Starting phenix.real_space_refine on Sun Oct 12 14:14:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0q_42866/10_2025/8v0q_42866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0q_42866/10_2025/8v0q_42866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0q_42866/10_2025/8v0q_42866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0q_42866/10_2025/8v0q_42866.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0q_42866/10_2025/8v0q_42866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0q_42866/10_2025/8v0q_42866.cif" } resolution = 3.9 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= 0.020 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 114 5.16 5 C 15813 2.51 5 N 4068 2.21 5 O 4800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24795 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.72, per 1000 atoms: 0.23 Number of scatterers: 24795 At special positions: 0 Unit cell: (137.16, 130.68, 174.96, 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 114 16.00 O 4800 8.00 N 4068 7.00 C 15813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN C 234 " " NAG C1301 " - " ASN A 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN C 801 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 886.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 49 sheets defined 24.3% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.556A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.723A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.568A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.565A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.003A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.654A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.979A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.717A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.672A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.645A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.672A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.399A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.786A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.588A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.538A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.578A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.806A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.515A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.033A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.006A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.633A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.749A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.604A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.149A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.807A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.571A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.595A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.052A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.582A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.864A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.561A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.877A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.190A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.626A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.691A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.708A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.674A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.617A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.563A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.358A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.790A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.343A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.111A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.735A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.735A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.354A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.556A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.556A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.693A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.596A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.818A pdb=" N VAL B 127 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.669A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 7.045A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.712A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.819A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.568A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.391A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.532A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.582A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.173A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.893A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.965A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.554A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.575A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.611A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.273A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.635A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.856A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 909 hydrogen bonds defined for protein. 2502 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: 5.78 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7859 1.34 - 1.47: 6366 1.47 - 1.60: 10978 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25344 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C1 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.48e+00 ... (remaining 25339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 34053 2.99 - 5.99: 354 5.99 - 8.98: 47 8.98 - 11.97: 11 11.97 - 14.96: 5 Bond angle restraints: 34470 Sorted by residual: angle pdb=" C LEU C 945 " pdb=" N GLY C 946 " pdb=" CA GLY C 946 " ideal model delta sigma weight residual 119.98 126.18 -6.20 1.11e+00 8.12e-01 3.11e+01 angle pdb=" C LEU A 518 " pdb=" N HIS A 519 " pdb=" CA HIS A 519 " ideal model delta sigma weight residual 121.54 130.45 -8.91 1.91e+00 2.74e-01 2.18e+01 angle pdb=" C LEU A 518 " pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " ideal model delta sigma weight residual 115.79 110.44 5.35 1.19e+00 7.06e-01 2.02e+01 angle pdb=" C SER A 116 " pdb=" N LEU A 117 " pdb=" CA LEU A 117 " ideal model delta sigma weight residual 120.82 127.39 -6.57 1.47e+00 4.63e-01 2.00e+01 angle pdb=" CB MET C1050 " pdb=" CG MET C1050 " pdb=" SD MET C1050 " ideal model delta sigma weight residual 112.70 126.07 -13.37 3.00e+00 1.11e-01 1.98e+01 ... (remaining 34465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 14455 21.92 - 43.84: 1037 43.84 - 65.77: 127 65.77 - 87.69: 36 87.69 - 109.61: 5 Dihedral angle restraints: 15660 sinusoidal: 6627 harmonic: 9033 Sorted by residual: dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N PHE B 92 " pdb=" CA PHE B 92 " ideal model delta harmonic sigma weight residual -180.00 -132.40 -47.60 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CA LYS B 462 " pdb=" C LYS B 462 " pdb=" N PRO B 463 " pdb=" CA PRO B 463 " ideal model delta harmonic sigma weight residual -180.00 -136.95 -43.05 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -18.25 -67.75 1 1.00e+01 1.00e-02 5.96e+01 ... (remaining 15657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3945 0.124 - 0.248: 90 0.248 - 0.373: 9 0.373 - 0.497: 2 0.497 - 0.621: 1 Chirality restraints: 4047 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C2 NAG C1301 " pdb=" C1 NAG C1301 " pdb=" C3 NAG C1301 " pdb=" N2 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 4044 not shown) Planarity restraints: 4434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 91 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C TYR B 91 " -0.064 2.00e-02 2.50e+03 pdb=" O TYR B 91 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE B 92 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO C 521 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 118 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C LEU C 118 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU C 118 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE C 119 " 0.014 2.00e-02 2.50e+03 ... (remaining 4431 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6318 2.80 - 3.33: 20145 3.33 - 3.85: 39830 3.85 - 4.38: 42999 4.38 - 4.90: 77033 Nonbonded interactions: 186325 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.279 3.040 nonbonded pdb=" O ASP B 294 " pdb=" OG SER B 297 " model vdw 2.287 3.040 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.300 3.040 nonbonded pdb=" O VAL A 308 " pdb=" OG1 THR A 602 " model vdw 2.303 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.304 3.040 ... (remaining 186320 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' selection = (chain 'B' and resid 24 through 1309) selection = (chain 'C' and resid 24 through 1309) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.200 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.970 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.004 0.100 25428 Z= 0.218 Angle : 0.853 19.090 34676 Z= 0.425 Chirality : 0.055 0.621 4047 Planarity : 0.006 0.068 4398 Dihedral : 14.492 109.610 9726 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.14), residues: 3057 helix: -0.68 (0.17), residues: 665 sheet: -0.08 (0.21), residues: 539 loop : -1.80 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C1107 TYR 0.018 0.001 TYR A 453 PHE 0.036 0.002 PHE A 201 TRP 0.015 0.002 TRP B 64 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00439 (25344) covalent geometry : angle 0.82083 (34470) SS BOND : bond 0.00427 ( 40) SS BOND : angle 1.60354 ( 80) hydrogen bonds : bond 0.22872 ( 873) hydrogen bonds : angle 8.28533 ( 2502) Misc. bond : bond 0.00884 ( 2) link_BETA1-4 : bond 0.00645 ( 6) link_BETA1-4 : angle 1.49273 ( 18) link_NAG-ASN : bond 0.00652 ( 36) link_NAG-ASN : angle 4.00754 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8511 (m-30) cc_final: 0.8300 (m-30) REVERT: A 353 TRP cc_start: 0.8791 (p-90) cc_final: 0.7161 (p-90) REVERT: B 740 MET cc_start: 0.7769 (mmt) cc_final: 0.7442 (mmt) REVERT: B 1019 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7323 (ttp80) REVERT: C 549 THR cc_start: 0.8336 (m) cc_final: 0.8022 (p) REVERT: C 979 ASP cc_start: 0.8681 (m-30) cc_final: 0.8460 (m-30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1543 time to fit residues: 66.3626 Evaluate side-chains 183 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 755 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 926 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.135016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101097 restraints weight = 58390.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099079 restraints weight = 39403.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100277 restraints weight = 31730.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100959 restraints weight = 26030.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101220 restraints weight = 23445.181| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25428 Z= 0.139 Angle : 0.618 13.368 34676 Z= 0.307 Chirality : 0.046 0.481 4047 Planarity : 0.004 0.045 4398 Dihedral : 8.226 97.875 4200 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 0.63 % Allowed : 7.61 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.15), residues: 3057 helix: 0.94 (0.20), residues: 675 sheet: -0.13 (0.20), residues: 595 loop : -1.58 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.020 0.001 TYR A1067 PHE 0.020 0.001 PHE A 906 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00313 (25344) covalent geometry : angle 0.59778 (34470) SS BOND : bond 0.00309 ( 40) SS BOND : angle 1.17391 ( 80) hydrogen bonds : bond 0.05048 ( 873) hydrogen bonds : angle 5.65153 ( 2502) Misc. bond : bond 0.00101 ( 2) link_BETA1-4 : bond 0.00381 ( 6) link_BETA1-4 : angle 1.11591 ( 18) link_NAG-ASN : bond 0.00484 ( 36) link_NAG-ASN : angle 2.71884 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.8823 (p-90) cc_final: 0.7453 (p-90) REVERT: A 1039 ARG cc_start: 0.7603 (mtp180) cc_final: 0.7111 (mtm-85) REVERT: B 87 ASN cc_start: 0.6986 (t0) cc_final: 0.6752 (t0) REVERT: B 91 TYR cc_start: 0.7810 (t80) cc_final: 0.7598 (t80) REVERT: B 740 MET cc_start: 0.7854 (mmt) cc_final: 0.7597 (mmt) REVERT: C 453 TYR cc_start: 0.7524 (p90) cc_final: 0.7068 (p90) REVERT: C 869 MET cc_start: 0.7893 (mpp) cc_final: 0.7487 (mpp) REVERT: C 900 MET cc_start: 0.8414 (mtm) cc_final: 0.8178 (mtm) REVERT: C 979 ASP cc_start: 0.8600 (m-30) cc_final: 0.8087 (m-30) outliers start: 17 outliers final: 11 residues processed: 207 average time/residue: 0.1642 time to fit residues: 55.3071 Evaluate side-chains 184 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 519 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 42 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 658 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 710 ASN C 914 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.131377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.096653 restraints weight = 58834.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097205 restraints weight = 35562.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.098075 restraints weight = 33054.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098473 restraints weight = 25117.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099297 restraints weight = 22707.317| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25428 Z= 0.198 Angle : 0.640 13.410 34676 Z= 0.317 Chirality : 0.047 0.466 4047 Planarity : 0.004 0.092 4398 Dihedral : 7.923 95.102 4200 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 1.34 % Allowed : 10.88 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 3057 helix: 1.32 (0.20), residues: 663 sheet: -0.33 (0.20), residues: 590 loop : -1.48 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1039 TYR 0.019 0.001 TYR B 91 PHE 0.024 0.002 PHE B 888 TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00463 (25344) covalent geometry : angle 0.61776 (34470) SS BOND : bond 0.00360 ( 40) SS BOND : angle 1.31256 ( 80) hydrogen bonds : bond 0.05381 ( 873) hydrogen bonds : angle 5.37715 ( 2502) Misc. bond : bond 0.00116 ( 2) link_BETA1-4 : bond 0.00235 ( 6) link_BETA1-4 : angle 1.29971 ( 18) link_NAG-ASN : bond 0.00545 ( 36) link_NAG-ASN : angle 2.82316 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.8785 (p-90) cc_final: 0.7493 (p-90) REVERT: A 697 MET cc_start: 0.7121 (tpt) cc_final: 0.6815 (mmm) REVERT: A 873 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: B 87 ASN cc_start: 0.7264 (t0) cc_final: 0.6931 (t0) REVERT: B 91 TYR cc_start: 0.7821 (t80) cc_final: 0.7618 (t80) REVERT: B 392 PHE cc_start: 0.7651 (m-10) cc_final: 0.7361 (m-10) REVERT: B 740 MET cc_start: 0.7867 (mmt) cc_final: 0.7523 (mmt) REVERT: B 869 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8747 (mtm) REVERT: C 104 TRP cc_start: 0.7391 (m-90) cc_final: 0.7141 (m-90) REVERT: C 453 TYR cc_start: 0.7431 (p90) cc_final: 0.6984 (p90) REVERT: C 900 MET cc_start: 0.8569 (mtm) cc_final: 0.8349 (mtm) REVERT: C 979 ASP cc_start: 0.8565 (m-30) cc_final: 0.8084 (m-30) outliers start: 36 outliers final: 23 residues processed: 209 average time/residue: 0.1704 time to fit residues: 57.3864 Evaluate side-chains 191 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 104 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.130653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095661 restraints weight = 58111.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.095378 restraints weight = 35809.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096070 restraints weight = 32029.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096965 restraints weight = 25306.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.097090 restraints weight = 22721.936| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25428 Z= 0.179 Angle : 0.611 13.051 34676 Z= 0.302 Chirality : 0.046 0.459 4047 Planarity : 0.004 0.045 4398 Dihedral : 7.614 91.314 4200 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 2.12 % Allowed : 12.58 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.15), residues: 3057 helix: 1.56 (0.20), residues: 659 sheet: -0.36 (0.20), residues: 610 loop : -1.38 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.019 0.001 TYR A1067 PHE 0.027 0.001 PHE A 106 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00417 (25344) covalent geometry : angle 0.58854 (34470) SS BOND : bond 0.00362 ( 40) SS BOND : angle 1.30405 ( 80) hydrogen bonds : bond 0.04973 ( 873) hydrogen bonds : angle 5.15145 ( 2502) Misc. bond : bond 0.00204 ( 2) link_BETA1-4 : bond 0.00417 ( 6) link_BETA1-4 : angle 1.22864 ( 18) link_NAG-ASN : bond 0.00475 ( 36) link_NAG-ASN : angle 2.75833 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.9117 (p-90) cc_final: 0.7795 (p-90) REVERT: A 873 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: B 87 ASN cc_start: 0.7566 (t0) cc_final: 0.7183 (t0) REVERT: B 378 LYS cc_start: 0.8124 (pptt) cc_final: 0.7913 (tmmt) REVERT: B 542 ASN cc_start: 0.8643 (t0) cc_final: 0.8349 (t0) REVERT: B 740 MET cc_start: 0.7847 (mmt) cc_final: 0.7410 (mmt) REVERT: B 869 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8843 (mtm) REVERT: C 453 TYR cc_start: 0.7581 (p90) cc_final: 0.7059 (p90) REVERT: C 979 ASP cc_start: 0.8590 (m-30) cc_final: 0.8022 (m-30) outliers start: 57 outliers final: 42 residues processed: 236 average time/residue: 0.1584 time to fit residues: 61.1079 Evaluate side-chains 221 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 21 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 301 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.131082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096068 restraints weight = 57918.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095808 restraints weight = 36080.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.096510 restraints weight = 31994.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097271 restraints weight = 25300.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097430 restraints weight = 22870.350| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25428 Z= 0.140 Angle : 0.588 13.075 34676 Z= 0.289 Chirality : 0.045 0.463 4047 Planarity : 0.004 0.049 4398 Dihedral : 7.350 87.272 4200 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 2.04 % Allowed : 14.40 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.15), residues: 3057 helix: 1.77 (0.21), residues: 657 sheet: -0.32 (0.20), residues: 608 loop : -1.31 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.018 0.001 TYR A1067 PHE 0.027 0.001 PHE A 342 TRP 0.013 0.001 TRP C 104 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00325 (25344) covalent geometry : angle 0.56392 (34470) SS BOND : bond 0.00378 ( 40) SS BOND : angle 1.51432 ( 80) hydrogen bonds : bond 0.04716 ( 873) hydrogen bonds : angle 5.02769 ( 2502) Misc. bond : bond 0.00363 ( 2) link_BETA1-4 : bond 0.00256 ( 6) link_BETA1-4 : angle 1.15639 ( 18) link_NAG-ASN : bond 0.00464 ( 36) link_NAG-ASN : angle 2.77390 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.9124 (p-90) cc_final: 0.7832 (p-90) REVERT: A 697 MET cc_start: 0.6984 (tpt) cc_final: 0.6343 (mmm) REVERT: A 873 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: B 87 ASN cc_start: 0.7529 (t0) cc_final: 0.7118 (t0) REVERT: B 378 LYS cc_start: 0.8123 (pptt) cc_final: 0.7884 (tmmt) REVERT: B 392 PHE cc_start: 0.7723 (m-10) cc_final: 0.7484 (m-10) REVERT: B 740 MET cc_start: 0.7882 (mmt) cc_final: 0.7471 (mmt) REVERT: B 869 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8859 (mtm) REVERT: C 453 TYR cc_start: 0.7587 (p90) cc_final: 0.7075 (p90) REVERT: C 979 ASP cc_start: 0.8565 (m-30) cc_final: 0.7987 (m-30) outliers start: 55 outliers final: 40 residues processed: 226 average time/residue: 0.1611 time to fit residues: 59.9435 Evaluate side-chains 222 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 124 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 307 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 51 optimal weight: 0.2980 chunk 270 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.130969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.096165 restraints weight = 58411.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095451 restraints weight = 36453.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096377 restraints weight = 32902.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.096904 restraints weight = 26539.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097160 restraints weight = 24325.207| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25428 Z= 0.138 Angle : 0.579 14.100 34676 Z= 0.284 Chirality : 0.045 0.453 4047 Planarity : 0.004 0.053 4398 Dihedral : 7.028 75.905 4200 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 2.26 % Allowed : 15.22 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 3057 helix: 1.73 (0.20), residues: 671 sheet: -0.30 (0.20), residues: 610 loop : -1.28 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.039 0.001 TYR B 91 PHE 0.029 0.001 PHE A 106 TRP 0.016 0.001 TRP C 104 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00322 (25344) covalent geometry : angle 0.55660 (34470) SS BOND : bond 0.00343 ( 40) SS BOND : angle 1.33121 ( 80) hydrogen bonds : bond 0.04575 ( 873) hydrogen bonds : angle 4.90295 ( 2502) Misc. bond : bond 0.00157 ( 2) link_BETA1-4 : bond 0.00303 ( 6) link_BETA1-4 : angle 1.12679 ( 18) link_NAG-ASN : bond 0.00443 ( 36) link_NAG-ASN : angle 2.70520 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3494 (mmm) cc_final: 0.3183 (mmm) REVERT: A 353 TRP cc_start: 0.9122 (p-90) cc_final: 0.7828 (p-90) REVERT: A 501 TYR cc_start: 0.8361 (m-10) cc_final: 0.7628 (m-10) REVERT: A 697 MET cc_start: 0.6933 (tpt) cc_final: 0.6362 (mmm) REVERT: A 873 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8474 (m-80) REVERT: B 87 ASN cc_start: 0.7560 (t0) cc_final: 0.7118 (t0) REVERT: B 392 PHE cc_start: 0.7855 (m-10) cc_final: 0.7648 (m-10) REVERT: B 740 MET cc_start: 0.7809 (mmt) cc_final: 0.7430 (mmt) REVERT: B 869 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8646 (mtm) REVERT: C 453 TYR cc_start: 0.7685 (p90) cc_final: 0.7169 (p90) REVERT: C 900 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7904 (mtm) REVERT: C 979 ASP cc_start: 0.8514 (m-30) cc_final: 0.7951 (m-30) outliers start: 61 outliers final: 49 residues processed: 234 average time/residue: 0.1590 time to fit residues: 61.5609 Evaluate side-chains 226 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 61 optimal weight: 3.9990 chunk 245 optimal weight: 0.0030 chunk 275 optimal weight: 0.6980 chunk 43 optimal weight: 0.0000 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.133022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099611 restraints weight = 58231.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097499 restraints weight = 37843.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098763 restraints weight = 31743.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099509 restraints weight = 25370.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099741 restraints weight = 22752.113| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25428 Z= 0.097 Angle : 0.571 12.642 34676 Z= 0.275 Chirality : 0.045 0.455 4047 Planarity : 0.004 0.056 4398 Dihedral : 6.661 59.837 4200 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 1.63 % Allowed : 16.18 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.15), residues: 3057 helix: 2.05 (0.21), residues: 663 sheet: -0.19 (0.20), residues: 615 loop : -1.18 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 905 TYR 0.033 0.001 TYR B 91 PHE 0.030 0.001 PHE A 106 TRP 0.017 0.001 TRP C 104 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00215 (25344) covalent geometry : angle 0.54926 (34470) SS BOND : bond 0.00299 ( 40) SS BOND : angle 1.17252 ( 80) hydrogen bonds : bond 0.04111 ( 873) hydrogen bonds : angle 4.71125 ( 2502) Misc. bond : bond 0.00095 ( 2) link_BETA1-4 : bond 0.00301 ( 6) link_BETA1-4 : angle 1.00326 ( 18) link_NAG-ASN : bond 0.00430 ( 36) link_NAG-ASN : angle 2.66709 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: A 353 TRP cc_start: 0.9077 (p-90) cc_final: 0.7786 (p-90) REVERT: A 501 TYR cc_start: 0.8398 (m-10) cc_final: 0.7674 (m-10) REVERT: A 697 MET cc_start: 0.7034 (tpt) cc_final: 0.6496 (mmm) REVERT: A 873 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: B 87 ASN cc_start: 0.7407 (t0) cc_final: 0.6968 (t0) REVERT: B 380 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: B 392 PHE cc_start: 0.7841 (m-10) cc_final: 0.7630 (m-10) REVERT: B 740 MET cc_start: 0.7788 (mmt) cc_final: 0.7409 (mmt) REVERT: B 869 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8642 (mtm) REVERT: C 453 TYR cc_start: 0.7660 (p90) cc_final: 0.7127 (p90) REVERT: C 900 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7899 (mtm) REVERT: C 979 ASP cc_start: 0.8579 (m-30) cc_final: 0.7942 (m-30) outliers start: 44 outliers final: 29 residues processed: 222 average time/residue: 0.1574 time to fit residues: 57.5127 Evaluate side-chains 210 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1030 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 192 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.129487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094484 restraints weight = 58698.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094234 restraints weight = 37329.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094897 restraints weight = 33556.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.095680 restraints weight = 26613.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095826 restraints weight = 24041.559| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25428 Z= 0.188 Angle : 0.634 12.941 34676 Z= 0.312 Chirality : 0.046 0.430 4047 Planarity : 0.004 0.052 4398 Dihedral : 6.673 59.819 4200 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 2.04 % Allowed : 16.63 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.15), residues: 3057 helix: 1.70 (0.20), residues: 670 sheet: -0.29 (0.20), residues: 607 loop : -1.26 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1039 TYR 0.019 0.001 TYR A 489 PHE 0.021 0.002 PHE B 888 TRP 0.015 0.001 TRP C 104 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00441 (25344) covalent geometry : angle 0.61165 (34470) SS BOND : bond 0.00370 ( 40) SS BOND : angle 1.41798 ( 80) hydrogen bonds : bond 0.04884 ( 873) hydrogen bonds : angle 4.94251 ( 2502) Misc. bond : bond 0.00225 ( 2) link_BETA1-4 : bond 0.00265 ( 6) link_BETA1-4 : angle 1.24347 ( 18) link_NAG-ASN : bond 0.00479 ( 36) link_NAG-ASN : angle 2.81713 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7945 (m-10) REVERT: A 177 MET cc_start: 0.4475 (mmm) cc_final: 0.4172 (mmm) REVERT: A 501 TYR cc_start: 0.8421 (m-10) cc_final: 0.7682 (m-10) REVERT: A 697 MET cc_start: 0.7126 (tpt) cc_final: 0.6600 (mmm) REVERT: A 873 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: A 1045 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7954 (mmtt) REVERT: B 87 ASN cc_start: 0.7619 (t0) cc_final: 0.7193 (t0) REVERT: B 392 PHE cc_start: 0.7948 (m-10) cc_final: 0.7729 (m-10) REVERT: B 740 MET cc_start: 0.7758 (mmt) cc_final: 0.7357 (mmt) REVERT: B 869 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8634 (mtm) REVERT: C 453 TYR cc_start: 0.7660 (p90) cc_final: 0.7104 (p90) REVERT: C 900 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7971 (mtm) REVERT: C 979 ASP cc_start: 0.8569 (m-30) cc_final: 0.8023 (m-30) outliers start: 55 outliers final: 50 residues processed: 229 average time/residue: 0.1636 time to fit residues: 61.6177 Evaluate side-chains 231 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 177 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 298 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 171 optimal weight: 0.4980 chunk 190 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.127907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.093056 restraints weight = 58249.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093466 restraints weight = 34991.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094171 restraints weight = 31497.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094974 restraints weight = 24255.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095145 restraints weight = 21754.274| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25428 Z= 0.225 Angle : 0.677 14.286 34676 Z= 0.334 Chirality : 0.047 0.425 4047 Planarity : 0.004 0.054 4398 Dihedral : 6.785 59.567 4200 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 2.12 % Allowed : 17.11 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 3057 helix: 1.46 (0.20), residues: 670 sheet: -0.47 (0.20), residues: 605 loop : -1.34 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 905 TYR 0.019 0.001 TYR A 489 PHE 0.021 0.002 PHE B1089 TRP 0.017 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00529 (25344) covalent geometry : angle 0.65385 (34470) SS BOND : bond 0.00425 ( 40) SS BOND : angle 1.64321 ( 80) hydrogen bonds : bond 0.05256 ( 873) hydrogen bonds : angle 5.12120 ( 2502) Misc. bond : bond 0.00093 ( 2) link_BETA1-4 : bond 0.00492 ( 6) link_BETA1-4 : angle 1.30537 ( 18) link_NAG-ASN : bond 0.00502 ( 36) link_NAG-ASN : angle 2.89156 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8074 (m-10) REVERT: A 697 MET cc_start: 0.7335 (tpt) cc_final: 0.6843 (mmm) REVERT: A 873 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: A 1045 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8066 (mmtt) REVERT: B 87 ASN cc_start: 0.7764 (t0) cc_final: 0.7384 (t0) REVERT: B 740 MET cc_start: 0.7726 (mmt) cc_final: 0.7379 (mmt) REVERT: B 869 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8653 (mtm) REVERT: C 453 TYR cc_start: 0.7649 (p90) cc_final: 0.7116 (p90) REVERT: C 900 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7992 (mtm) REVERT: C 979 ASP cc_start: 0.8548 (m-30) cc_final: 0.8007 (m-30) outliers start: 57 outliers final: 47 residues processed: 228 average time/residue: 0.1591 time to fit residues: 59.7650 Evaluate side-chains 220 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 47 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.0670 chunk 204 optimal weight: 2.9990 chunk 152 optimal weight: 0.0060 chunk 24 optimal weight: 0.7980 overall best weight: 0.3292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 901 GLN A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 487 ASN B 613 GLN B 675 GLN B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 762 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.132032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098754 restraints weight = 58132.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096617 restraints weight = 37768.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097955 restraints weight = 31475.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.098625 restraints weight = 25094.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098859 restraints weight = 22755.747| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25428 Z= 0.105 Angle : 0.600 13.778 34676 Z= 0.291 Chirality : 0.045 0.444 4047 Planarity : 0.004 0.059 4398 Dihedral : 6.478 59.144 4200 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 1.56 % Allowed : 18.00 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.15), residues: 3057 helix: 1.96 (0.20), residues: 681 sheet: -0.28 (0.20), residues: 613 loop : -1.18 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.017 0.001 TYR A1067 PHE 0.021 0.001 PHE A 106 TRP 0.027 0.001 TRP C 104 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00227 (25344) covalent geometry : angle 0.57877 (34470) SS BOND : bond 0.00309 ( 40) SS BOND : angle 1.09703 ( 80) hydrogen bonds : bond 0.04198 ( 873) hydrogen bonds : angle 4.75649 ( 2502) Misc. bond : bond 0.00367 ( 2) link_BETA1-4 : bond 0.00366 ( 6) link_BETA1-4 : angle 0.94488 ( 18) link_NAG-ASN : bond 0.00445 ( 36) link_NAG-ASN : angle 2.73934 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8049 (m-10) REVERT: A 104 TRP cc_start: 0.5167 (m100) cc_final: 0.3481 (m-90) REVERT: A 177 MET cc_start: 0.4898 (mmm) cc_final: 0.4645 (mmm) REVERT: A 353 TRP cc_start: 0.9071 (p-90) cc_final: 0.7844 (p-90) REVERT: A 420 ASP cc_start: 0.8664 (m-30) cc_final: 0.8310 (m-30) REVERT: A 697 MET cc_start: 0.7210 (tpt) cc_final: 0.6729 (mmm) REVERT: A 731 MET cc_start: 0.8685 (ptp) cc_final: 0.8222 (ptp) REVERT: A 873 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: B 87 ASN cc_start: 0.7787 (t0) cc_final: 0.7375 (t0) REVERT: B 740 MET cc_start: 0.7649 (mmt) cc_final: 0.7345 (mmt) REVERT: B 869 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8651 (mtm) REVERT: B 1107 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7920 (mtt90) REVERT: C 453 TYR cc_start: 0.7725 (p90) cc_final: 0.7210 (p90) REVERT: C 900 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7962 (mtm) outliers start: 42 outliers final: 32 residues processed: 211 average time/residue: 0.1625 time to fit residues: 56.2816 Evaluate side-chains 204 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 19 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 224 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.129832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.095193 restraints weight = 58475.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094797 restraints weight = 34876.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.095668 restraints weight = 32989.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096402 restraints weight = 25578.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096583 restraints weight = 23366.725| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25428 Z= 0.154 Angle : 0.610 13.128 34676 Z= 0.299 Chirality : 0.045 0.423 4047 Planarity : 0.004 0.055 4398 Dihedral : 6.471 59.312 4200 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 1.63 % Allowed : 17.82 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.15), residues: 3057 helix: 1.87 (0.20), residues: 676 sheet: -0.33 (0.20), residues: 612 loop : -1.20 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.017 0.001 TYR B1067 PHE 0.020 0.001 PHE B 275 TRP 0.020 0.001 TRP C 104 HIS 0.011 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00361 (25344) covalent geometry : angle 0.58881 (34470) SS BOND : bond 0.00359 ( 40) SS BOND : angle 1.42394 ( 80) hydrogen bonds : bond 0.04570 ( 873) hydrogen bonds : angle 4.83541 ( 2502) Misc. bond : bond 0.00209 ( 2) link_BETA1-4 : bond 0.00297 ( 6) link_BETA1-4 : angle 1.15711 ( 18) link_NAG-ASN : bond 0.00453 ( 36) link_NAG-ASN : angle 2.69323 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.70 seconds wall clock time: 61 minutes 27.02 seconds (3687.02 seconds total)