Starting phenix.real_space_refine on Mon Jul 6 02:30:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mxp_24075/07_2026/7mxp_24075.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mxp_24075/07_2026/7mxp_24075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mxp_24075/07_2026/7mxp_24075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mxp_24075/07_2026/7mxp_24075.map" model { file = "/net/cci-nas-00/data/ceres_data/7mxp_24075/07_2026/7mxp_24075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mxp_24075/07_2026/7mxp_24075.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mxp_24075/07_2026/7mxp_24075.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mxp_24075/07_2026/7mxp_24075.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 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 135 5.16 5 C 20115 2.51 5 N 5207 2.21 5 O 6207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31664 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8555 Classifications: {'peptide': 1098} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8577 Classifications: {'peptide': 1101} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1047} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8494 Classifications: {'peptide': 1090} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 53, 'TRANS': 1036} Chain breaks: 5 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "E" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {'BMA': 2, 'FUC': 1, 'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 chiralities: 2 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {'BMA': 2, 'FUC': 1, 'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {'BMA': 2, 'FUC': 1, 'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.69, per 1000 atoms: 0.21 Number of scatterers: 31664 At special positions: 0 Unit cell: (193.67, 200.09, 187.25, 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 135 16.00 O 6207 8.00 N 5207 7.00 C 20115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA N 3 " - " MAN N 4 " BETA1-2 " BMA E 3 " - " NAG E 6 " " MAN E 4 " - " NAG E 5 " " BMA F 3 " - " NAG F 6 " " MAN F 4 " - " NAG F 5 " " BMA N 3 " - " NAG N 6 " " MAN N 4 " - " NAG N 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " BETA1-6 " NAG E 1 " - " FUC E 8 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " BMA E 3 " - " BMA E 7 " " NAG F 1 " - " FUC F 8 " " BMA F 3 " - " BMA F 7 " " NAG N 1 " - " FUC N 8 " " BMA N 3 " - " BMA N 7 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 122 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 165 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 165 " " NAG D 1 " - " ASN B 149 " " NAG E 1 " - " ASN B 17 " " NAG F 1 " - " ASN A 17 " " NAG M 1 " - " ASN A 149 " " NAG N 1 " - " ASN C 17 " " NAG O 1 " - " ASN C 149 " " NAG Y 1 " - " ASN C 122 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7356 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 56 sheets defined 18.3% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.632A pdb=" N LEU A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.668A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.508A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 387' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 751 through 757 removed outlier: 3.961A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.953A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.536A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.534A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.612A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 963 removed outlier: 3.532A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.521A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.951A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A1011 " --> pdb=" O TYR A1007 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.663A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.830A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.675A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.910A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.703A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.806A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.845A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 4.086A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.777A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.928A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 removed outlier: 3.533A pdb=" N GLU B 988 " --> pdb=" O ASP B 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 985 through 988' Processing helix chain 'B' and resid 989 through 1033 removed outlier: 4.696A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.298A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.533A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 4.035A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.573A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.527A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.140A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 946 through 968 removed outlier: 3.828A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.435A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 28 removed outlier: 4.093A pdb=" N LEU J 27 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER J 28 " --> pdb=" O ASP J 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 24 through 28' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.525A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 64 removed outlier: 4.046A pdb=" N LYS I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'K' and resid 24 through 28 removed outlier: 4.104A pdb=" N SER K 28 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 4.153A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.785A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.553A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.121A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.938A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.992A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.486A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.486A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.045A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.526A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.549A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.096A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 356 through 358 removed outlier: 5.136A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.589A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.782A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 703 removed outlier: 5.922A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.663A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.663A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.187A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.620A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.802A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.140A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 318 removed outlier: 3.511A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.675A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.623A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.823A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.556A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.743A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1047 through 1048 removed outlier: 4.022A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.986A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL G 109 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA G 88 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 32 through 35 Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.969A pdb=" N SER I 70 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 43 through 47 removed outlier: 7.109A pdb=" N TRP K 34 " --> pdb=" O VAL K 46 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.071A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.699A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY H 33 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.122A pdb=" N VAL L 10 " --> pdb=" O THR L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.873A pdb=" N CYS L 22 " --> pdb=" O ILE L 70 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 45 through 47 removed outlier: 7.123A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP L 84 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 983 hydrogen bonds defined for protein. 2682 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: 8.12 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7384 1.33 - 1.46: 9748 1.46 - 1.59: 15088 1.59 - 1.72: 5 1.72 - 1.84: 171 Bond restraints: 32396 Sorted by residual: bond pdb=" C LYS B 986 " pdb=" N VAL B 987 " ideal model delta sigma weight residual 1.335 1.454 -0.119 1.09e-02 8.42e+03 1.19e+02 bond pdb=" C LYS C 986 " pdb=" N VAL C 987 " ideal model delta sigma weight residual 1.335 1.446 -0.111 1.21e-02 6.83e+03 8.38e+01 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.519 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N VAL B 289 " pdb=" CA VAL B 289 " ideal model delta sigma weight residual 1.459 1.522 -0.063 1.22e-02 6.72e+03 2.70e+01 ... (remaining 32391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 43069 4.22 - 8.44: 905 8.44 - 12.66: 93 12.66 - 16.88: 13 16.88 - 21.10: 2 Bond angle restraints: 44082 Sorted by residual: angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 121.14 -7.34 1.00e+00 1.00e+00 5.38e+01 angle pdb=" CA VAL B 42 " pdb=" CB VAL B 42 " pdb=" CG1 VAL B 42 " ideal model delta sigma weight residual 110.40 122.57 -12.17 1.70e+00 3.46e-01 5.12e+01 angle pdb=" CG1 ILE A 624 " pdb=" CB ILE A 624 " pdb=" CG2 ILE A 624 " ideal model delta sigma weight residual 110.70 89.60 21.10 3.00e+00 1.11e-01 4.95e+01 angle pdb=" N LYS C 986 " pdb=" CA LYS C 986 " pdb=" C LYS C 986 " ideal model delta sigma weight residual 111.71 119.41 -7.70 1.15e+00 7.56e-01 4.49e+01 angle pdb=" C GLY B 744 " pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 122.08 131.59 -9.51 1.47e+00 4.63e-01 4.18e+01 ... (remaining 44077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 16670 18.03 - 36.05: 1687 36.05 - 54.08: 238 54.08 - 72.11: 68 72.11 - 90.14: 29 Dihedral angle restraints: 18692 sinusoidal: 7206 harmonic: 11486 Sorted by residual: dihedral pdb=" CA ASP C 294 " pdb=" C ASP C 294 " pdb=" N PRO C 295 " pdb=" CA PRO C 295 " ideal model delta harmonic sigma weight residual -180.00 -120.07 -59.93 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA LEU C 293 " pdb=" C LEU C 293 " pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta harmonic sigma weight residual 180.00 123.97 56.03 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA ASP A 290 " pdb=" C ASP A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta harmonic sigma weight residual -180.00 -124.36 -55.64 0 5.00e+00 4.00e-02 1.24e+02 ... (remaining 18689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4813 0.149 - 0.299: 261 0.299 - 0.448: 34 0.448 - 0.598: 12 0.598 - 0.747: 2 Chirality restraints: 5122 Sorted by residual: chirality pdb=" CB ILE B 119 " pdb=" CA ILE B 119 " pdb=" CG1 ILE B 119 " pdb=" CG2 ILE B 119 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CB VAL K 74 " pdb=" CA VAL K 74 " pdb=" CG1 VAL K 74 " pdb=" CG2 VAL K 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" CB ILE C 794 " pdb=" CA ILE C 794 " pdb=" CG1 ILE C 794 " pdb=" CG2 ILE C 794 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.19e+00 ... (remaining 5119 not shown) Planarity restraints: 5643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 285 " 0.034 2.00e-02 2.50e+03 7.10e-02 5.04e+01 pdb=" C ILE B 285 " -0.123 2.00e-02 2.50e+03 pdb=" O ILE B 285 " 0.049 2.00e-02 2.50e+03 pdb=" N THR B 286 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 855 " -0.021 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C PHE B 855 " 0.076 2.00e-02 2.50e+03 pdb=" O PHE B 855 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN B 856 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 42 " -0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C VAL B 42 " 0.071 2.00e-02 2.50e+03 pdb=" O VAL B 42 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE B 43 " -0.024 2.00e-02 2.50e+03 ... (remaining 5640 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8818 2.80 - 3.33: 26603 3.33 - 3.85: 59817 3.85 - 4.38: 62986 4.38 - 4.90: 105580 Nonbonded interactions: 263804 Sorted by model distance: nonbonded pdb=" O LEU B 276 " pdb=" N ALA B 288 " model vdw 2.280 3.120 nonbonded pdb=" O PHE L 61 " pdb=" OG1 THR L 73 " model vdw 2.294 3.040 nonbonded pdb=" NE2 GLN H 81 " pdb=" OG1 THR H 82A" model vdw 2.315 3.120 nonbonded pdb=" O LEU C 877 " pdb=" OG1 THR C 881 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR A 396 " pdb=" O ILE B 231 " model vdw 2.334 3.040 ... (remaining 263799 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 14 through 828 or resid 851 or resid 855 through 1309)) selection = (chain 'B' and (resid 14 through 828 or resid 840 or resid 855 through 1309)) selection = (chain 'C' and (resid 14 through 828 or resid 851 or resid 855 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 9.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.420 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.010 0.119 32499 Z= 0.472 Angle : 1.502 21.103 44345 Z= 0.816 Chirality : 0.084 0.747 5122 Planarity : 0.010 0.100 5612 Dihedral : 14.746 89.288 11198 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.50 % Favored : 91.35 % Rotamer: Outliers : 0.23 % Allowed : 1.09 % Favored : 98.68 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.69 % Twisted General : 0.67 % 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: -3.74 (0.11), residues: 3919 helix: -3.23 (0.14), residues: 632 sheet: -1.64 (0.17), residues: 826 loop : -2.71 (0.10), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG C 634 TYR 0.044 0.004 TYR B 204 PHE 0.055 0.004 PHE J 48 TRP 0.046 0.005 TRP K 34 HIS 0.015 0.003 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00959 / 0.47 (32396) covalent geometry : angle 1.46956 / 0.81 (44082) SS BOND : bond 0.00707 / 0.44 ( 46) SS BOND : angle 2.87248 / 2.01 ( 92) hydrogen bonds : bond 0.24563 / 16.46 ( 940) hydrogen bonds : angle 10.57133 / 7.27 ( 2682) link_ALPHA1-3 : bond 0.00384 / 0.20 ( 3) link_ALPHA1-3 : angle 2.53132 / 1.53 ( 9) link_BETA1-2 : bond 0.00786 / 0.37 ( 6) link_BETA1-2 : angle 3.07332 / 1.95 ( 18) link_BETA1-4 : bond 0.01305 / 0.73 ( 11) link_BETA1-4 : angle 4.32555 / 3.11 ( 33) link_BETA1-6 : bond 0.00908 / 0.43 ( 6) link_BETA1-6 : angle 2.81139 / 1.73 ( 18) link_NAG-ASN : bond 0.01417 / 0.88 ( 31) link_NAG-ASN : angle 5.72713 / 3.99 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 650 LEU cc_start: 0.9650 (pt) cc_final: 0.9248 (tp) REVERT: A 740 MET cc_start: 0.9681 (tpt) cc_final: 0.9453 (tpp) REVERT: A 902 MET cc_start: 0.9649 (mmp) cc_final: 0.9430 (mmm) REVERT: A 1029 MET cc_start: 0.9528 (mtm) cc_final: 0.9115 (mtm) REVERT: B 106 PHE cc_start: 0.9358 (m-80) cc_final: 0.9143 (m-80) REVERT: B 117 LEU cc_start: 0.9686 (tp) cc_final: 0.9294 (tp) REVERT: B 740 MET cc_start: 0.9338 (tpt) cc_final: 0.8716 (tpp) REVERT: C 177 MET cc_start: 0.9030 (pmm) cc_final: 0.8822 (pmm) REVERT: C 900 MET cc_start: 0.9681 (mpp) cc_final: 0.9460 (ptp) REVERT: C 1010 GLN cc_start: 0.9664 (tp-100) cc_final: 0.9353 (tp-100) REVERT: G 82 MET cc_start: 0.2979 (ptt) cc_final: 0.2516 (ptt) REVERT: I 18 LEU cc_start: 0.8270 (tp) cc_final: 0.7773 (tt) REVERT: I 100 PHE cc_start: 0.7640 (m-80) cc_final: 0.7168 (m-10) REVERT: H 105 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.9138 (pm20) outliers start: 8 outliers final: 2 residues processed: 106 average time/residue: 0.2143 time to fit residues: 37.0387 Evaluate side-chains 68 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 66 HIS A 173 GLN A 824 ASN A 965 GLN B 146 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1010 GLN B1058 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 540 ASN C 762 GLN I 13 GLN L 41 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.039226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.029064 restraints weight = 526486.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.030006 restraints weight = 322462.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.030730 restraints weight = 227241.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.031236 restraints weight = 176773.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.031613 restraints weight = 147560.869| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32499 Z= 0.152 Angle : 0.734 11.806 44345 Z= 0.380 Chirality : 0.047 0.256 5122 Planarity : 0.006 0.086 5612 Dihedral : 7.228 48.631 4271 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.19 % 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: -2.97 (0.12), residues: 3919 helix: -1.44 (0.17), residues: 650 sheet: -1.60 (0.17), residues: 855 loop : -2.37 (0.11), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 53 TYR 0.035 0.002 TYR A 917 PHE 0.017 0.001 PHE B 833 TRP 0.020 0.002 TRP K 34 HIS 0.005 0.001 HIS K 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (32396) covalent geometry : angle 0.70810 / 0.37 (44082) SS BOND : bond 0.00337 / 0.21 ( 46) SS BOND : angle 1.49487 / 1.06 ( 92) hydrogen bonds : bond 0.05044 / 3.32 ( 940) hydrogen bonds : angle 7.43125 / 5.11 ( 2682) link_ALPHA1-3 : bond 0.00879 / 0.44 ( 3) link_ALPHA1-3 : angle 1.19708 / 0.77 ( 9) link_BETA1-2 : bond 0.00469 / 0.24 ( 6) link_BETA1-2 : angle 1.23100 / 0.78 ( 18) link_BETA1-4 : bond 0.00847 / 0.45 ( 11) link_BETA1-4 : angle 1.62251 / 1.19 ( 33) link_BETA1-6 : bond 0.00529 / 0.28 ( 6) link_BETA1-6 : angle 2.22854 / 1.36 ( 18) link_NAG-ASN : bond 0.00666 / 0.46 ( 31) link_NAG-ASN : angle 3.81134 / 2.65 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9726 (ppt170) cc_final: 0.9429 (ttp80) REVERT: A 1029 MET cc_start: 0.9288 (mtm) cc_final: 0.8980 (mtm) REVERT: B 117 LEU cc_start: 0.9630 (tp) cc_final: 0.9418 (mm) REVERT: B 194 PHE cc_start: 0.8128 (m-10) cc_final: 0.7912 (m-80) REVERT: B 740 MET cc_start: 0.9179 (tpt) cc_final: 0.8267 (tpp) REVERT: C 1010 GLN cc_start: 0.9498 (tp-100) cc_final: 0.9186 (tp-100) REVERT: C 1050 MET cc_start: 0.9772 (pmm) cc_final: 0.9543 (pmm) REVERT: G 82 MET cc_start: 0.2273 (ptt) cc_final: 0.1851 (ptt) REVERT: I 100 PHE cc_start: 0.7663 (m-80) cc_final: 0.7290 (m-10) outliers start: 2 outliers final: 1 residues processed: 91 average time/residue: 0.1944 time to fit residues: 29.6543 Evaluate side-chains 62 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 255 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 261 optimal weight: 20.0000 chunk 247 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 361 optimal weight: 50.0000 chunk 257 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 371 optimal weight: 0.0070 overall best weight: 2.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 625 HIS A1106 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 935 GLN B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 536 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.038395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.028209 restraints weight = 531361.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.029239 restraints weight = 325021.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.029955 restraints weight = 232200.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.030490 restraints weight = 181463.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.030845 restraints weight = 151547.205| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32499 Z= 0.158 Angle : 0.695 12.428 44345 Z= 0.357 Chirality : 0.046 0.298 5122 Planarity : 0.005 0.075 5612 Dihedral : 6.545 42.729 4271 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.27 % Favored : 92.70 % Rotamer: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.13 % 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: -2.64 (0.12), residues: 3919 helix: -0.58 (0.19), residues: 663 sheet: -1.67 (0.17), residues: 879 loop : -2.21 (0.11), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 273 TYR 0.021 0.002 TYR C 369 PHE 0.018 0.002 PHE B 306 TRP 0.014 0.001 TRP K 34 HIS 0.009 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (32396) covalent geometry : angle 0.66887 / 0.35 (44082) SS BOND : bond 0.00311 / 0.21 ( 46) SS BOND : angle 1.45548 / 1.03 ( 92) hydrogen bonds : bond 0.04565 / 3.02 ( 940) hydrogen bonds : angle 6.84880 / 4.71 ( 2682) link_ALPHA1-3 : bond 0.00858 / 0.44 ( 3) link_ALPHA1-3 : angle 1.23225 / 0.78 ( 9) link_BETA1-2 : bond 0.00594 / 0.29 ( 6) link_BETA1-2 : angle 1.36799 / 0.85 ( 18) link_BETA1-4 : bond 0.00693 / 0.39 ( 11) link_BETA1-4 : angle 1.70493 / 1.25 ( 33) link_BETA1-6 : bond 0.00640 / 0.34 ( 6) link_BETA1-6 : angle 1.88121 / 1.14 ( 18) link_NAG-ASN : bond 0.00657 / 0.41 ( 31) link_NAG-ASN : angle 3.70520 / 2.70 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9752 (ppt170) cc_final: 0.9448 (ttp80) REVERT: A 1029 MET cc_start: 0.9355 (mtm) cc_final: 0.8943 (mtm) REVERT: B 117 LEU cc_start: 0.9451 (tp) cc_final: 0.9223 (mm) REVERT: B 194 PHE cc_start: 0.8177 (m-10) cc_final: 0.7925 (m-80) REVERT: B 740 MET cc_start: 0.9217 (tpt) cc_final: 0.8401 (tpp) REVERT: C 118 LEU cc_start: 0.9825 (tt) cc_final: 0.9489 (mp) REVERT: C 177 MET cc_start: 0.8686 (pmm) cc_final: 0.8486 (pmm) REVERT: C 1010 GLN cc_start: 0.9520 (tp-100) cc_final: 0.9234 (tp-100) REVERT: C 1050 MET cc_start: 0.9779 (pmm) cc_final: 0.9523 (pmm) REVERT: G 82 MET cc_start: 0.2368 (ptt) cc_final: 0.1982 (ptt) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2186 time to fit residues: 30.8004 Evaluate side-chains 62 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 15 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 373 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 chunk 342 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 355 optimal weight: 0.5980 chunk 272 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A1011 GLN B 66 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 30 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.037007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.026959 restraints weight = 539456.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.027991 restraints weight = 337745.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.028682 restraints weight = 243756.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.029191 restraints weight = 191953.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.029578 restraints weight = 161053.367| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 32499 Z= 0.190 Angle : 0.709 12.978 44345 Z= 0.363 Chirality : 0.046 0.379 5122 Planarity : 0.005 0.069 5612 Dihedral : 6.236 41.092 4271 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.40 % Favored : 92.57 % Rotamer: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.05 % 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: -2.41 (0.12), residues: 3919 helix: -0.13 (0.19), residues: 660 sheet: -1.61 (0.17), residues: 856 loop : -2.11 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 16 TYR 0.027 0.002 TYR C 369 PHE 0.029 0.002 PHE B 59 TRP 0.017 0.002 TRP C 104 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (32396) covalent geometry : angle 0.68463 / 0.36 (44082) SS BOND : bond 0.00382 / 0.25 ( 46) SS BOND : angle 1.48497 / 1.01 ( 92) hydrogen bonds : bond 0.04324 / 2.85 ( 940) hydrogen bonds : angle 6.70406 / 4.59 ( 2682) link_ALPHA1-3 : bond 0.00870 / 0.45 ( 3) link_ALPHA1-3 : angle 1.28175 / 0.78 ( 9) link_BETA1-2 : bond 0.00564 / 0.27 ( 6) link_BETA1-2 : angle 1.32920 / 0.84 ( 18) link_BETA1-4 : bond 0.00581 / 0.33 ( 11) link_BETA1-4 : angle 1.59061 / 1.15 ( 33) link_BETA1-6 : bond 0.00556 / 0.30 ( 6) link_BETA1-6 : angle 1.95671 / 1.18 ( 18) link_NAG-ASN : bond 0.00940 / 0.58 ( 31) link_NAG-ASN : angle 3.62891 / 2.63 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9751 (ppt170) cc_final: 0.9442 (ttp80) REVERT: A 1029 MET cc_start: 0.9290 (mtm) cc_final: 0.8923 (mtm) REVERT: B 194 PHE cc_start: 0.8396 (m-10) cc_final: 0.8189 (m-80) REVERT: B 740 MET cc_start: 0.9279 (tpt) cc_final: 0.8468 (tpp) REVERT: C 118 LEU cc_start: 0.9805 (tt) cc_final: 0.9498 (mp) REVERT: C 1050 MET cc_start: 0.9782 (pmm) cc_final: 0.9496 (pmm) REVERT: G 82 MET cc_start: 0.3010 (ptt) cc_final: 0.2523 (ptt) outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 0.2203 time to fit residues: 31.1954 Evaluate side-chains 57 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 341 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 388 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 334 optimal weight: 20.0000 chunk 283 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 498 GLN ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 703 ASN B 955 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 317 ASN C 448 ASN C 613 GLN C 784 GLN C 787 GLN C 955 ASN C 992 GLN C1011 GLN C1023 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.033823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.024544 restraints weight = 562273.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.025293 restraints weight = 369414.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.025835 restraints weight = 275601.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.026238 restraints weight = 223454.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.026520 restraints weight = 191942.065| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 32499 Z= 0.361 Angle : 0.918 14.390 44345 Z= 0.476 Chirality : 0.050 0.341 5122 Planarity : 0.006 0.072 5612 Dihedral : 6.888 42.899 4271 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 31.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.28 % Favored : 89.69 % Rotamer: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.82 (0.12), residues: 3919 helix: -0.78 (0.19), residues: 657 sheet: -1.96 (0.17), residues: 806 loop : -2.24 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 567 TYR 0.027 0.003 TYR C 756 PHE 0.033 0.003 PHE J 48 TRP 0.024 0.003 TRP A 152 HIS 0.014 0.003 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.36 (32396) covalent geometry : angle 0.89184 / 0.47 (44082) SS BOND : bond 0.01477 / 0.94 ( 46) SS BOND : angle 2.27234 / 1.56 ( 92) hydrogen bonds : bond 0.05546 / 3.64 ( 940) hydrogen bonds : angle 7.47257 / 5.08 ( 2682) link_ALPHA1-3 : bond 0.00965 / 0.50 ( 3) link_ALPHA1-3 : angle 1.91705 / 1.13 ( 9) link_BETA1-2 : bond 0.00729 / 0.35 ( 6) link_BETA1-2 : angle 1.98200 / 1.28 ( 18) link_BETA1-4 : bond 0.00740 / 0.38 ( 11) link_BETA1-4 : angle 1.82431 / 1.31 ( 33) link_BETA1-6 : bond 0.00619 / 0.34 ( 6) link_BETA1-6 : angle 2.34700 / 1.38 ( 18) link_NAG-ASN : bond 0.01045 / 0.58 ( 31) link_NAG-ASN : angle 4.01024 / 2.88 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9498 (mmp) cc_final: 0.9298 (mmm) REVERT: A 1019 ARG cc_start: 0.9741 (ppt170) cc_final: 0.9465 (ttp80) REVERT: B 740 MET cc_start: 0.9401 (tpt) cc_final: 0.8565 (tpp) REVERT: C 118 LEU cc_start: 0.9810 (tt) cc_final: 0.9447 (mp) REVERT: C 177 MET cc_start: 0.8650 (pmm) cc_final: 0.8403 (pmm) REVERT: C 1050 MET cc_start: 0.9770 (pmm) cc_final: 0.9506 (pmm) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 0.2110 time to fit residues: 27.2781 Evaluate side-chains 56 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 75 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 313 optimal weight: 0.9990 chunk 353 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 384 optimal weight: 0.0170 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 824 ASN A 955 ASN A1106 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 992 GLN C1005 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.035668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.026099 restraints weight = 547332.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.026981 restraints weight = 344656.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.027634 restraints weight = 247150.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.028092 restraints weight = 194278.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.028376 restraints weight = 163295.285| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32499 Z= 0.170 Angle : 0.718 12.238 44345 Z= 0.365 Chirality : 0.048 0.574 5122 Planarity : 0.005 0.061 5612 Dihedral : 6.391 40.934 4271 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.06 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.50 (0.13), residues: 3919 helix: -0.04 (0.20), residues: 672 sheet: -1.90 (0.17), residues: 799 loop : -2.14 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 71 TYR 0.029 0.002 TYR B 38 PHE 0.022 0.002 PHE C 275 TRP 0.032 0.002 TRP G 52 HIS 0.010 0.002 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (32396) covalent geometry : angle 0.69115 / 0.36 (44082) SS BOND : bond 0.00362 / 0.23 ( 46) SS BOND : angle 1.79442 / 1.27 ( 92) hydrogen bonds : bond 0.04196 / 2.78 ( 940) hydrogen bonds : angle 6.87809 / 4.68 ( 2682) link_ALPHA1-3 : bond 0.00802 / 0.41 ( 3) link_ALPHA1-3 : angle 1.45606 / 0.79 ( 9) link_BETA1-2 : bond 0.00601 / 0.29 ( 6) link_BETA1-2 : angle 1.27475 / 0.83 ( 18) link_BETA1-4 : bond 0.00624 / 0.32 ( 11) link_BETA1-4 : angle 1.66790 / 1.22 ( 33) link_BETA1-6 : bond 0.00564 / 0.29 ( 6) link_BETA1-6 : angle 1.94610 / 1.18 ( 18) link_NAG-ASN : bond 0.00604 / 0.39 ( 31) link_NAG-ASN : angle 3.70450 / 2.64 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9714 (ppt170) cc_final: 0.9444 (ttp80) REVERT: B 106 PHE cc_start: 0.9314 (m-80) cc_final: 0.9102 (m-80) REVERT: B 177 MET cc_start: 0.8346 (pmm) cc_final: 0.8136 (pmm) REVERT: B 740 MET cc_start: 0.9330 (tpt) cc_final: 0.8456 (tpp) REVERT: C 118 LEU cc_start: 0.9815 (tt) cc_final: 0.9416 (mp) REVERT: C 177 MET cc_start: 0.8638 (pmm) cc_final: 0.8409 (pmm) REVERT: C 1050 MET cc_start: 0.9758 (pmm) cc_final: 0.9406 (pmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1957 time to fit residues: 25.5442 Evaluate side-chains 56 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 231 optimal weight: 0.6980 chunk 337 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 205 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 824 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.035669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.026129 restraints weight = 547329.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.027062 restraints weight = 338950.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.027728 restraints weight = 243535.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.028194 restraints weight = 191364.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.028500 restraints weight = 160883.252| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 32499 Z= 0.161 Angle : 0.687 11.206 44345 Z= 0.351 Chirality : 0.046 0.352 5122 Planarity : 0.005 0.064 5612 Dihedral : 6.156 41.732 4271 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.73 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.41 (0.13), residues: 3919 helix: 0.11 (0.20), residues: 680 sheet: -1.84 (0.17), residues: 811 loop : -2.11 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 765 TYR 0.026 0.002 TYR B 38 PHE 0.024 0.002 PHE J 61 TRP 0.021 0.002 TRP G 52 HIS 0.018 0.002 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (32396) covalent geometry : angle 0.66317 / 0.35 (44082) SS BOND : bond 0.00412 / 0.26 ( 46) SS BOND : angle 1.63931 / 1.13 ( 92) hydrogen bonds : bond 0.04009 / 2.65 ( 940) hydrogen bonds : angle 6.67914 / 4.55 ( 2682) link_ALPHA1-3 : bond 0.00844 / 0.44 ( 3) link_ALPHA1-3 : angle 1.29987 / 0.76 ( 9) link_BETA1-2 : bond 0.00390 / 0.20 ( 6) link_BETA1-2 : angle 1.36168 / 0.88 ( 18) link_BETA1-4 : bond 0.00679 / 0.35 ( 11) link_BETA1-4 : angle 1.64881 / 1.20 ( 33) link_BETA1-6 : bond 0.00555 / 0.28 ( 6) link_BETA1-6 : angle 1.88689 / 1.15 ( 18) link_NAG-ASN : bond 0.00563 / 0.35 ( 31) link_NAG-ASN : angle 3.43382 / 2.46 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9720 (ppt170) cc_final: 0.9435 (ttp80) REVERT: B 106 PHE cc_start: 0.9209 (m-80) cc_final: 0.9002 (m-80) REVERT: B 177 MET cc_start: 0.8204 (pmm) cc_final: 0.7965 (pmm) REVERT: B 740 MET cc_start: 0.9343 (tpt) cc_final: 0.8459 (tpp) REVERT: C 118 LEU cc_start: 0.9783 (tt) cc_final: 0.9426 (mp) REVERT: C 177 MET cc_start: 0.8583 (pmm) cc_final: 0.8370 (pmm) REVERT: C 1050 MET cc_start: 0.9761 (pmm) cc_final: 0.9391 (pmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2364 time to fit residues: 29.1252 Evaluate side-chains 54 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 42 optimal weight: 20.0000 chunk 361 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 chunk 324 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.033604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.024399 restraints weight = 568083.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.025299 restraints weight = 362089.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.025899 restraints weight = 264476.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.026317 restraints weight = 210805.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.026639 restraints weight = 178440.442| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 32499 Z= 0.268 Angle : 0.808 13.499 44345 Z= 0.414 Chirality : 0.048 0.340 5122 Planarity : 0.005 0.095 5612 Dihedral : 6.432 40.903 4271 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.77 % Favored : 89.21 % Rotamer: Outliers : 0.03 % Allowed : 1.58 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.63 (0.13), residues: 3919 helix: -0.35 (0.19), residues: 670 sheet: -1.86 (0.18), residues: 770 loop : -2.21 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 71 TYR 0.027 0.003 TYR B 837 PHE 0.023 0.003 PHE B 135 TRP 0.030 0.003 TRP G 52 HIS 0.011 0.002 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.27 (32396) covalent geometry : angle 0.78240 / 0.41 (44082) SS BOND : bond 0.00435 / 0.29 ( 46) SS BOND : angle 1.87037 / 1.27 ( 92) hydrogen bonds : bond 0.04693 / 3.10 ( 940) hydrogen bonds : angle 7.10984 / 4.84 ( 2682) link_ALPHA1-3 : bond 0.01123 / 0.58 ( 3) link_ALPHA1-3 : angle 1.54342 / 0.91 ( 9) link_BETA1-2 : bond 0.00600 / 0.29 ( 6) link_BETA1-2 : angle 1.62346 / 1.05 ( 18) link_BETA1-4 : bond 0.00684 / 0.36 ( 11) link_BETA1-4 : angle 1.68703 / 1.20 ( 33) link_BETA1-6 : bond 0.00595 / 0.32 ( 6) link_BETA1-6 : angle 2.10307 / 1.25 ( 18) link_NAG-ASN : bond 0.00847 / 0.51 ( 31) link_NAG-ASN : angle 3.89849 / 2.73 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9735 (ppt170) cc_final: 0.9442 (ttp80) REVERT: B 106 PHE cc_start: 0.9161 (m-80) cc_final: 0.8948 (m-80) REVERT: B 177 MET cc_start: 0.8225 (pmm) cc_final: 0.7947 (pmm) REVERT: B 740 MET cc_start: 0.9426 (tpt) cc_final: 0.8577 (tpp) REVERT: B 869 MET cc_start: 0.9487 (mtp) cc_final: 0.9277 (mtp) REVERT: C 118 LEU cc_start: 0.9816 (tt) cc_final: 0.9434 (mp) REVERT: C 177 MET cc_start: 0.8473 (pmm) cc_final: 0.8252 (pmm) REVERT: C 1050 MET cc_start: 0.9760 (pmm) cc_final: 0.9477 (pmm) REVERT: I 34 MET cc_start: 0.9456 (mmp) cc_final: 0.9215 (mmm) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.2343 time to fit residues: 28.8763 Evaluate side-chains 56 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 191 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 254 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 384 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 350 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 241 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.034597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.025336 restraints weight = 559387.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.026275 restraints weight = 343779.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.026903 restraints weight = 245672.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.027358 restraints weight = 193277.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.027627 restraints weight = 161727.126| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32499 Z= 0.172 Angle : 0.712 13.769 44345 Z= 0.362 Chirality : 0.047 0.614 5122 Planarity : 0.005 0.062 5612 Dihedral : 6.197 40.836 4271 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.03 % Favored : 90.94 % Rotamer: Outliers : 0.03 % Allowed : 0.73 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.48 (0.13), residues: 3919 helix: 0.05 (0.20), residues: 675 sheet: -1.82 (0.17), residues: 799 loop : -2.18 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 246 TYR 0.034 0.002 TYR L 31 PHE 0.024 0.002 PHE C 275 TRP 0.037 0.002 TRP K 34 HIS 0.008 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (32396) covalent geometry : angle 0.68583 / 0.36 (44082) SS BOND : bond 0.00391 / 0.23 ( 46) SS BOND : angle 1.82002 / 1.22 ( 92) hydrogen bonds : bond 0.04032 / 2.67 ( 940) hydrogen bonds : angle 6.77815 / 4.61 ( 2682) link_ALPHA1-3 : bond 0.00946 / 0.49 ( 3) link_ALPHA1-3 : angle 1.33499 / 0.75 ( 9) link_BETA1-2 : bond 0.00496 / 0.24 ( 6) link_BETA1-2 : angle 1.34573 / 0.89 ( 18) link_BETA1-4 : bond 0.00647 / 0.33 ( 11) link_BETA1-4 : angle 1.68612 / 1.20 ( 33) link_BETA1-6 : bond 0.00567 / 0.29 ( 6) link_BETA1-6 : angle 1.89357 / 1.15 ( 18) link_NAG-ASN : bond 0.00581 / 0.37 ( 31) link_NAG-ASN : angle 3.67235 / 2.57 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9718 (ppt170) cc_final: 0.9425 (ttp80) REVERT: B 106 PHE cc_start: 0.9143 (m-80) cc_final: 0.8899 (m-80) REVERT: B 177 MET cc_start: 0.8059 (pmm) cc_final: 0.7758 (pmm) REVERT: B 194 PHE cc_start: 0.8627 (m-80) cc_final: 0.8219 (m-80) REVERT: B 740 MET cc_start: 0.9392 (tpt) cc_final: 0.8531 (tpp) REVERT: B 1019 ARG cc_start: 0.9228 (tpt-90) cc_final: 0.9025 (tpp80) REVERT: C 118 LEU cc_start: 0.9799 (tt) cc_final: 0.9425 (mp) REVERT: C 177 MET cc_start: 0.8505 (pmm) cc_final: 0.8288 (pmm) REVERT: C 1050 MET cc_start: 0.9728 (pmm) cc_final: 0.9350 (pmm) REVERT: I 34 MET cc_start: 0.9396 (mmp) cc_final: 0.9179 (mmm) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.2287 time to fit residues: 29.3844 Evaluate side-chains 57 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 168 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 384 optimal weight: 0.5980 chunk 5 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 369 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 387 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.033677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.024651 restraints weight = 570729.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.025503 restraints weight = 352713.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.026086 restraints weight = 253070.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.026523 restraints weight = 199143.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.026789 restraints weight = 167380.229| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 32499 Z= 0.207 Angle : 0.740 12.500 44345 Z= 0.378 Chirality : 0.047 0.458 5122 Planarity : 0.005 0.059 5612 Dihedral : 6.211 40.772 4271 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.39 % Favored : 89.59 % Rotamer: Outliers : 0.03 % Allowed : 0.50 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.53 (0.13), residues: 3919 helix: -0.13 (0.20), residues: 678 sheet: -1.84 (0.17), residues: 812 loop : -2.17 (0.12), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 765 TYR 0.028 0.002 TYR B 38 PHE 0.025 0.002 PHE C 275 TRP 0.032 0.002 TRP K 34 HIS 0.009 0.002 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (32396) covalent geometry : angle 0.71704 / 0.37 (44082) SS BOND : bond 0.00406 / 0.26 ( 46) SS BOND : angle 1.78647 / 1.21 ( 92) hydrogen bonds : bond 0.04205 / 2.79 ( 940) hydrogen bonds : angle 6.88279 / 4.67 ( 2682) link_ALPHA1-3 : bond 0.00986 / 0.51 ( 3) link_ALPHA1-3 : angle 1.37037 / 0.81 ( 9) link_BETA1-2 : bond 0.00701 / 0.34 ( 6) link_BETA1-2 : angle 1.48401 / 0.97 ( 18) link_BETA1-4 : bond 0.00667 / 0.35 ( 11) link_BETA1-4 : angle 1.66328 / 1.18 ( 33) link_BETA1-6 : bond 0.00587 / 0.31 ( 6) link_BETA1-6 : angle 1.98393 / 1.20 ( 18) link_NAG-ASN : bond 0.00671 / 0.40 ( 31) link_NAG-ASN : angle 3.47770 / 2.46 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9747 (ppt170) cc_final: 0.9451 (ttp80) REVERT: B 106 PHE cc_start: 0.9172 (m-80) cc_final: 0.8926 (m-80) REVERT: B 177 MET cc_start: 0.8194 (pmm) cc_final: 0.7913 (pmm) REVERT: B 194 PHE cc_start: 0.8735 (m-80) cc_final: 0.8404 (m-80) REVERT: B 869 MET cc_start: 0.9488 (mtp) cc_final: 0.9272 (mtp) REVERT: C 118 LEU cc_start: 0.9807 (tt) cc_final: 0.9417 (mp) REVERT: C 177 MET cc_start: 0.8503 (pmm) cc_final: 0.8291 (pmm) REVERT: C 900 MET cc_start: 0.9579 (mpp) cc_final: 0.9307 (ptp) REVERT: C 1050 MET cc_start: 0.9756 (pmm) cc_final: 0.9391 (pmm) REVERT: G 34 MET cc_start: -0.3451 (pmm) cc_final: -0.3670 (pmm) REVERT: I 34 MET cc_start: 0.9428 (mmp) cc_final: 0.9192 (mmm) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.2219 time to fit residues: 27.9341 Evaluate side-chains 57 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 348 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 309 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 613 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.032501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.023727 restraints weight = 564384.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.024550 restraints weight = 358647.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.025116 restraints weight = 259950.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.025505 restraints weight = 206739.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.025813 restraints weight = 174836.561| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 32499 Z= 0.265 Angle : 0.818 14.143 44345 Z= 0.419 Chirality : 0.049 0.434 5122 Planarity : 0.005 0.062 5612 Dihedral : 6.557 40.759 4271 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 30.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.20 % Favored : 88.77 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.79 (0.13), residues: 3919 helix: -0.51 (0.19), residues: 669 sheet: -1.95 (0.18), residues: 775 loop : -2.31 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 765 TYR 0.030 0.003 TYR H 97 PHE 0.045 0.003 PHE C 497 TRP 0.031 0.003 TRP G 52 HIS 0.015 0.002 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.27 (32396) covalent geometry : angle 0.79454 / 0.41 (44082) SS BOND : bond 0.00436 / 0.27 ( 46) SS BOND : angle 1.94391 / 1.34 ( 92) hydrogen bonds : bond 0.04559 / 3.01 ( 940) hydrogen bonds : angle 7.24939 / 4.92 ( 2682) link_ALPHA1-3 : bond 0.01059 / 0.55 ( 3) link_ALPHA1-3 : angle 1.61505 / 0.95 ( 9) link_BETA1-2 : bond 0.00599 / 0.29 ( 6) link_BETA1-2 : angle 1.72853 / 1.13 ( 18) link_BETA1-4 : bond 0.00759 / 0.39 ( 11) link_BETA1-4 : angle 1.81069 / 1.27 ( 33) link_BETA1-6 : bond 0.00582 / 0.30 ( 6) link_BETA1-6 : angle 2.12440 / 1.26 ( 18) link_NAG-ASN : bond 0.00778 / 0.46 ( 31) link_NAG-ASN : angle 3.65278 / 2.67 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5758.36 seconds wall clock time: 101 minutes 23.25 seconds (6083.25 seconds total)