363 " pdb=" CA ARG B 363 " pdb=" C ARG B 363 " ideal model delta sigma weight residual 110.48 104.22 6.26 1.48e+00 4.57e-01 1.79e+01 angle pdb=" N ASP A 216 " pdb=" CA ASP A 216 " pdb=" C ASP A 216 " ideal model delta sigma weight residual 114.64 108.94 5.70 1.52e+00 4.33e-01 1.41e+01 angle pdb=" N THR B 820 " pdb=" CA THR B 820 " pdb=" C THR B 820 " ideal model delta sigma weight residual 113.55 108.84 4.71 1.26e+00 6.30e-01 1.40e+01 angle pdb=" CA ILE A 122 " pdb=" C ILE A 122 " pdb=" O ILE A 122 " ideal model delta sigma weight residual 121.67 117.85 3.82 1.05e+00 9.07e-01 1.32e+01 ... (remaining 20878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 8603 21.70 - 43.41: 682 43.41 - 65.11: 106 65.11 - 86.82: 43 86.82 - 108.52: 20 Dihedral angle restraints: 9454 sinusoidal: 4119 harmonic: 5335 Sorted by residual: dihedral pdb=" CA TYR A 362 " pdb=" C TYR A 362 " pdb=" N ARG A 363 " pdb=" CA ARG A 363 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.81 108.52 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" CA TYR B 161 " pdb=" C TYR B 161 " pdb=" N LEU B 162 " pdb=" CA LEU B 162 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 9451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2241 0.114 - 0.228: 107 0.228 - 0.342: 7 0.342 - 0.455: 1 0.455 - 0.569: 2 Chirality restraints: 2358 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.29e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.85e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.45e+01 ... (remaining 2355 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.122 2.00e-02 2.50e+03 1.01e-01 1.29e+02 pdb=" C7 NAG F 2 " 0.031 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.166 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.080 2.00e-02 2.50e+03 6.75e-02 5.70e+01 pdb=" C7 NAG J 1 " 0.014 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.108 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.047 2.00e-02 2.50e+03 3.95e-02 1.95e+01 pdb=" C7 NAG J 2 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.035 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.064 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.007 2.00e-02 2.50e+03 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 829 2.73 - 3.27: 15190 3.27 - 3.82: 25549 3.82 - 4.36: 32634 4.36 - 4.90: 54402 Nonbonded interactions: 128604 Sorted by model distance: nonbonded pdb=" OE1 GLU B 411 " pdb="ZN ZN B1002 " model vdw 2.189 2.230 nonbonded pdb=" O LEU A 491 " pdb=" OG SER A 492 " model vdw 2.190 3.040 nonbonded pdb=" O GLY B 931 " pdb=" OG1 THR B 934 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 317 " pdb=" OG1 THR A 321 " model vdw 2.215 3.040 nonbonded pdb=" N GLU B 636 " pdb=" OE1 GLU B 636 " model vdw 2.246 3.120 ... (remaining 128599 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 240 or (resid 241 and (name N or name CA or nam \ e C or name O or name CB )) or resid 242 through 640 or resid 643 through 699 or \ resid 701 through 757 or resid 759 through 1004)) selection = (chain 'B' and (resid 67 through 640 or resid 643 through 699 or resid 701 throu \ gh 757 or resid 759 through 1004)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.02 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: 3.030 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.890 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15358 Z= 0.331 Angle : 0.755 11.425 20972 Z= 0.474 Chirality : 0.055 0.569 2358 Planarity : 0.006 0.121 2669 Dihedral : 16.831 108.521 5994 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 1.62 % Allowed : 18.90 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.20), residues: 1812 helix: 0.57 (0.18), residues: 830 sheet: 1.02 (0.31), residues: 254 loop : 0.12 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 537 TYR 0.019 0.001 TYR A 891 PHE 0.023 0.001 PHE B 490 TRP 0.020 0.001 TRP B 619 HIS 0.007 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00514 (15325) covalent geometry : angle 0.73947 (20883) SS BOND : bond 0.00301 ( 4) SS BOND : angle 2.70415 ( 8) hydrogen bonds : bond 0.14719 ( 751) hydrogen bonds : angle 6.54413 ( 2135) metal coordination : bond 0.00270 ( 2) link_BETA1-4 : bond 0.00248 ( 12) link_BETA1-4 : angle 0.97407 ( 36) link_NAG-ASN : bond 0.00696 ( 15) link_NAG-ASN : angle 3.16861 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 MET cc_start: 0.8650 (mmt) cc_final: 0.8398 (mmm) REVERT: B 411 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8154 (mm-30) outliers start: 26 outliers final: 17 residues processed: 150 average time/residue: 0.7303 time to fit residues: 119.1357 Evaluate side-chains 104 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 782 ASN Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 898 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 HIS B 392 HIS B 746 ASN B 925 ASN A 392 HIS A 732 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.087154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.071037 restraints weight = 92083.210| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.99 r_work: 0.2740 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.768 15358 Z= 0.239 Angle : 0.557 11.418 20972 Z= 0.284 Chirality : 0.043 0.230 2358 Planarity : 0.004 0.046 2669 Dihedral : 8.696 67.166 2550 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.17 % Favored : 97.72 % Rotamer: Outliers : 2.00 % Allowed : 18.53 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.20), residues: 1812 helix: 1.52 (0.18), residues: 842 sheet: 0.97 (0.31), residues: 266 loop : 0.22 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 537 TYR 0.014 0.001 TYR A 503 PHE 0.022 0.001 PHE B 490 TRP 0.017 0.001 TRP B 619 HIS 0.006 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00265 (15325) covalent geometry : angle 0.53883 (20883) SS BOND : bond 0.00415 ( 4) SS BOND : angle 2.00711 ( 8) hydrogen bonds : bond 0.04247 ( 751) hydrogen bonds : angle 4.64215 ( 2135) metal coordination : bond 0.54309 ( 2) link_BETA1-4 : bond 0.00370 ( 12) link_BETA1-4 : angle 1.89529 ( 36) link_NAG-ASN : bond 0.00509 ( 15) link_NAG-ASN : angle 2.54613 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 MET cc_start: 0.8645 (mmt) cc_final: 0.8381 (mmt) REVERT: B 411 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 604 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7482 (p0) REVERT: B 886 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8201 (tppt) REVERT: A 113 CYS cc_start: 0.9349 (t) cc_final: 0.8930 (t) REVERT: A 161 TYR cc_start: 0.8712 (m-80) cc_final: 0.8422 (m-80) outliers start: 32 outliers final: 12 residues processed: 121 average time/residue: 0.7055 time to fit residues: 93.2782 Evaluate side-chains 98 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 953 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 158 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 HIS A 516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.067365 restraints weight = 94731.262| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 4.02 r_work: 0.2699 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.841 15358 Z= 0.324 Angle : 0.597 11.552 20972 Z= 0.303 Chirality : 0.045 0.236 2358 Planarity : 0.004 0.044 2669 Dihedral : 6.671 55.976 2535 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 2.18 % Allowed : 18.03 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.20), residues: 1812 helix: 1.65 (0.18), residues: 842 sheet: 0.86 (0.31), residues: 266 loop : 0.11 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 595 TYR 0.022 0.002 TYR A 503 PHE 0.023 0.002 PHE B 490 TRP 0.013 0.001 TRP B 619 HIS 0.021 0.002 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00550 (15325) covalent geometry : angle 0.57674 (20883) SS BOND : bond 0.00503 ( 4) SS BOND : angle 2.97541 ( 8) hydrogen bonds : bond 0.04592 ( 751) hydrogen bonds : angle 4.62556 ( 2135) metal coordination : bond 0.59474 ( 2) link_BETA1-4 : bond 0.00393 ( 12) link_BETA1-4 : angle 1.93952 ( 36) link_NAG-ASN : bond 0.00523 ( 15) link_NAG-ASN : angle 2.68626 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 MET cc_start: 0.8899 (mmt) cc_final: 0.8596 (mmt) REVERT: B 837 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8415 (mt-10) REVERT: A 113 CYS cc_start: 0.9270 (t) cc_final: 0.8916 (t) REVERT: A 161 TYR cc_start: 0.8972 (m-80) cc_final: 0.8666 (m-80) REVERT: A 722 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9227 (mm) outliers start: 35 outliers final: 17 residues processed: 109 average time/residue: 0.6751 time to fit residues: 80.3895 Evaluate side-chains 98 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 392 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 837 GLU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 953 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.068370 restraints weight = 93924.685| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 4.03 r_work: 0.2689 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.813 15358 Z= 0.251 Angle : 0.531 11.651 20972 Z= 0.269 Chirality : 0.042 0.234 2358 Planarity : 0.004 0.042 2669 Dihedral : 5.533 56.213 2534 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 1.81 % Allowed : 18.34 % Favored : 79.85 % 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: 1.42 (0.20), residues: 1812 helix: 1.76 (0.18), residues: 840 sheet: 0.75 (0.32), residues: 246 loop : 0.14 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 640 TYR 0.018 0.001 TYR B 891 PHE 0.021 0.001 PHE B 490 TRP 0.011 0.001 TRP B 619 HIS 0.014 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00279 (15325) covalent geometry : angle 0.51224 (20883) SS BOND : bond 0.00376 ( 4) SS BOND : angle 2.13726 ( 8) hydrogen bonds : bond 0.03942 ( 751) hydrogen bonds : angle 4.44982 ( 2135) metal coordination : bond 0.57505 ( 2) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 1.72208 ( 36) link_NAG-ASN : bond 0.00495 ( 15) link_NAG-ASN : angle 2.56487 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 MET cc_start: 0.8879 (mmt) cc_final: 0.8589 (mmt) REVERT: B 886 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8146 (tppt) REVERT: A 113 CYS cc_start: 0.9311 (t) cc_final: 0.8854 (t) REVERT: A 161 TYR cc_start: 0.8971 (m-80) cc_final: 0.8629 (m-80) REVERT: A 722 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9190 (mm) outliers start: 29 outliers final: 18 residues processed: 110 average time/residue: 0.6415 time to fit residues: 77.9708 Evaluate side-chains 98 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 392 HIS Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 957 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.067687 restraints weight = 92856.933| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.99 r_work: 0.2674 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.823 15358 Z= 0.270 Angle : 0.539 11.606 20972 Z= 0.274 Chirality : 0.042 0.232 2358 Planarity : 0.004 0.042 2669 Dihedral : 5.155 56.658 2532 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 2.37 % Allowed : 17.78 % Favored : 79.85 % 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: 1.44 (0.20), residues: 1812 helix: 1.76 (0.18), residues: 842 sheet: 0.73 (0.32), residues: 246 loop : 0.17 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 640 TYR 0.017 0.001 TYR A 503 PHE 0.021 0.001 PHE B 490 TRP 0.010 0.001 TRP B 619 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00363 (15325) covalent geometry : angle 0.51829 (20883) SS BOND : bond 0.00621 ( 4) SS BOND : angle 3.50453 ( 8) hydrogen bonds : bond 0.03984 ( 751) hydrogen bonds : angle 4.43446 ( 2135) metal coordination : bond 0.58239 ( 2) link_BETA1-4 : bond 0.00397 ( 12) link_BETA1-4 : angle 1.62756 ( 36) link_NAG-ASN : bond 0.00487 ( 15) link_NAG-ASN : angle 2.57730 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.8533 (tmm-80) cc_final: 0.8190 (tmm-80) REVERT: B 212 MET cc_start: 0.8914 (mmt) cc_final: 0.8564 (mmt) REVERT: B 886 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8065 (tppt) REVERT: A 113 CYS cc_start: 0.9321 (t) cc_final: 0.8837 (t) REVERT: A 161 TYR cc_start: 0.9034 (m-80) cc_final: 0.8677 (m-80) REVERT: A 591 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9100 (pt) REVERT: A 967 LYS cc_start: 0.8577 (mttm) cc_final: 0.8232 (mtpp) outliers start: 38 outliers final: 23 residues processed: 110 average time/residue: 0.6891 time to fit residues: 83.1196 Evaluate side-chains 103 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 392 HIS Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 957 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 83 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 140 optimal weight: 0.0040 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 0.0980 chunk 155 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.084731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.068409 restraints weight = 97453.845| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 4.09 r_work: 0.2688 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.865 15358 Z= 0.261 Angle : 0.518 11.568 20972 Z= 0.263 Chirality : 0.041 0.229 2358 Planarity : 0.004 0.040 2669 Dihedral : 4.949 57.252 2532 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 1.93 % Allowed : 17.84 % Favored : 80.22 % 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: 1.51 (0.20), residues: 1812 helix: 1.81 (0.18), residues: 842 sheet: 0.66 (0.32), residues: 256 loop : 0.26 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 595 TYR 0.018 0.001 TYR B 891 PHE 0.020 0.001 PHE B 490 TRP 0.009 0.001 TRP B 619 HIS 0.006 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00270 (15325) covalent geometry : angle 0.49857 (20883) SS BOND : bond 0.00380 ( 4) SS BOND : angle 2.79916 ( 8) hydrogen bonds : bond 0.03732 ( 751) hydrogen bonds : angle 4.35500 ( 2135) metal coordination : bond 0.61215 ( 2) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 1.49302 ( 36) link_NAG-ASN : bond 0.00496 ( 15) link_NAG-ASN : angle 2.52909 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.8563 (tmm-80) cc_final: 0.8239 (tmm-80) REVERT: B 197 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8269 (mt-10) REVERT: B 212 MET cc_start: 0.8932 (mmt) cc_final: 0.8629 (mmt) REVERT: B 547 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7831 (ttp) REVERT: B 560 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8248 (m) REVERT: B 636 GLU cc_start: 0.8885 (mp0) cc_final: 0.8653 (mm-30) REVERT: B 688 GLU cc_start: 0.8863 (pt0) cc_final: 0.8504 (pp20) REVERT: B 886 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8157 (tppt) REVERT: A 113 CYS cc_start: 0.9290 (t) cc_final: 0.8875 (t) REVERT: A 161 TYR cc_start: 0.9035 (m-80) cc_final: 0.8663 (m-80) REVERT: A 722 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9175 (mm) REVERT: A 967 LYS cc_start: 0.8532 (mttm) cc_final: 0.8228 (mtpp) outliers start: 31 outliers final: 23 residues processed: 110 average time/residue: 0.7088 time to fit residues: 85.2174 Evaluate side-chains 106 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 392 HIS Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 957 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.085192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.069273 restraints weight = 79441.011| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.75 r_work: 0.2722 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.901 15358 Z= 0.266 Angle : 0.519 11.470 20972 Z= 0.264 Chirality : 0.041 0.227 2358 Planarity : 0.004 0.040 2669 Dihedral : 4.826 57.845 2532 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 1.81 % Allowed : 17.90 % Favored : 80.29 % 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: 1.54 (0.20), residues: 1812 helix: 1.83 (0.18), residues: 842 sheet: 0.64 (0.32), residues: 256 loop : 0.29 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 595 TYR 0.018 0.001 TYR B 891 PHE 0.020 0.001 PHE B 490 TRP 0.009 0.001 TRP B 619 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00251 (15325) covalent geometry : angle 0.49871 (20883) SS BOND : bond 0.00255 ( 4) SS BOND : angle 3.75844 ( 8) hydrogen bonds : bond 0.03599 ( 751) hydrogen bonds : angle 4.30663 ( 2135) metal coordination : bond 0.63713 ( 2) link_BETA1-4 : bond 0.00367 ( 12) link_BETA1-4 : angle 1.39167 ( 36) link_NAG-ASN : bond 0.00500 ( 15) link_NAG-ASN : angle 2.49324 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.8563 (tmm-80) cc_final: 0.8236 (tmm-80) REVERT: B 197 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 212 MET cc_start: 0.8935 (mmt) cc_final: 0.8588 (mmt) REVERT: B 560 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8213 (m) REVERT: B 688 GLU cc_start: 0.8838 (pt0) cc_final: 0.8480 (pp20) REVERT: B 886 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8197 (tppt) REVERT: A 113 CYS cc_start: 0.9246 (t) cc_final: 0.8864 (t) REVERT: A 161 TYR cc_start: 0.9023 (m-80) cc_final: 0.8691 (m-80) REVERT: A 722 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9164 (mm) REVERT: A 967 LYS cc_start: 0.8495 (mttm) cc_final: 0.8200 (mtpp) outliers start: 29 outliers final: 23 residues processed: 108 average time/residue: 0.7020 time to fit residues: 82.8188 Evaluate side-chains 107 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 392 HIS Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 957 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 172 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.083840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.067363 restraints weight = 105953.975| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.23 r_work: 0.2669 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15358 Z= 0.161 Angle : 0.542 11.329 20972 Z= 0.276 Chirality : 0.042 0.227 2358 Planarity : 0.004 0.040 2669 Dihedral : 4.820 57.793 2532 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 1.87 % Allowed : 17.97 % Favored : 80.16 % 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: 1.50 (0.20), residues: 1812 helix: 1.81 (0.18), residues: 842 sheet: 0.62 (0.32), residues: 256 loop : 0.27 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 204 TYR 0.018 0.001 TYR B 891 PHE 0.021 0.001 PHE A 490 TRP 0.009 0.001 TRP B 619 HIS 0.014 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00379 (15325) covalent geometry : angle 0.52200 (20883) SS BOND : bond 0.00289 ( 4) SS BOND : angle 3.76055 ( 8) hydrogen bonds : bond 0.03848 ( 751) hydrogen bonds : angle 4.35249 ( 2135) metal coordination : bond 0.00864 ( 2) link_BETA1-4 : bond 0.00393 ( 12) link_BETA1-4 : angle 1.42758 ( 36) link_NAG-ASN : bond 0.00479 ( 15) link_NAG-ASN : angle 2.53760 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.8602 (tmm-80) cc_final: 0.8261 (tmm-80) REVERT: B 197 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8259 (mt-10) REVERT: B 212 MET cc_start: 0.8982 (mmt) cc_final: 0.8673 (mmt) REVERT: B 560 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8346 (m) REVERT: B 688 GLU cc_start: 0.8885 (pt0) cc_final: 0.8510 (pp20) REVERT: B 886 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8188 (tppt) REVERT: A 113 CYS cc_start: 0.9286 (t) cc_final: 0.8901 (t) REVERT: A 161 TYR cc_start: 0.9095 (m-80) cc_final: 0.8763 (m-80) REVERT: A 722 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9198 (mm) REVERT: A 967 LYS cc_start: 0.8567 (mttm) cc_final: 0.8234 (mtpp) outliers start: 30 outliers final: 24 residues processed: 108 average time/residue: 0.6776 time to fit residues: 80.1708 Evaluate side-chains 105 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 392 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 957 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.085129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.068897 restraints weight = 94771.595| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.05 r_work: 0.2700 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.819 15358 Z= 0.250 Angle : 0.521 12.591 20972 Z= 0.264 Chirality : 0.041 0.226 2358 Planarity : 0.004 0.040 2669 Dihedral : 4.747 58.139 2532 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.55 % Rotamer: Outliers : 1.75 % Allowed : 18.09 % Favored : 80.16 % 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: 1.54 (0.20), residues: 1812 helix: 1.82 (0.18), residues: 842 sheet: 0.66 (0.32), residues: 256 loop : 0.31 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 204 TYR 0.018 0.001 TYR B 891 PHE 0.020 0.001 PHE B 490 TRP 0.008 0.001 TRP B 619 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00272 (15325) covalent geometry : angle 0.50058 (20883) SS BOND : bond 0.00266 ( 4) SS BOND : angle 3.99810 ( 8) hydrogen bonds : bond 0.03609 ( 751) hydrogen bonds : angle 4.28158 ( 2135) metal coordination : bond 0.57894 ( 2) link_BETA1-4 : bond 0.00399 ( 12) link_BETA1-4 : angle 1.33447 ( 36) link_NAG-ASN : bond 0.00492 ( 15) link_NAG-ASN : angle 2.45944 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.8602 (tmm-80) cc_final: 0.8291 (tmm-80) REVERT: B 160 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7748 (pt0) REVERT: B 183 GLU cc_start: 0.8208 (tt0) cc_final: 0.7514 (tm-30) REVERT: B 197 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 212 MET cc_start: 0.8969 (mmt) cc_final: 0.8618 (mmt) REVERT: B 560 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8359 (m) REVERT: B 688 GLU cc_start: 0.8897 (pt0) cc_final: 0.8526 (pp20) REVERT: B 886 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8218 (tppt) REVERT: A 113 CYS cc_start: 0.9255 (t) cc_final: 0.8871 (t) REVERT: A 161 TYR cc_start: 0.9064 (m-80) cc_final: 0.8727 (m-80) REVERT: A 722 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9175 (mm) REVERT: A 967 LYS cc_start: 0.8540 (mttm) cc_final: 0.8212 (mtpp) outliers start: 28 outliers final: 23 residues processed: 109 average time/residue: 0.6673 time to fit residues: 80.0385 Evaluate side-chains 104 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 392 HIS Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 957 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.085094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.068733 restraints weight = 103187.117| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 4.20 r_work: 0.2691 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.731 15358 Z= 0.230 Angle : 0.520 12.735 20972 Z= 0.264 Chirality : 0.041 0.224 2358 Planarity : 0.004 0.040 2669 Dihedral : 4.712 56.797 2532 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 1.56 % Allowed : 18.28 % Favored : 80.16 % 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: 1.56 (0.20), residues: 1812 helix: 1.84 (0.18), residues: 842 sheet: 0.68 (0.32), residues: 256 loop : 0.31 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 204 TYR 0.018 0.001 TYR B 891 PHE 0.020 0.001 PHE B 490 TRP 0.008 0.001 TRP B 619 HIS 0.005 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00276 (15325) covalent geometry : angle 0.49990 (20883) SS BOND : bond 0.00261 ( 4) SS BOND : angle 3.95154 ( 8) hydrogen bonds : bond 0.03598 ( 751) hydrogen bonds : angle 4.26244 ( 2135) metal coordination : bond 0.51677 ( 2) link_BETA1-4 : bond 0.00396 ( 12) link_BETA1-4 : angle 1.33169 ( 36) link_NAG-ASN : bond 0.00484 ( 15) link_NAG-ASN : angle 2.44327 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.8615 (tmm-80) cc_final: 0.8307 (tmm-80) REVERT: B 183 GLU cc_start: 0.8248 (tt0) cc_final: 0.7473 (tm-30) REVERT: B 197 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 212 MET cc_start: 0.8977 (mmt) cc_final: 0.8623 (mmt) REVERT: B 560 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8369 (m) REVERT: B 688 GLU cc_start: 0.8932 (pt0) cc_final: 0.8564 (pp20) REVERT: B 886 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8243 (tppt) REVERT: A 113 CYS cc_start: 0.9267 (t) cc_final: 0.8883 (t) REVERT: A 161 TYR cc_start: 0.9075 (m-80) cc_final: 0.8738 (m-80) REVERT: A 722 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 967 LYS cc_start: 0.8535 (mttm) cc_final: 0.8204 (mtpp) outliers start: 25 outliers final: 23 residues processed: 103 average time/residue: 0.6366 time to fit residues: 72.2823 Evaluate side-chains 104 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 392 HIS Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 957 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 87 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.067445 restraints weight = 103284.930| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 4.19 r_work: 0.2672 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.645 15358 Z= 0.233 Angle : 0.541 13.047 20972 Z= 0.275 Chirality : 0.042 0.224 2358 Planarity : 0.004 0.041 2669 Dihedral : 4.747 56.815 2532 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 1.50 % Allowed : 18.47 % Favored : 80.04 % 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: 1.54 (0.20), residues: 1812 helix: 1.82 (0.18), residues: 842 sheet: 0.68 (0.32), residues: 256 loop : 0.30 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 204 TYR 0.017 0.001 TYR B 891 PHE 0.021 0.001 PHE A 490 TRP 0.008 0.001 TRP B 619 HIS 0.009 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00369 (15325) covalent geometry : angle 0.52108 (20883) SS BOND : bond 0.00264 ( 4) SS BOND : angle 4.07834 ( 8) hydrogen bonds : bond 0.03811 ( 751) hydrogen bonds : angle 4.30593 ( 2135) metal coordination : bond 0.45586 ( 2) link_BETA1-4 : bond 0.00386 ( 12) link_BETA1-4 : angle 1.36520 ( 36) link_NAG-ASN : bond 0.00473 ( 15) link_NAG-ASN : angle 2.47700 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3884.37 seconds wall clock time: 67 minutes 18.46 seconds (4038.46 seconds total)