Starting phenix.real_space_refine on Tue Oct 27 16:10:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yvg_73523/10_2026/9yvg_73523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yvg_73523/10_2026/9yvg_73523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yvg_73523/10_2026/9yvg_73523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yvg_73523/10_2026/9yvg_73523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yvg_73523/10_2026/9yvg_73523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yvg_73523/10_2026/9yvg_73523.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 107 5.16 5 C 15628 2.51 5 N 4050 2.21 5 O 4681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24466 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8052 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 56, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8081 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 8081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8081 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "S" 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: "U" 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 Time building chain proxies: 4.83, per 1000 atoms: 0.20 Number of scatterers: 24466 At special positions: 0 Unit cell: (135.456, 131.915, 187.691, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 107 16.00 O 4681 8.00 N 4050 7.00 C 15628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS A 733 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 744 " distance=2.04 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1038 " distance=2.03 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 533 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 644 " distance=2.04 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS B 666 " distance=2.03 Simple disulfide: pdb=" SG CYS B 733 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 744 " distance=2.04 Simple disulfide: pdb=" SG CYS B1027 " - pdb=" SG CYS B1038 " distance=2.03 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 533 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 644 " distance=2.05 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.04 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " 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 D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG D 1 " - " ASN A 712 " " NAG I 1 " - " ASN A1093 " " NAG M 1 " - " ASN A1129 " " NAG N 1 " - " ASN B 712 " " NAG O 1 " - " ASN B 796 " " NAG P 1 " - " ASN B1093 " " NAG Q 1 " - " ASN B1129 " " NAG S 1 " - " ASN C 796 " " NAG U 1 " - " ASN C1129 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 981.2 milliseconds 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 47 sheets defined 25.2% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.621A pdb=" N VAL A 362 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.952A pdb=" N ASN A 383 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 750 through 752 No H-bonds generated for 'chain 'A' and resid 750 through 752' Processing helix chain 'A' and resid 753 through 778 Processing helix chain 'A' and resid 811 through 821 Processing helix chain 'A' and resid 861 through 880 Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 892 through 904 Processing helix chain 'A' and resid 907 through 913 removed outlier: 4.191A pdb=" N LEU A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 Processing helix chain 'A' and resid 940 through 960 removed outlier: 3.827A pdb=" N GLN A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'A' and resid 980 through 1028 removed outlier: 5.415A pdb=" N VAL A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1142 removed outlier: 4.113A pdb=" N GLU A1139 " --> pdb=" O PRO A1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.603A pdb=" N VAL B 362 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 367 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.937A pdb=" N ASN B 383 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 741 through 749 Processing helix chain 'B' and resid 750 through 752 No H-bonds generated for 'chain 'B' and resid 750 through 752' Processing helix chain 'B' and resid 753 through 778 Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 846 through 851 removed outlier: 3.597A pdb=" N ASN B 851 " --> pdb=" O ALA B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 880 Processing helix chain 'B' and resid 881 through 886 removed outlier: 3.907A pdb=" N ALA B 885 " --> pdb=" O TRP B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 904 Processing helix chain 'B' and resid 907 through 913 removed outlier: 4.130A pdb=" N LEU B 911 " --> pdb=" O THR B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 removed outlier: 3.655A pdb=" N GLN B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 960 removed outlier: 3.794A pdb=" N VAL B 946 " --> pdb=" O LYS B 942 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 971 through 979 Processing helix chain 'B' and resid 980 through 1027 removed outlier: 5.608A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN B 987 " --> pdb=" O GLU B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1142 removed outlier: 4.130A pdb=" N GLU B1139 " --> pdb=" O PRO B1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.722A pdb=" N TYR C 364 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 382 removed outlier: 3.698A pdb=" N LEU C 382 " --> pdb=" O PRO C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 402 No H-bonds generated for 'chain 'C' and resid 400 through 402' Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'C' and resid 497 through 500 Processing helix chain 'C' and resid 732 through 739 Processing helix chain 'C' and resid 741 through 750 removed outlier: 3.658A pdb=" N GLN C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 778 Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 846 through 851 Processing helix chain 'C' and resid 861 through 880 Processing helix chain 'C' and resid 881 through 886 removed outlier: 3.892A pdb=" N ALA C 885 " --> pdb=" O TRP C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 904 Processing helix chain 'C' and resid 907 through 913 removed outlier: 4.238A pdb=" N LEU C 911 " --> pdb=" O THR C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 removed outlier: 3.573A pdb=" N SER C 934 " --> pdb=" O GLN C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 960 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 971 through 979 Processing helix chain 'C' and resid 980 through 1028 removed outlier: 5.248A pdb=" N VAL C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1142 removed outlier: 4.127A pdb=" N GLU C1139 " --> pdb=" O PRO C1135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 7.617A pdb=" N ASN A 58 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR A 264 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27 removed outlier: 7.617A pdb=" N ASN A 58 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR A 264 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 222 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER A 200 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 52 removed outlier: 3.567A pdb=" N ASP A 282 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 removed outlier: 6.435A pdb=" N ARG A 97 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 116 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 165 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 314 removed outlier: 7.227A pdb=" N VAL A 590 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN A 312 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY A 588 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY A 589 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 320 through 323 removed outlier: 3.560A pdb=" N LEU A 541 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 353 Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 357 removed outlier: 6.692A pdb=" N CYS A 356 " --> pdb=" O CYS A 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AB1, first strand: chain 'A' and resid 447 through 449 Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AB3, first strand: chain 'A' and resid 649 through 650 removed outlier: 6.124A pdb=" N GLU A 649 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N THR A 691 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 706 through 710 Processing sheet with id=AB5, first strand: chain 'A' and resid 713 through 723 removed outlier: 3.540A pdb=" N MET A1045 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR A1062 " --> pdb=" O HIS A1043 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N HIS A1043 " --> pdb=" O TYR A1062 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 728 through 730 removed outlier: 4.465A pdb=" N LYS A 728 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1115 through 1117 Processing sheet with id=AB8, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id=AB9, first strand: chain 'B' and resid 23 through 27 removed outlier: 3.526A pdb=" N TYR B 260 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 23 through 27 removed outlier: 3.526A pdb=" N TYR B 260 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 186 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 190 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N SER B 200 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.571A pdb=" N PHE B 40 " --> pdb=" O PHE C 560 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C 562 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY C 561 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 44 through 52 removed outlier: 6.694A pdb=" N LYS B 273 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.729A pdb=" N ARG B 97 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN B 116 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 165 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 306 through 309 Processing sheet with id=AC6, first strand: chain 'B' and resid 319 through 323 removed outlier: 4.429A pdb=" N GLU B 319 " --> pdb=" O CYS B 533 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 349 through 353 Processing sheet with id=AC8, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AC9, first strand: chain 'B' and resid 468 through 469 Processing sheet with id=AD1, first strand: chain 'B' and resid 548 through 549 removed outlier: 3.594A pdb=" N THR B 548 " --> pdb=" O ASP B 581 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 578 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 649 through 650 removed outlier: 6.124A pdb=" N GLU B 649 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR B 691 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 706 through 723 removed outlier: 6.702A pdb=" N GLN B1066 " --> pdb=" O THR B 711 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE B 713 " --> pdb=" O PRO B1064 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 715 " --> pdb=" O TYR B1062 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B1062 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 717 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1060 " --> pdb=" O VAL B 717 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR B 719 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1058 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE B 721 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL B1056 " --> pdb=" O ILE B 721 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY B1054 " --> pdb=" O PRO B 723 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B1045 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR B1062 " --> pdb=" O HIS B1043 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS B1043 " --> pdb=" O TYR B1062 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 706 through 723 removed outlier: 6.702A pdb=" N GLN B1066 " --> pdb=" O THR B 711 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE B 713 " --> pdb=" O PRO B1064 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 715 " --> pdb=" O TYR B1062 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B1062 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 717 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1060 " --> pdb=" O VAL B 717 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR B 719 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1058 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE B 721 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL B1056 " --> pdb=" O ILE B 721 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY B1054 " --> pdb=" O PRO B 723 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B1071 " --> pdb=" O SER B1092 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 728 through 731 removed outlier: 4.427A pdb=" N LYS B 728 " --> pdb=" O LEU B 856 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1115 through 1117 Processing sheet with id=AD7, first strand: chain 'C' and resid 23 through 27 removed outlier: 5.759A pdb=" N ALA C 259 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR C 90 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 190 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 196 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 223 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 198 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 44 through 52 removed outlier: 6.811A pdb=" N LYS C 273 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 79 through 80 removed outlier: 6.506A pdb=" N ARG C 97 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN C 116 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 165 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 306 through 314 removed outlier: 3.541A pdb=" N THR C 594 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 590 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASN C 312 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY C 588 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 589 " --> pdb=" O GLN C 608 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 319 through 320 removed outlier: 6.852A pdb=" N GLU C 319 " --> pdb=" O ASN C 535 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN C 537 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 349 through 353 Processing sheet with id=AE4, first strand: chain 'C' and resid 356 through 357 removed outlier: 6.657A pdb=" N CYS C 356 " --> pdb=" O CYS C 520 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AE6, first strand: chain 'C' and resid 468 through 469 Processing sheet with id=AE7, first strand: chain 'C' and resid 649 through 650 removed outlier: 6.112A pdb=" N GLU C 649 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR C 691 " --> pdb=" O GLU C 649 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 706 through 710 removed outlier: 3.768A pdb=" N THR C1071 " --> pdb=" O SER C1092 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA C1073 " --> pdb=" O PHE C1090 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE C1090 " --> pdb=" O ALA C1073 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 713 through 723 removed outlier: 3.523A pdb=" N MET C1045 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR C1062 " --> pdb=" O HIS C1043 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS C1043 " --> pdb=" O TYR C1062 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 728 through 731 removed outlier: 4.535A pdb=" N LYS C 728 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1076 through 1077 1006 hydrogen bonds defined for protein. 2748 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: 6.59 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7800 1.35 - 1.47: 6340 1.47 - 1.60: 10765 1.60 - 1.72: 0 1.72 - 1.85: 131 Bond restraints: 25036 Sorted by residual: bond pdb=" C LEU A 224 " pdb=" N PRO A 225 " ideal model delta sigma weight residual 1.331 1.360 -0.029 7.90e-03 1.60e+04 1.34e+01 bond pdb=" N ASN B1093 " pdb=" CA ASN B1093 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.12e-02 7.97e+03 1.06e+01 bond pdb=" N VAL B1091 " pdb=" CA VAL B1091 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.61e+00 bond pdb=" N VAL B1128 " pdb=" CA VAL B1128 " ideal model delta sigma weight residual 1.457 1.489 -0.033 1.15e-02 7.56e+03 8.05e+00 bond pdb=" N ASN A 712 " pdb=" CA ASN A 712 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.16e-02 7.43e+03 7.51e+00 ... (remaining 25031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 32988 1.86 - 3.72: 856 3.72 - 5.58: 221 5.58 - 7.44: 18 7.44 - 9.30: 1 Bond angle restraints: 34084 Sorted by residual: angle pdb=" N ASN B1093 " pdb=" CA ASN B1093 " pdb=" C ASN B1093 " ideal model delta sigma weight residual 112.97 108.74 4.23 1.06e+00 8.90e-01 1.60e+01 angle pdb=" N THR C1095 " pdb=" CA THR C1095 " pdb=" C THR C1095 " ideal model delta sigma weight residual 113.43 108.76 4.67 1.26e+00 6.30e-01 1.37e+01 angle pdb=" CA THR A 711 " pdb=" CB THR A 711 " pdb=" OG1 THR A 711 " ideal model delta sigma weight residual 109.60 104.10 5.50 1.50e+00 4.44e-01 1.34e+01 angle pdb=" CA THR C 711 " pdb=" CB THR C 711 " pdb=" OG1 THR C 711 " ideal model delta sigma weight residual 109.60 104.13 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C ASN B1093 " pdb=" CA ASN B1093 " pdb=" CB ASN B1093 " ideal model delta sigma weight residual 111.17 116.73 -5.56 1.53e+00 4.27e-01 1.32e+01 ... (remaining 34079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14330 17.80 - 35.59: 695 35.59 - 53.39: 106 53.39 - 71.18: 23 71.18 - 88.98: 15 Dihedral angle restraints: 15169 sinusoidal: 6142 harmonic: 9027 Sorted by residual: dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 644 " pdb=" CB CYS C 644 " ideal model delta sinusoidal sigma weight residual 93.00 8.07 84.93 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 644 " pdb=" CB CYS B 644 " ideal model delta sinusoidal sigma weight residual -86.00 -38.89 -47.11 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CB CYS A 733 " pdb=" SG CYS A 733 " pdb=" SG CYS A 755 " pdb=" CB CYS A 755 " ideal model delta sinusoidal sigma weight residual -86.00 -130.91 44.91 1 1.00e+01 1.00e-02 2.80e+01 ... (remaining 15166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3714 0.113 - 0.227: 202 0.227 - 0.340: 2 0.340 - 0.454: 0 0.454 - 0.567: 2 Chirality restraints: 3920 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.38e+01 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.67e+01 ... (remaining 3917 not shown) Planarity restraints: 4402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 2 " 0.335 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG U 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG U 2 " 0.051 2.00e-02 2.50e+03 pdb=" N2 NAG U 2 " -0.506 2.00e-02 2.50e+03 pdb=" O7 NAG U 2 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " -0.324 2.00e-02 2.50e+03 2.76e-01 9.54e+02 pdb=" C7 NAG U 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " 0.483 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " -0.307 2.00e-02 2.50e+03 2.58e-01 8.31e+02 pdb=" C7 NAG Q 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " 0.441 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " -0.028 2.00e-02 2.50e+03 ... (remaining 4399 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 270 2.65 - 3.21: 21709 3.21 - 3.78: 34887 3.78 - 4.34: 49447 4.34 - 4.90: 83048 Nonbonded interactions: 189361 Sorted by model distance: nonbonded pdb=" OG SER A 962 " pdb=" OD2 ASP B 566 " model vdw 2.089 3.040 nonbonded pdb=" OG SER A 703 " pdb=" OG SER A 706 " model vdw 2.127 3.040 nonbonded pdb=" ND2 ASN A 973 " pdb=" OG1 THR B 542 " model vdw 2.148 3.120 nonbonded pdb=" OH TYR C 34 " pdb=" OD2 ASP C 50 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR B 195 " pdb=" OE1 GLU C 511 " model vdw 2.193 3.040 ... (remaining 189356 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 22 through 822 or resid 850 through 1142)) selection = (chain 'B' and (resid 22 through 822 or resid 850 through 1142)) selection = (chain 'C' and (resid 22 through 822 or resid 850 through 1142)) } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.200 Find NCS groups from input model: 0.490 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 0.051 25093 Z= 0.213 Angle : 0.768 10.511 34216 Z= 0.395 Chirality : 0.051 0.567 3920 Planarity : 0.010 0.289 4393 Dihedral : 10.877 88.980 9240 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.07 % Allowed : 0.15 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3050 helix: 2.32 (0.20), residues: 663 sheet: 0.15 (0.19), residues: 665 loop : -1.46 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 352 TYR 0.022 0.001 TYR A 899 PHE 0.030 0.002 PHE C 196 TRP 0.041 0.002 TRP A 628 HIS 0.006 0.001 HIS C1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (25036) covalent geometry : angle 0.74777 / 0.39 (34084) SS BOND : bond 0.00396 / 0.24 ( 39) SS BOND : angle 1.62876 / 1.18 ( 78) hydrogen bonds : bond 0.16699 / 10.79 ( 970) hydrogen bonds : angle 7.41803 / 5.06 ( 2748) link_BETA1-4 : bond 0.03142 / 2.01 ( 9) link_BETA1-4 : angle 3.17969 / 1.92 ( 27) link_NAG-ASN : bond 0.00715 / 0.50 ( 9) link_NAG-ASN : angle 4.80580 / 2.98 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.8406 (t80) cc_final: 0.8201 (t80) REVERT: A 226 ILE cc_start: 0.7642 (mp) cc_final: 0.7190 (pt) REVERT: A 628 TRP cc_start: 0.6646 (p-90) cc_final: 0.5767 (p-90) REVERT: B 560 PHE cc_start: 0.8638 (p90) cc_final: 0.8325 (p90) REVERT: B 1045 MET cc_start: 0.8795 (pmm) cc_final: 0.8573 (ptp) REVERT: B 1133 TYR cc_start: 0.7996 (t80) cc_final: 0.7747 (t80) REVERT: C 136 LEU cc_start: 0.8962 (tp) cc_final: 0.8645 (tp) REVERT: C 221 LEU cc_start: 0.8385 (tp) cc_final: 0.8172 (tp) REVERT: C 330 LEU cc_start: 0.8397 (tt) cc_final: 0.8136 (mm) REVERT: C 510 PHE cc_start: 0.7157 (m-80) cc_final: 0.6430 (m-80) REVERT: C 1096 HIS cc_start: 0.8359 (m90) cc_final: 0.8061 (m90) REVERT: C 1130 ASN cc_start: 0.8369 (t0) cc_final: 0.8045 (t0) REVERT: C 1133 TYR cc_start: 0.8172 (t80) cc_final: 0.7775 (t80) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.1305 time to fit residues: 32.9439 Evaluate side-chains 110 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1095 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.0870 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 HIS ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 312 ASN A 500 HIS A 608 GLN A 704 ASN A 799 GLN A 973 ASN B 266 GLN C 757 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.128279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.079430 restraints weight = 62730.203| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.90 r_work: 0.3065 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25093 Z= 0.114 Angle : 0.536 8.136 34216 Z= 0.273 Chirality : 0.044 0.273 3920 Planarity : 0.004 0.043 4393 Dihedral : 4.356 25.356 3699 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.33 % Allowed : 3.18 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3050 helix: 2.55 (0.20), residues: 676 sheet: 0.59 (0.20), residues: 678 loop : -1.29 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 323 TYR 0.016 0.001 TYR A1062 PHE 0.020 0.001 PHE B 196 TRP 0.017 0.001 TRP A 628 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (25036) covalent geometry : angle 0.52775 / 0.27 (34084) SS BOND : bond 0.00213 / 0.15 ( 39) SS BOND : angle 0.99838 / 0.77 ( 78) hydrogen bonds : bond 0.04354 / 2.78 ( 970) hydrogen bonds : angle 5.79992 / 3.93 ( 2748) link_BETA1-4 : bond 0.00545 / 0.32 ( 9) link_BETA1-4 : angle 1.38958 / 0.87 ( 27) link_NAG-ASN : bond 0.00640 / 0.49 ( 9) link_NAG-ASN : angle 2.65466 / 1.62 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7370 (m-90) cc_final: 0.6693 (m-90) REVERT: A 226 ILE cc_start: 0.7400 (mp) cc_final: 0.6900 (pt) REVERT: B 195 TYR cc_start: 0.8994 (m-80) cc_final: 0.8575 (t80) REVERT: B 196 PHE cc_start: 0.8615 (t80) cc_final: 0.8324 (t80) REVERT: B 560 PHE cc_start: 0.8478 (p90) cc_final: 0.8176 (p90) REVERT: B 897 MET cc_start: 0.9102 (mmm) cc_final: 0.8884 (tpt) REVERT: B 1133 TYR cc_start: 0.8104 (t80) cc_final: 0.7798 (t80) REVERT: C 136 LEU cc_start: 0.8924 (tp) cc_final: 0.8595 (tp) REVERT: C 221 LEU cc_start: 0.8514 (tp) cc_final: 0.8273 (tp) REVERT: C 510 PHE cc_start: 0.7068 (m-80) cc_final: 0.6407 (m-80) REVERT: C 567 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7776 (p) REVERT: C 1096 HIS cc_start: 0.8428 (m90) cc_final: 0.8220 (m90) REVERT: C 1130 ASN cc_start: 0.8471 (t0) cc_final: 0.8053 (t0) REVERT: C 1133 TYR cc_start: 0.8250 (t80) cc_final: 0.7796 (t80) outliers start: 9 outliers final: 6 residues processed: 123 average time/residue: 0.1316 time to fit residues: 28.3623 Evaluate side-chains 104 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 568 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [278, 80, 68, 126, 221, 202, 63, 283, 81, 33, 174] chunk 278 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 221 optimal weight: 0.0570 chunk 202 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 174 optimal weight: 0.0470 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 500 HIS A 973 ASN A 997 GLN B 266 GLN B 608 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.132028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081233 restraints weight = 57512.106| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 4.28 r_work: 0.3069 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25093 Z= 0.120 Angle : 0.501 8.610 34216 Z= 0.256 Chirality : 0.043 0.232 3920 Planarity : 0.004 0.042 4393 Dihedral : 4.074 27.444 3699 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.44 % Allowed : 4.92 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3050 helix: 2.69 (0.20), residues: 667 sheet: 0.67 (0.19), residues: 693 loop : -1.18 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 352 TYR 0.016 0.001 TYR A1062 PHE 0.018 0.001 PHE C 333 TRP 0.014 0.001 TRP A 628 HIS 0.004 0.001 HIS A1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (25036) covalent geometry : angle 0.49391 / 0.25 (34084) SS BOND : bond 0.00228 / 0.16 ( 39) SS BOND : angle 0.98425 / 0.75 ( 78) hydrogen bonds : bond 0.04383 / 2.79 ( 970) hydrogen bonds : angle 5.43410 / 3.68 ( 2748) link_BETA1-4 : bond 0.00241 / 0.14 ( 9) link_BETA1-4 : angle 1.37151 / 0.85 ( 27) link_NAG-ASN : bond 0.00465 / 0.35 ( 9) link_NAG-ASN : angle 2.24436 / 1.35 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7439 (m-90) cc_final: 0.6754 (m-90) REVERT: A 124 LYS cc_start: 0.6984 (mmtt) cc_final: 0.6712 (ptpp) REVERT: B 195 TYR cc_start: 0.8980 (m-80) cc_final: 0.8773 (t80) REVERT: B 223 ASP cc_start: 0.8583 (p0) cc_final: 0.8331 (m-30) REVERT: B 560 PHE cc_start: 0.8561 (p90) cc_final: 0.8169 (p90) REVERT: B 897 MET cc_start: 0.9185 (mmm) cc_final: 0.8910 (tpt) REVERT: B 1045 MET cc_start: 0.9169 (ptp) cc_final: 0.8961 (ptt) REVERT: B 1133 TYR cc_start: 0.8153 (t80) cc_final: 0.7843 (t80) REVERT: C 99 TRP cc_start: 0.7198 (m-90) cc_final: 0.6952 (m-90) REVERT: C 136 LEU cc_start: 0.8969 (tp) cc_final: 0.8623 (tp) REVERT: C 363 LEU cc_start: 0.7362 (tt) cc_final: 0.7050 (mt) REVERT: C 510 PHE cc_start: 0.7270 (m-80) cc_final: 0.6490 (m-80) REVERT: C 567 THR cc_start: 0.8182 (m) cc_final: 0.7776 (p) REVERT: C 1096 HIS cc_start: 0.8478 (m90) cc_final: 0.8261 (m90) REVERT: C 1130 ASN cc_start: 0.8525 (t0) cc_final: 0.7968 (t0) REVERT: C 1133 TYR cc_start: 0.8229 (t80) cc_final: 0.7747 (t80) outliers start: 12 outliers final: 7 residues processed: 118 average time/residue: 0.1286 time to fit residues: 25.9879 Evaluate side-chains 106 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 989 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [101, 284, 135, 236, 245, 304, 224, 239, 86, 218, 29] chunk 101 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 135 optimal weight: 40.0000 chunk 236 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 304 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 239 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN B 500 HIS ** B 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 HIS C 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.121469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071344 restraints weight = 61206.036| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.94 r_work: 0.2973 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25093 Z= 0.195 Angle : 0.560 10.559 34216 Z= 0.290 Chirality : 0.045 0.199 3920 Planarity : 0.004 0.055 4393 Dihedral : 4.306 29.760 3699 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.63 % Allowed : 5.51 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3050 helix: 2.57 (0.20), residues: 654 sheet: 0.58 (0.19), residues: 715 loop : -1.10 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 760 TYR 0.018 0.001 TYR A1062 PHE 0.017 0.001 PHE B 324 TRP 0.037 0.002 TRP C 628 HIS 0.005 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (25036) covalent geometry : angle 0.55428 / 0.29 (34084) SS BOND : bond 0.00287 / 0.21 ( 39) SS BOND : angle 1.18376 / 0.89 ( 78) hydrogen bonds : bond 0.05334 / 3.39 ( 970) hydrogen bonds : angle 5.45362 / 3.69 ( 2748) link_BETA1-4 : bond 0.00266 / 0.16 ( 9) link_BETA1-4 : angle 1.30013 / 0.84 ( 27) link_NAG-ASN : bond 0.00496 / 0.36 ( 9) link_NAG-ASN : angle 2.08935 / 1.29 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7603 (m-90) cc_final: 0.6816 (m-90) REVERT: A 226 ILE cc_start: 0.7941 (mp) cc_final: 0.7533 (tp) REVERT: A 636 ASN cc_start: 0.7769 (m110) cc_final: 0.7171 (t0) REVERT: B 195 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8770 (t80) REVERT: B 897 MET cc_start: 0.9221 (mmm) cc_final: 0.8920 (tpt) REVERT: C 99 TRP cc_start: 0.7319 (m-90) cc_final: 0.7044 (m-90) REVERT: C 136 LEU cc_start: 0.8947 (tp) cc_final: 0.8489 (tp) REVERT: C 567 THR cc_start: 0.8276 (m) cc_final: 0.7863 (p) REVERT: C 1096 HIS cc_start: 0.8584 (m90) cc_final: 0.8298 (m90) REVERT: C 1133 TYR cc_start: 0.8240 (t80) cc_final: 0.7707 (t80) outliers start: 17 outliers final: 10 residues processed: 115 average time/residue: 0.1266 time to fit residues: 25.6661 Evaluate side-chains 103 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 1045 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [292, 185, 248, 257, 267, 117, 1, 218, 281, 94, 55] chunk 292 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 267 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 281 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 ASN ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN B 705 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.125983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.077430 restraints weight = 63524.150| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.80 r_work: 0.2932 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25093 Z= 0.235 Angle : 0.581 8.866 34216 Z= 0.301 Chirality : 0.045 0.180 3920 Planarity : 0.004 0.048 4393 Dihedral : 4.527 32.790 3699 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.07 % Allowed : 6.91 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 3050 helix: 2.40 (0.20), residues: 665 sheet: 0.36 (0.19), residues: 722 loop : -1.24 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 185 TYR 0.019 0.001 TYR A1062 PHE 0.014 0.001 PHE C 333 TRP 0.019 0.002 TRP B 99 HIS 0.005 0.001 HIS A1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (25036) covalent geometry : angle 0.57513 / 0.30 (34084) SS BOND : bond 0.00379 / 0.27 ( 39) SS BOND : angle 1.26392 / 0.94 ( 78) hydrogen bonds : bond 0.05588 / 3.55 ( 970) hydrogen bonds : angle 5.48756 / 3.72 ( 2748) link_BETA1-4 : bond 0.00201 / 0.13 ( 9) link_BETA1-4 : angle 1.28091 / 0.81 ( 27) link_NAG-ASN : bond 0.00522 / 0.38 ( 9) link_NAG-ASN : angle 2.08326 / 1.29 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7393 (m-90) cc_final: 0.6933 (m-90) REVERT: A 398 ARG cc_start: 0.6520 (mtm180) cc_final: 0.5513 (mtp85) REVERT: A 636 ASN cc_start: 0.7955 (m110) cc_final: 0.7312 (t0) REVERT: B 568 THR cc_start: 0.8258 (m) cc_final: 0.7895 (p) REVERT: B 897 MET cc_start: 0.9239 (mmm) cc_final: 0.8865 (tpt) REVERT: B 985 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: C 99 TRP cc_start: 0.7321 (m-90) cc_final: 0.7052 (m-90) REVERT: C 136 LEU cc_start: 0.8969 (tp) cc_final: 0.8495 (tp) REVERT: C 381 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6734 (ttpt) REVERT: C 567 THR cc_start: 0.8307 (m) cc_final: 0.7893 (p) REVERT: C 1096 HIS cc_start: 0.8701 (m90) cc_final: 0.8385 (m90) REVERT: C 1133 TYR cc_start: 0.8240 (t80) cc_final: 0.7645 (t80) outliers start: 29 outliers final: 18 residues processed: 122 average time/residue: 0.1387 time to fit residues: 29.2076 Evaluate side-chains 107 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 1045 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [57, 128, 154, 232, 196, 126, 106, 93, 213, 38, 186] chunk 57 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 213 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.118726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.069337 restraints weight = 62735.757| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.81 r_work: 0.2954 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25093 Z= 0.148 Angle : 0.516 8.366 34216 Z= 0.266 Chirality : 0.044 0.190 3920 Planarity : 0.004 0.048 4393 Dihedral : 4.345 32.164 3699 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.03 % Allowed : 7.83 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3050 helix: 2.54 (0.20), residues: 666 sheet: 0.40 (0.19), residues: 730 loop : -1.19 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 352 TYR 0.023 0.001 TYR A 375 PHE 0.023 0.001 PHE B 196 TRP 0.023 0.001 TRP B 99 HIS 0.004 0.001 HIS A1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (25036) covalent geometry : angle 0.51066 / 0.26 (34084) SS BOND : bond 0.00270 / 0.19 ( 39) SS BOND : angle 1.04399 / 0.80 ( 78) hydrogen bonds : bond 0.05015 / 3.18 ( 970) hydrogen bonds : angle 5.30990 / 3.60 ( 2748) link_BETA1-4 : bond 0.00297 / 0.19 ( 9) link_BETA1-4 : angle 1.14489 / 0.73 ( 27) link_NAG-ASN : bond 0.00504 / 0.38 ( 9) link_NAG-ASN : angle 1.94818 / 1.22 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7472 (m-90) cc_final: 0.6994 (m-90) REVERT: A 398 ARG cc_start: 0.6579 (mtm180) cc_final: 0.5569 (mtp85) REVERT: A 636 ASN cc_start: 0.7953 (m110) cc_final: 0.7400 (t0) REVERT: B 985 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: C 99 TRP cc_start: 0.7333 (m-90) cc_final: 0.7017 (m-90) REVERT: C 136 LEU cc_start: 0.8984 (tp) cc_final: 0.8534 (tp) REVERT: C 381 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.6735 (mtpt) REVERT: C 567 THR cc_start: 0.8320 (m) cc_final: 0.7897 (p) REVERT: C 631 TYR cc_start: 0.7332 (t80) cc_final: 0.7100 (t80) REVERT: C 1096 HIS cc_start: 0.8695 (m90) cc_final: 0.8377 (m90) REVERT: C 1133 TYR cc_start: 0.8243 (t80) cc_final: 0.7660 (t80) outliers start: 28 outliers final: 20 residues processed: 122 average time/residue: 0.1301 time to fit residues: 27.7019 Evaluate side-chains 113 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 1045 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [210, 7, 229, 183, 111, 28, 155, 76, 169, 84, 212] chunk 210 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 229 optimal weight: 0.0170 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 76 optimal weight: 0.2980 chunk 169 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN C 400 ASN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.119607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070674 restraints weight = 63194.978| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.80 r_work: 0.2993 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25093 Z= 0.098 Angle : 0.482 9.237 34216 Z= 0.245 Chirality : 0.043 0.197 3920 Planarity : 0.004 0.048 4393 Dihedral : 4.007 30.192 3699 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.85 % Allowed : 8.54 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3050 helix: 2.67 (0.20), residues: 672 sheet: 0.50 (0.19), residues: 740 loop : -1.09 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 352 TYR 0.019 0.001 TYR B1133 PHE 0.018 0.001 PHE B 324 TRP 0.025 0.001 TRP B 99 HIS 0.002 0.000 HIS A1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (25036) covalent geometry : angle 0.47768 / 0.24 (34084) SS BOND : bond 0.00230 / 0.17 ( 39) SS BOND : angle 0.84278 / 0.64 ( 78) hydrogen bonds : bond 0.04117 / 2.60 ( 970) hydrogen bonds : angle 5.05461 / 3.42 ( 2748) link_BETA1-4 : bond 0.00369 / 0.22 ( 9) link_BETA1-4 : angle 0.97549 / 0.63 ( 27) link_NAG-ASN : bond 0.00484 / 0.38 ( 9) link_NAG-ASN : angle 1.83764 / 1.16 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7468 (m-90) cc_final: 0.6982 (m-90) REVERT: B 52 PHE cc_start: 0.8065 (m-80) cc_final: 0.7606 (m-80) REVERT: B 985 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: C 136 LEU cc_start: 0.8963 (tp) cc_final: 0.8499 (tp) REVERT: C 381 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6724 (mtpt) REVERT: C 567 THR cc_start: 0.8305 (m) cc_final: 0.7864 (p) REVERT: C 631 TYR cc_start: 0.7236 (t80) cc_final: 0.7002 (t80) REVERT: C 1096 HIS cc_start: 0.8685 (m90) cc_final: 0.8368 (m90) REVERT: C 1133 TYR cc_start: 0.8197 (t80) cc_final: 0.7683 (t80) outliers start: 23 outliers final: 16 residues processed: 130 average time/residue: 0.1319 time to fit residues: 29.7621 Evaluate side-chains 117 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 989 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [149, 80, 289, 24, 296, 75, 89, 41, 290, 230, 231] chunk 149 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 231 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN B 952 GLN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.119410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070486 restraints weight = 62522.606| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.79 r_work: 0.2966 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25093 Z= 0.144 Angle : 0.509 10.322 34216 Z= 0.259 Chirality : 0.043 0.193 3920 Planarity : 0.004 0.047 4393 Dihedral : 4.024 29.227 3699 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.96 % Allowed : 8.68 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3050 helix: 2.70 (0.20), residues: 665 sheet: 0.41 (0.19), residues: 750 loop : -1.06 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 398 TYR 0.016 0.001 TYR A1062 PHE 0.024 0.001 PHE B 196 TRP 0.025 0.001 TRP B 99 HIS 0.003 0.001 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (25036) covalent geometry : angle 0.50400 / 0.26 (34084) SS BOND : bond 0.00242 / 0.18 ( 39) SS BOND : angle 0.93480 / 0.71 ( 78) hydrogen bonds : bond 0.04610 / 2.92 ( 970) hydrogen bonds : angle 5.09943 / 3.45 ( 2748) link_BETA1-4 : bond 0.00242 / 0.16 ( 9) link_BETA1-4 : angle 1.07841 / 0.70 ( 27) link_NAG-ASN : bond 0.00464 / 0.35 ( 9) link_NAG-ASN : angle 1.95158 / 1.21 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7430 (m-90) cc_final: 0.6968 (m-90) REVERT: B 985 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: B 987 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: C 136 LEU cc_start: 0.8911 (tp) cc_final: 0.8425 (tp) REVERT: C 330 LEU cc_start: 0.8585 (tt) cc_final: 0.8284 (mm) REVERT: C 381 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6817 (mtpt) REVERT: C 567 THR cc_start: 0.8283 (m) cc_final: 0.7834 (p) REVERT: C 631 TYR cc_start: 0.7273 (t80) cc_final: 0.7036 (t80) REVERT: C 1096 HIS cc_start: 0.8701 (m90) cc_final: 0.8372 (m90) REVERT: C 1133 TYR cc_start: 0.8240 (t80) cc_final: 0.7723 (t80) outliers start: 26 outliers final: 18 residues processed: 124 average time/residue: 0.1327 time to fit residues: 28.4060 Evaluate side-chains 118 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 989 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [168, 96, 264, 70, 201, 118, 112, 165, 249, 91, 195] chunk 168 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 264 optimal weight: 0.8980 chunk 70 optimal weight: 0.0070 chunk 201 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 165 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN B 575 GLN B 670 GLN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 GLN C 608 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.119993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071612 restraints weight = 63464.394| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.76 r_work: 0.3024 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25093 Z= 0.088 Angle : 0.477 9.250 34216 Z= 0.241 Chirality : 0.043 0.200 3920 Planarity : 0.004 0.048 4393 Dihedral : 3.785 27.527 3699 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.85 % Allowed : 8.87 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3050 helix: 2.79 (0.20), residues: 671 sheet: 0.42 (0.19), residues: 767 loop : -0.99 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 398 TYR 0.015 0.001 TYR A1062 PHE 0.017 0.001 PHE C 163 TRP 0.030 0.001 TRP B 99 HIS 0.002 0.000 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (25036) covalent geometry : angle 0.47313 / 0.24 (34084) SS BOND : bond 0.00208 / 0.15 ( 39) SS BOND : angle 0.75308 / 0.57 ( 78) hydrogen bonds : bond 0.03776 / 2.39 ( 970) hydrogen bonds : angle 4.89358 / 3.31 ( 2748) link_BETA1-4 : bond 0.00426 / 0.25 ( 9) link_BETA1-4 : angle 0.90732 / 0.60 ( 27) link_NAG-ASN : bond 0.00484 / 0.38 ( 9) link_NAG-ASN : angle 1.80489 / 1.14 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7402 (m-90) cc_final: 0.6933 (m-90) REVERT: A 375 TYR cc_start: 0.6387 (m-10) cc_final: 0.6183 (m-10) REVERT: B 987 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8126 (mm-40) REVERT: C 136 LEU cc_start: 0.8944 (tp) cc_final: 0.8443 (tp) REVERT: C 330 LEU cc_start: 0.8571 (tt) cc_final: 0.8294 (mm) REVERT: C 381 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6873 (mtpt) REVERT: C 567 THR cc_start: 0.8329 (m) cc_final: 0.7890 (p) REVERT: C 631 TYR cc_start: 0.7296 (t80) cc_final: 0.7094 (t80) REVERT: C 1096 HIS cc_start: 0.8668 (m90) cc_final: 0.8318 (m90) REVERT: C 1133 TYR cc_start: 0.8168 (t80) cc_final: 0.7684 (t80) outliers start: 23 outliers final: 20 residues processed: 130 average time/residue: 0.1275 time to fit residues: 28.7017 Evaluate side-chains 125 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 989 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [151, 96, 21, 261, 242, 157, 83, 125, 22, 19, 305] chunk 151 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 261 optimal weight: 0.7980 chunk 242 optimal weight: 30.0000 chunk 157 optimal weight: 0.0370 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 HIS B 266 GLN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.120292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071961 restraints weight = 62566.131| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.76 r_work: 0.3003 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25093 Z= 0.100 Angle : 0.487 9.543 34216 Z= 0.246 Chirality : 0.043 0.196 3920 Planarity : 0.004 0.046 4393 Dihedral : 3.740 25.703 3699 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.85 % Allowed : 9.02 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3050 helix: 2.75 (0.20), residues: 671 sheet: 0.41 (0.19), residues: 758 loop : -0.96 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 398 TYR 0.016 0.001 TYR B1133 PHE 0.024 0.001 PHE B 196 TRP 0.028 0.001 TRP B 99 HIS 0.002 0.000 HIS A1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (25036) covalent geometry : angle 0.48299 / 0.25 (34084) SS BOND : bond 0.00200 / 0.15 ( 39) SS BOND : angle 0.77868 / 0.59 ( 78) hydrogen bonds : bond 0.03902 / 2.47 ( 970) hydrogen bonds : angle 4.88041 / 3.30 ( 2748) link_BETA1-4 : bond 0.00332 / 0.19 ( 9) link_BETA1-4 : angle 0.97754 / 0.65 ( 27) link_NAG-ASN : bond 0.00458 / 0.36 ( 9) link_NAG-ASN : angle 1.86738 / 1.18 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7402 (m-90) cc_final: 0.6933 (m-90) REVERT: B 165 TYR cc_start: 0.8808 (t80) cc_final: 0.8554 (t80) REVERT: B 987 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8168 (mm-40) REVERT: C 136 LEU cc_start: 0.8925 (tp) cc_final: 0.8409 (tp) REVERT: C 330 LEU cc_start: 0.8569 (tt) cc_final: 0.8275 (mm) REVERT: C 381 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7058 (mtmt) REVERT: C 567 THR cc_start: 0.8323 (m) cc_final: 0.7866 (p) REVERT: C 631 TYR cc_start: 0.7252 (t80) cc_final: 0.7040 (t80) REVERT: C 1096 HIS cc_start: 0.8626 (m90) cc_final: 0.8274 (m90) REVERT: C 1133 TYR cc_start: 0.8236 (t80) cc_final: 0.7765 (t80) outliers start: 23 outliers final: 19 residues processed: 129 average time/residue: 0.1226 time to fit residues: 27.4137 Evaluate side-chains 125 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 989 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: [110, 88, 165, 185, 52, 209, 171, 245, 104, 78, 240] chunk 110 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 185 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 209 optimal weight: 0.0270 chunk 171 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 240 optimal weight: 30.0000 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN ** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.120433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072342 restraints weight = 63123.477| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.77 r_work: 0.3017 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25093 Z= 0.090 Angle : 0.479 9.444 34216 Z= 0.242 Chirality : 0.042 0.196 3920 Planarity : 0.004 0.047 4393 Dihedral : 3.689 24.481 3699 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.81 % Allowed : 8.91 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3050 helix: 2.78 (0.20), residues: 672 sheet: 0.44 (0.19), residues: 748 loop : -0.92 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 398 TYR 0.023 0.001 TYR A 375 PHE 0.017 0.001 PHE B 324 TRP 0.029 0.001 TRP B 99 HIS 0.002 0.000 HIS B1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (25036) covalent geometry : angle 0.47549 / 0.24 (34084) SS BOND : bond 0.00193 / 0.14 ( 39) SS BOND : angle 0.72035 / 0.55 ( 78) hydrogen bonds : bond 0.03708 / 2.35 ( 970) hydrogen bonds : angle 4.81777 / 3.26 ( 2748) link_BETA1-4 : bond 0.00384 / 0.24 ( 9) link_BETA1-4 : angle 0.92501 / 0.61 ( 27) link_NAG-ASN : bond 0.00476 / 0.37 ( 9) link_NAG-ASN : angle 1.82830 / 1.15 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6976.90 seconds wall clock time: 119 minutes 42.94 seconds (7182.94 seconds total)