Starting phenix.real_space_refine on Mon Jul 6 11:59:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zr7_14885/07_2026/7zr7_14885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr7_14885/07_2026/7zr7_14885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zr7_14885/07_2026/7zr7_14885.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zr7_14885/07_2026/7zr7_14885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zr7_14885/07_2026/7zr7_14885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr7_14885/07_2026/7zr7_14885.map" model { file = "/net/cci-nas-00/data/ceres_data/7zr7_14885/07_2026/7zr7_14885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr7_14885/07_2026/7zr7_14885.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5153 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19566 2.51 5 N 5048 2.21 5 O 6018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30764 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8281 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 783 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 783 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 937 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 783 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.07, per 1000 atoms: 0.23 Number of scatterers: 30764 At special positions: 0 Unit cell: (161.02, 157.7, 209.16, 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 132 16.00 O 6018 8.00 N 5048 7.00 C 19566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 340 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 340 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 328 " " NAG C1304 " - " ASN C 600 " " NAG C1305 " - " ASN C 613 " " NAG C1306 " - " ASN C 654 " " NAG C1307 " - " ASN C 706 " " NAG C1308 " - " ASN C1071 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 340 " " NAG I 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN A 714 " " NAG O 1 " - " ASN A 798 " " NAG P 1 " - " ASN A1095 " " NAG Q 1 " - " ASN A1131 " " NAG R 1 " - " ASN C 714 " " NAG S 1 " - " ASN C 798 " " NAG T 1 " - " ASN C1095 " " NAG U 1 " - " ASN C1131 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7158 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 21.7% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 387 removed outlier: 3.803A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.936A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.836A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.603A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.224A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.467A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.955A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.652A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.802A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.632A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 938 removed outlier: 3.507A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.533A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.612A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.874A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.673A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 380 through 387 removed outlier: 3.652A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.802A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.631A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 909 through 938 removed outlier: 4.224A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.533A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.612A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.874A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.673A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 105 through 111 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'G' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.626A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.982A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.416A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.976A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.090A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'B' and resid 661 through 664 removed outlier: 6.509A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AB6, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.936A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.371A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 785 through 786 removed outlier: 5.727A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.862A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AC3, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.726A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.787A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.492A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AD1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AD2, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.846A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD4, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AD5, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.427A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AD7, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.070A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.589A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.520A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AE2, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.726A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.787A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 143 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.492A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 322 through 325 Processing sheet with id=AE9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AF1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.846A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.426A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AF6, first strand: chain 'C' and resid 715 through 725 removed outlier: 7.070A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.589A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.520A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL H 114 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.259A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AG6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY D 10 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY D 10 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 114 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.259A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 9 through 13 Processing sheet with id=AH3, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AH4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 114 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.258A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AH9, first strand: chain 'G' and resid 18 through 23 1348 hydrogen bonds defined for protein. 3612 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: 10.16 Time building geometry restraints manager: 3.91 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: 9770 1.34 - 1.46: 7907 1.46 - 1.58: 13625 1.58 - 1.70: 3 1.70 - 1.82: 168 Bond restraints: 31473 Sorted by residual: bond pdb=" CA VAL A 317 " pdb=" C VAL A 317 " ideal model delta sigma weight residual 1.523 1.618 -0.095 1.14e-02 7.69e+03 6.91e+01 bond pdb=" N THR B 304 " pdb=" CA THR B 304 " ideal model delta sigma weight residual 1.457 1.544 -0.087 1.23e-02 6.61e+03 4.97e+01 bond pdb=" CA PHE B 303 " pdb=" C PHE B 303 " ideal model delta sigma weight residual 1.521 1.616 -0.095 1.36e-02 5.41e+03 4.89e+01 bond pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 1.453 1.548 -0.095 1.64e-02 3.72e+03 3.35e+01 bond pdb=" CA GLN A 318 " pdb=" C GLN A 318 " ideal model delta sigma weight residual 1.524 1.581 -0.057 1.28e-02 6.10e+03 1.99e+01 ... (remaining 31468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 42372 2.24 - 4.48: 430 4.48 - 6.73: 15 6.73 - 8.97: 3 8.97 - 11.21: 2 Bond angle restraints: 42822 Sorted by residual: angle pdb=" N ASN C 328 " pdb=" CA ASN C 328 " pdb=" C ASN C 328 " ideal model delta sigma weight residual 112.38 123.59 -11.21 1.22e+00 6.72e-01 8.44e+01 angle pdb=" N GLN A 318 " pdb=" CA GLN A 318 " pdb=" C GLN A 318 " ideal model delta sigma weight residual 110.39 117.76 -7.37 1.30e+00 5.92e-01 3.21e+01 angle pdb=" N ASN C 328 " pdb=" CA ASN C 328 " pdb=" CB ASN C 328 " ideal model delta sigma weight residual 110.32 101.08 9.24 1.70e+00 3.46e-01 2.96e+01 angle pdb=" N SER B 588 " pdb=" CA SER B 588 " pdb=" C SER B 588 " ideal model delta sigma weight residual 110.35 117.72 -7.37 1.40e+00 5.10e-01 2.77e+01 angle pdb=" CA VAL A 317 " pdb=" C VAL A 317 " pdb=" N GLN A 318 " ideal model delta sigma weight residual 116.30 122.11 -5.81 1.13e+00 7.83e-01 2.64e+01 ... (remaining 42817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 17431 17.73 - 35.46: 597 35.46 - 53.19: 113 53.19 - 70.92: 27 70.92 - 88.65: 16 Dihedral angle restraints: 18184 sinusoidal: 6990 harmonic: 11194 Sorted by residual: dihedral pdb=" CA THR C 596 " pdb=" C THR C 596 " pdb=" N PRO C 597 " pdb=" CA PRO C 597 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR A 596 " pdb=" C THR A 596 " pdb=" N PRO A 597 " pdb=" CA PRO A 597 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 18181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4504 0.085 - 0.170: 452 0.170 - 0.255: 5 0.255 - 0.340: 2 0.340 - 0.425: 2 Chirality restraints: 4965 Sorted by residual: chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.83 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA VAL A 317 " pdb=" N VAL A 317 " pdb=" C VAL A 317 " pdb=" CB VAL A 317 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ASN C 328 " pdb=" N ASN C 328 " pdb=" C ASN C 328 " pdb=" CB ASN C 328 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 4962 not shown) Planarity restraints: 5507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 340 " -0.147 2.00e-02 2.50e+03 1.56e-01 3.03e+02 pdb=" CG ASN A 340 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 340 " 0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 340 " 0.224 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1071 " -0.130 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" CG ASN C1071 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C1071 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN C1071 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 340 " -0.122 2.00e-02 2.50e+03 1.27e-01 2.01e+02 pdb=" CG ASN C 340 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 340 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN C 340 " 0.184 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " -0.163 2.00e-02 2.50e+03 ... (remaining 5504 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 338 2.61 - 3.18: 27050 3.18 - 3.75: 46131 3.75 - 4.33: 67856 4.33 - 4.90: 112975 Nonbonded interactions: 254350 Sorted by model distance: nonbonded pdb=" OD1 ASN A 537 " pdb=" OG1 THR A 546 " model vdw 2.034 3.040 nonbonded pdb=" OD1 ASN C 537 " pdb=" OG1 THR C 546 " model vdw 2.035 3.040 nonbonded pdb=" OD2 ASP B 575 " pdb=" OG1 THR B 578 " model vdw 2.040 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.044 3.040 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.069 3.040 ... (remaining 254345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 619 or resid 638 through 1310)) selection = chain 'B' selection = (chain 'C' and (resid 13 through 619 or resid 638 through 1310)) } ncs_group { reference = (chain 'D' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 86 or (resid 87 through 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 125)) selection = (chain 'F' and (resid 1 through 13 or resid 17 through 18 or (resid 19 and (name \ N or name CA or name C or name O or name CB )) or resid 20 through 125)) selection = (chain 'H' and (resid 1 through 13 or resid 17 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 86 or (resid \ 87 through 88 and (name N or name CA or name C or name O or name CB )) or resid \ 89 through 125)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.970 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 0.095 31575 Z= 0.197 Angle : 0.588 18.006 43080 Z= 0.304 Chirality : 0.045 0.425 4965 Planarity : 0.003 0.034 5465 Dihedral : 9.857 88.654 10882 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 0.75 % Allowed : 4.09 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 3822 helix: 0.33 (0.20), residues: 721 sheet: -0.20 (0.15), residues: 1042 loop : -0.75 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1016 TYR 0.013 0.001 TYR B1064 PHE 0.012 0.001 PHE B 65 TRP 0.009 0.001 TRP B 883 HIS 0.004 0.001 HIS C1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.20 (31473) covalent geometry : angle 0.53754 / 0.29 (42822) SS BOND : bond 0.00219 / 0.15 ( 48) SS BOND : angle 0.76305 / 0.56 ( 96) hydrogen bonds : bond 0.13911 / 9.14 ( 1262) hydrogen bonds : angle 7.67951 / 5.46 ( 3612) link_BETA1-4 : bond 0.00216 / 0.16 ( 12) link_BETA1-4 : angle 0.90363 / 0.62 ( 36) link_NAG-ASN : bond 0.00456 / 0.32 ( 42) link_NAG-ASN : angle 4.38140 / 2.72 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 339 time to evaluate : 1.137 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: 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: B 55 PHE cc_start: 0.8220 (m-80) cc_final: 0.7258 (m-80) REVERT: B 88 ASP cc_start: 0.8772 (m-30) cc_final: 0.8167 (p0) REVERT: B 191 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8007 (pm20) REVERT: B 275 LYS cc_start: 0.9232 (tmtt) cc_final: 0.9018 (ptmt) REVERT: B 529 ASN cc_start: 0.8813 (t0) cc_final: 0.8612 (t0) REVERT: B 555 LYS cc_start: 0.9384 (tptt) cc_final: 0.8680 (ttpp) REVERT: B 778 VAL cc_start: 0.9587 (t) cc_final: 0.9180 (m) REVERT: B 866 MET cc_start: 0.9117 (mtt) cc_final: 0.8806 (mmt) REVERT: B 910 GLN cc_start: 0.7718 (pt0) cc_final: 0.7390 (pm20) REVERT: B 1034 SER cc_start: 0.8274 (t) cc_final: 0.7301 (p) REVERT: A 760 LEU cc_start: 0.9353 (mt) cc_final: 0.8414 (mt) REVERT: C 229 LEU cc_start: 0.8389 (mt) cc_final: 0.7916 (mp) REVERT: C 998 LEU cc_start: 0.8974 (tp) cc_final: 0.8750 (pp) REVERT: H 80 TYR cc_start: 0.8833 (m-80) cc_final: 0.8546 (m-10) REVERT: L 47 LYS cc_start: 0.8474 (tttt) cc_final: 0.7840 (mptt) REVERT: D 48 VAL cc_start: 0.6382 (t) cc_final: 0.5186 (t) REVERT: F 95 TYR cc_start: 0.8316 (m-80) cc_final: 0.8099 (m-80) outliers start: 25 outliers final: 6 residues processed: 361 average time/residue: 0.2183 time to fit residues: 122.7475 Evaluate side-chains 158 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain C residue 65 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 331 ASN B 603 ASN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 ASN B1008 GLN A 490 GLN A 610 GLN A 999 GLN A1008 GLN C 318 GLN C 962 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.083283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.053324 restraints weight = 164998.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.055178 restraints weight = 72816.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.056305 restraints weight = 44163.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.056972 restraints weight = 32323.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.057397 restraints weight = 26678.748| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31575 Z= 0.161 Angle : 0.589 11.089 43080 Z= 0.302 Chirality : 0.044 0.221 4965 Planarity : 0.004 0.060 5465 Dihedral : 4.081 34.197 4169 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.36 % Rotamer: Outliers : 1.53 % Allowed : 7.58 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 3822 helix: 1.28 (0.19), residues: 719 sheet: -0.00 (0.15), residues: 1074 loop : -0.57 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 102 TYR 0.024 0.001 TYR A1064 PHE 0.021 0.001 PHE B 135 TRP 0.010 0.001 TRP F 36 HIS 0.005 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (31473) covalent geometry : angle 0.57774 / 0.30 (42822) SS BOND : bond 0.00450 / 0.22 ( 48) SS BOND : angle 0.58755 / 0.42 ( 96) hydrogen bonds : bond 0.03991 / 2.63 ( 1262) hydrogen bonds : angle 5.81175 / 4.11 ( 3612) link_BETA1-4 : bond 0.00474 / 0.33 ( 12) link_BETA1-4 : angle 1.04915 / 0.75 ( 36) link_NAG-ASN : bond 0.00235 / 0.14 ( 42) link_NAG-ASN : angle 2.11135 / 1.42 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 1.144 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9060 (tp) REVERT: B 55 PHE cc_start: 0.8441 (m-80) cc_final: 0.7673 (m-80) REVERT: B 88 ASP cc_start: 0.8955 (m-30) cc_final: 0.7750 (p0) REVERT: B 177 MET cc_start: -0.1511 (ttm) cc_final: -0.1738 (mtt) REVERT: B 191 GLU cc_start: 0.8620 (mt-10) cc_final: 0.7916 (pm20) REVERT: B 275 LYS cc_start: 0.9096 (tttt) cc_final: 0.8756 (ptmt) REVERT: B 510 LEU cc_start: 0.9804 (mm) cc_final: 0.9580 (tp) REVERT: B 529 ASN cc_start: 0.8927 (t0) cc_final: 0.8649 (t0) REVERT: B 555 LYS cc_start: 0.9420 (tptt) cc_final: 0.8622 (ttpp) REVERT: B 737 MET cc_start: 0.9152 (ttt) cc_final: 0.8883 (ttt) REVERT: B 866 MET cc_start: 0.9073 (mtt) cc_final: 0.8775 (mmt) REVERT: B 910 GLN cc_start: 0.7902 (pt0) cc_final: 0.7514 (pm20) REVERT: B 945 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9059 (mt) REVERT: A 737 MET cc_start: 0.9053 (tpp) cc_final: 0.8191 (tpp) REVERT: A 759 GLN cc_start: 0.8575 (pp30) cc_final: 0.8102 (pp30) REVERT: A 879 ILE cc_start: 0.9272 (mt) cc_final: 0.9040 (tt) REVERT: A 897 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8954 (mtm) REVERT: C 177 MET cc_start: -0.3340 (mtt) cc_final: -0.3554 (mtt) REVERT: C 284 ASP cc_start: 0.9107 (t0) cc_final: 0.8850 (t0) REVERT: C 375 LYS cc_start: 0.9611 (mttt) cc_final: 0.9403 (mmtt) REVERT: C 777 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8628 (mt-10) outliers start: 51 outliers final: 27 residues processed: 194 average time/residue: 0.1892 time to fit residues: 60.4782 Evaluate side-chains 147 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain L residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 63 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 352 optimal weight: 6.9990 chunk 313 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 341 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 311 GLN B 447 ASN B 610 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 610 GLN C 962 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.081825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051707 restraints weight = 165566.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.053522 restraints weight = 73895.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.054634 restraints weight = 45165.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.055295 restraints weight = 33150.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055642 restraints weight = 27548.710| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31575 Z= 0.166 Angle : 0.541 11.687 43080 Z= 0.279 Chirality : 0.043 0.177 4965 Planarity : 0.004 0.037 5465 Dihedral : 3.984 35.886 4165 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Rotamer: Outliers : 1.53 % Allowed : 8.60 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 3822 helix: 1.70 (0.20), residues: 727 sheet: 0.28 (0.15), residues: 1030 loop : -0.47 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 102 TYR 0.026 0.001 TYR C 366 PHE 0.013 0.001 PHE B 135 TRP 0.022 0.001 TRP F 36 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (31473) covalent geometry : angle 0.53211 / 0.28 (42822) SS BOND : bond 0.00227 / 0.15 ( 48) SS BOND : angle 0.66141 / 0.46 ( 96) hydrogen bonds : bond 0.03736 / 2.48 ( 1262) hydrogen bonds : angle 5.49517 / 3.89 ( 3612) link_BETA1-4 : bond 0.00144 / 0.08 ( 12) link_BETA1-4 : angle 1.03682 / 0.72 ( 36) link_NAG-ASN : bond 0.00296 / 0.19 ( 42) link_NAG-ASN : angle 1.81086 / 1.24 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 1.149 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: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8649 (m-80) cc_final: 0.7763 (m-80) REVERT: B 88 ASP cc_start: 0.9024 (m-30) cc_final: 0.8162 (p0) REVERT: B 191 GLU cc_start: 0.8668 (mt-10) cc_final: 0.7921 (pm20) REVERT: B 510 LEU cc_start: 0.9810 (mm) cc_final: 0.9608 (tp) REVERT: B 529 ASN cc_start: 0.8992 (t0) cc_final: 0.8701 (t0) REVERT: B 555 LYS cc_start: 0.9415 (tptt) cc_final: 0.8623 (ttpp) REVERT: B 737 MET cc_start: 0.9187 (ttt) cc_final: 0.8900 (ttt) REVERT: A 737 MET cc_start: 0.9202 (tpp) cc_final: 0.8337 (tpp) REVERT: A 760 LEU cc_start: 0.9337 (mt) cc_final: 0.8865 (mt) REVERT: A 816 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8495 (mp0) REVERT: A 897 MET cc_start: 0.9306 (mtm) cc_final: 0.9037 (mtm) REVERT: A 1026 MET cc_start: 0.9253 (tpp) cc_final: 0.8947 (mmm) REVERT: C 229 LEU cc_start: 0.8229 (mt) cc_final: 0.7660 (tp) REVERT: C 284 ASP cc_start: 0.9185 (t0) cc_final: 0.8854 (t70) REVERT: C 375 LYS cc_start: 0.9614 (mttt) cc_final: 0.9403 (mmtt) REVERT: C 571 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8208 (p0) REVERT: C 694 MET cc_start: 0.8552 (pmm) cc_final: 0.7776 (pmm) REVERT: C 770 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7234 (tm-30) REVERT: H 83 MET cc_start: 0.7062 (mtm) cc_final: 0.6674 (mpp) REVERT: D 83 MET cc_start: 0.0998 (ptp) cc_final: 0.0619 (ptp) REVERT: G 71 ASN cc_start: 0.8416 (m-40) cc_final: 0.8130 (m-40) outliers start: 51 outliers final: 27 residues processed: 166 average time/residue: 0.1850 time to fit residues: 51.3678 Evaluate side-chains 142 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 107 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 161 optimal weight: 0.0070 chunk 169 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 345 optimal weight: 8.9990 chunk 315 optimal weight: 0.7980 chunk 293 optimal weight: 0.5980 chunk 240 optimal weight: 0.6980 chunk 347 optimal weight: 20.0000 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.082043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051874 restraints weight = 164003.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.053701 restraints weight = 72587.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.054796 restraints weight = 44119.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.055430 restraints weight = 32515.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.055847 restraints weight = 27048.612| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31575 Z= 0.108 Angle : 0.495 8.643 43080 Z= 0.256 Chirality : 0.042 0.162 4965 Planarity : 0.003 0.034 5465 Dihedral : 3.827 35.554 4164 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 1.59 % Allowed : 9.03 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 3822 helix: 2.08 (0.20), residues: 703 sheet: 0.41 (0.15), residues: 1059 loop : -0.42 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 992 TYR 0.018 0.001 TYR B 498 PHE 0.013 0.001 PHE A 65 TRP 0.008 0.001 TRP F 115 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (31473) covalent geometry : angle 0.48909 / 0.25 (42822) SS BOND : bond 0.00160 / 0.09 ( 48) SS BOND : angle 0.46481 / 0.32 ( 96) hydrogen bonds : bond 0.03392 / 2.26 ( 1262) hydrogen bonds : angle 5.21784 / 3.70 ( 3612) link_BETA1-4 : bond 0.00352 / 0.24 ( 12) link_BETA1-4 : angle 0.88278 / 0.62 ( 36) link_NAG-ASN : bond 0.00167 / 0.11 ( 42) link_NAG-ASN : angle 1.48999 / 1.05 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 1.190 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8697 (m-80) cc_final: 0.7753 (m-80) REVERT: B 88 ASP cc_start: 0.9047 (m-30) cc_final: 0.8126 (p0) REVERT: B 191 GLU cc_start: 0.8630 (mt-10) cc_final: 0.7858 (pm20) REVERT: B 200 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8330 (t80) REVERT: B 510 LEU cc_start: 0.9830 (mm) cc_final: 0.9605 (tp) REVERT: B 737 MET cc_start: 0.9064 (ttt) cc_final: 0.8755 (ttt) REVERT: B 756 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8058 (m-10) REVERT: A 737 MET cc_start: 0.9242 (tpp) cc_final: 0.8328 (tpp) REVERT: A 759 GLN cc_start: 0.8739 (pp30) cc_final: 0.8317 (pp30) REVERT: A 760 LEU cc_start: 0.9417 (mt) cc_final: 0.9058 (mt) REVERT: A 897 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8726 (mtm) REVERT: A 999 GLN cc_start: 0.9005 (tt0) cc_final: 0.8682 (tm-30) REVERT: A 1026 MET cc_start: 0.9244 (tpp) cc_final: 0.8916 (mmm) REVERT: C 284 ASP cc_start: 0.9144 (t0) cc_final: 0.8829 (t0) REVERT: C 375 LYS cc_start: 0.9616 (mttt) cc_final: 0.9410 (mmtt) REVERT: C 571 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8218 (p0) REVERT: C 694 MET cc_start: 0.8768 (pmm) cc_final: 0.7894 (pmm) REVERT: C 770 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7234 (tm-30) REVERT: C 954 GLN cc_start: 0.9074 (tp40) cc_final: 0.8842 (tm-30) REVERT: H 83 MET cc_start: 0.7049 (mtm) cc_final: 0.6796 (mpp) REVERT: L 18 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.6132 (p) REVERT: L 77 VAL cc_start: 0.9052 (t) cc_final: 0.8829 (p) REVERT: D 46 GLU cc_start: 0.7233 (tp30) cc_final: 0.6836 (tp30) REVERT: D 83 MET cc_start: 0.0634 (ptp) cc_final: 0.0202 (ptp) REVERT: G 71 ASN cc_start: 0.8436 (m-40) cc_final: 0.8168 (m-40) outliers start: 53 outliers final: 31 residues processed: 161 average time/residue: 0.1878 time to fit residues: 50.5311 Evaluate side-chains 149 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 147 optimal weight: 3.9990 chunk 357 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 366 optimal weight: 0.8980 chunk 329 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 369 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 533 ASN B 687 GLN B 759 GLN B 975 ASN B 999 GLN B1116 ASN B1132 ASN A 66 HIS A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 533 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 687 GLN C 66 HIS C 447 ASN C 610 GLN C 638 ASN C1002 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.084319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.057998 restraints weight = 194327.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.059100 restraints weight = 103029.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.059669 restraints weight = 59135.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.059730 restraints weight = 50398.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.059638 restraints weight = 43569.296| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 31575 Z= 0.389 Angle : 0.779 11.011 43080 Z= 0.396 Chirality : 0.046 0.232 4965 Planarity : 0.005 0.055 5465 Dihedral : 4.743 41.174 4164 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 2.08 % Allowed : 9.33 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 3822 helix: 1.08 (0.19), residues: 709 sheet: 0.09 (0.15), residues: 1064 loop : -0.58 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 44 TYR 0.023 0.002 TYR C 276 PHE 0.026 0.003 PHE B 903 TRP 0.015 0.002 TRP F 36 HIS 0.012 0.002 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00837 / 0.39 (31473) covalent geometry : angle 0.76618 / 0.39 (42822) SS BOND : bond 0.00396 / 0.24 ( 48) SS BOND : angle 1.18730 / 0.87 ( 96) hydrogen bonds : bond 0.04685 / 3.17 ( 1262) hydrogen bonds : angle 5.94615 / 4.17 ( 3612) link_BETA1-4 : bond 0.00624 / 0.43 ( 12) link_BETA1-4 : angle 1.82153 / 1.24 ( 36) link_NAG-ASN : bond 0.00870 / 0.57 ( 42) link_NAG-ASN : angle 2.47601 / 1.74 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 109 time to evaluate : 1.341 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.9114 (m-30) cc_final: 0.8123 (p0) REVERT: B 200 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8684 (t80) REVERT: B 753 TYR cc_start: 0.9316 (m-80) cc_final: 0.8934 (m-80) REVERT: B 899 MET cc_start: 0.9550 (tpp) cc_final: 0.9340 (tpt) REVERT: B 909 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8816 (p) REVERT: B 999 GLN cc_start: 0.9224 (tt0) cc_final: 0.8437 (tp40) REVERT: A 737 MET cc_start: 0.9325 (tpp) cc_final: 0.8591 (tpp) REVERT: A 897 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9211 (mpp) REVERT: A 966 ASN cc_start: 0.9038 (m-40) cc_final: 0.8615 (t0) REVERT: C 694 MET cc_start: 0.8851 (pmm) cc_final: 0.8286 (pmm) REVERT: C 866 MET cc_start: 0.9045 (mtm) cc_final: 0.8399 (ptp) REVERT: C 1047 MET cc_start: 0.8535 (ptt) cc_final: 0.8221 (mtm) outliers start: 69 outliers final: 47 residues processed: 167 average time/residue: 0.1837 time to fit residues: 51.5075 Evaluate side-chains 144 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 94 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 57 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 363 optimal weight: 1.9990 chunk 294 optimal weight: 0.4980 chunk 270 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 GLN A 962 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.078330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.047989 restraints weight = 168545.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049669 restraints weight = 75658.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050677 restraints weight = 46640.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.051311 restraints weight = 34708.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.051665 restraints weight = 28959.551| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31575 Z= 0.174 Angle : 0.548 12.949 43080 Z= 0.283 Chirality : 0.043 0.202 4965 Planarity : 0.003 0.048 5465 Dihedral : 4.259 38.378 4164 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.91 % Rotamer: Outliers : 1.81 % Allowed : 9.96 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 3822 helix: 1.93 (0.20), residues: 696 sheet: 0.17 (0.15), residues: 1072 loop : -0.47 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 992 TYR 0.015 0.001 TYR A 263 PHE 0.016 0.001 PHE B 556 TRP 0.013 0.001 TRP F 36 HIS 0.005 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (31473) covalent geometry : angle 0.54008 / 0.28 (42822) SS BOND : bond 0.00219 / 0.13 ( 48) SS BOND : angle 0.67852 / 0.48 ( 96) hydrogen bonds : bond 0.03723 / 2.50 ( 1262) hydrogen bonds : angle 5.45486 / 3.85 ( 3612) link_BETA1-4 : bond 0.00282 / 0.15 ( 12) link_BETA1-4 : angle 1.11038 / 0.76 ( 36) link_NAG-ASN : bond 0.00279 / 0.19 ( 42) link_NAG-ASN : angle 1.63092 / 1.17 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 105 time to evaluate : 1.105 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: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.8915 (m-30) cc_final: 0.8278 (p0) REVERT: B 200 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8463 (t80) REVERT: B 510 LEU cc_start: 0.9686 (tp) cc_final: 0.9361 (pp) REVERT: B 574 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.9020 (ttm-80) REVERT: B 737 MET cc_start: 0.9137 (ttt) cc_final: 0.8832 (ttt) REVERT: B 999 GLN cc_start: 0.9167 (tt0) cc_final: 0.8515 (tp-100) REVERT: A 737 MET cc_start: 0.9383 (tpp) cc_final: 0.8585 (tpp) REVERT: A 897 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.8807 (mtm) REVERT: A 966 ASN cc_start: 0.9060 (m-40) cc_final: 0.8750 (t0) REVERT: A 999 GLN cc_start: 0.9053 (tt0) cc_final: 0.8416 (tm-30) REVERT: C 694 MET cc_start: 0.8859 (pmm) cc_final: 0.8196 (pmm) REVERT: C 866 MET cc_start: 0.9000 (mtm) cc_final: 0.8788 (mtm) REVERT: L 97 LYS cc_start: 0.8737 (pttt) cc_final: 0.8489 (tmtt) REVERT: E 97 LYS cc_start: 0.9167 (pttt) cc_final: 0.8835 (tmtt) REVERT: F 34 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9138 (tp) outliers start: 60 outliers final: 41 residues processed: 154 average time/residue: 0.1855 time to fit residues: 48.2773 Evaluate side-chains 145 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 35 HIS Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 128 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 294 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 379 optimal weight: 9.9990 chunk 300 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN A 391 ASN A 447 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.078126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.047776 restraints weight = 168117.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049470 restraints weight = 75760.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.050475 restraints weight = 46797.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051122 restraints weight = 34852.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.051432 restraints weight = 29028.716| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31575 Z= 0.178 Angle : 0.555 13.652 43080 Z= 0.283 Chirality : 0.042 0.191 4965 Planarity : 0.003 0.047 5465 Dihedral : 4.180 37.417 4164 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 1.93 % Allowed : 10.38 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.13), residues: 3822 helix: 1.87 (0.20), residues: 713 sheet: 0.14 (0.15), residues: 1068 loop : -0.44 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 63 TYR 0.014 0.001 TYR A 263 PHE 0.019 0.001 PHE E 64 TRP 0.012 0.001 TRP F 36 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (31473) covalent geometry : angle 0.54793 / 0.28 (42822) SS BOND : bond 0.00220 / 0.13 ( 48) SS BOND : angle 0.64467 / 0.45 ( 96) hydrogen bonds : bond 0.03647 / 2.45 ( 1262) hydrogen bonds : angle 5.34265 / 3.78 ( 3612) link_BETA1-4 : bond 0.00118 / 0.08 ( 12) link_BETA1-4 : angle 1.09610 / 0.75 ( 36) link_NAG-ASN : bond 0.00309 / 0.21 ( 42) link_NAG-ASN : angle 1.67269 / 1.20 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 104 time to evaluate : 1.298 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: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.8865 (m-30) cc_final: 0.8317 (p0) REVERT: B 200 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8465 (t80) REVERT: B 510 LEU cc_start: 0.9630 (tp) cc_final: 0.9312 (pp) REVERT: B 574 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8832 (ttm-80) REVERT: B 737 MET cc_start: 0.9064 (ttt) cc_final: 0.8746 (ttt) REVERT: A 357 ASN cc_start: 0.9088 (p0) cc_final: 0.8864 (m-40) REVERT: A 737 MET cc_start: 0.9407 (tpp) cc_final: 0.8590 (tpp) REVERT: A 897 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8835 (mtm) REVERT: A 999 GLN cc_start: 0.9105 (tt0) cc_final: 0.8563 (tm-30) REVERT: A 1026 MET cc_start: 0.9397 (mmm) cc_final: 0.9073 (tpp) REVERT: C 694 MET cc_start: 0.8859 (pmm) cc_final: 0.8192 (pmm) REVERT: C 866 MET cc_start: 0.8988 (mtm) cc_final: 0.8782 (mtm) REVERT: L 97 LYS cc_start: 0.8823 (pttt) cc_final: 0.8568 (tmtt) REVERT: E 97 LYS cc_start: 0.9158 (pttt) cc_final: 0.8801 (tmtt) REVERT: F 34 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9133 (tp) outliers start: 64 outliers final: 48 residues processed: 152 average time/residue: 0.1768 time to fit residues: 46.2374 Evaluate side-chains 149 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 35 HIS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 151 optimal weight: 8.9990 chunk 341 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 295 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN C 853 ASN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.076859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.046704 restraints weight = 169422.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.048387 restraints weight = 74825.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049412 restraints weight = 45686.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.050047 restraints weight = 33710.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.050404 restraints weight = 28004.945| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 31575 Z= 0.245 Angle : 0.604 13.177 43080 Z= 0.308 Chirality : 0.043 0.204 4965 Planarity : 0.004 0.050 5465 Dihedral : 4.315 37.239 4164 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 1.96 % Allowed : 10.74 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 3822 helix: 1.73 (0.20), residues: 711 sheet: 0.09 (0.15), residues: 1088 loop : -0.44 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 63 TYR 0.017 0.002 TYR A 263 PHE 0.017 0.002 PHE B 389 TRP 0.017 0.001 TRP F 36 HIS 0.006 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.25 (31473) covalent geometry : angle 0.59549 / 0.31 (42822) SS BOND : bond 0.00290 / 0.18 ( 48) SS BOND : angle 0.79186 / 0.57 ( 96) hydrogen bonds : bond 0.03851 / 2.60 ( 1262) hydrogen bonds : angle 5.45952 / 3.85 ( 3612) link_BETA1-4 : bond 0.00193 / 0.14 ( 12) link_BETA1-4 : angle 1.28686 / 0.86 ( 36) link_NAG-ASN : bond 0.00449 / 0.31 ( 42) link_NAG-ASN : angle 1.84320 / 1.32 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 102 time to evaluate : 1.126 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: symmetry clash REVERT: B 200 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8520 (t80) REVERT: B 510 LEU cc_start: 0.9680 (tp) cc_final: 0.9334 (pp) REVERT: B 737 MET cc_start: 0.9082 (ttt) cc_final: 0.8735 (ttt) REVERT: A 737 MET cc_start: 0.9434 (tpp) cc_final: 0.8646 (tpp) REVERT: A 897 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8792 (mtm) REVERT: A 999 GLN cc_start: 0.9162 (tt0) cc_final: 0.8796 (tm-30) REVERT: A 1026 MET cc_start: 0.9368 (mmm) cc_final: 0.9127 (tpt) REVERT: C 694 MET cc_start: 0.8872 (pmm) cc_final: 0.8148 (pmm) REVERT: C 866 MET cc_start: 0.9061 (mtm) cc_final: 0.8813 (mtm) REVERT: H 83 MET cc_start: 0.6483 (mtp) cc_final: 0.6221 (mtp) REVERT: L 16 GLN cc_start: 0.8712 (pp30) cc_final: 0.8467 (pp30) REVERT: L 97 LYS cc_start: 0.9015 (pttt) cc_final: 0.8790 (tmtt) REVERT: E 97 LYS cc_start: 0.9253 (pttt) cc_final: 0.8868 (tmtt) REVERT: F 34 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9169 (tp) REVERT: G 96 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8680 (t0) outliers start: 65 outliers final: 50 residues processed: 152 average time/residue: 0.1763 time to fit residues: 46.0518 Evaluate side-chains 152 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 98 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 35 HIS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 180 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 307 optimal weight: 0.8980 chunk 356 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 364 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.076588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.046643 restraints weight = 168592.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.048310 restraints weight = 74385.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.049333 restraints weight = 45556.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049933 restraints weight = 33580.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.050321 restraints weight = 28010.362| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31575 Z= 0.232 Angle : 0.594 10.261 43080 Z= 0.302 Chirality : 0.043 0.197 4965 Planarity : 0.004 0.048 5465 Dihedral : 4.310 36.785 4163 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 1.90 % Allowed : 10.95 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3822 helix: 1.73 (0.20), residues: 722 sheet: 0.09 (0.15), residues: 1084 loop : -0.46 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 63 TYR 0.016 0.002 TYR A 263 PHE 0.015 0.002 PHE A1086 TRP 0.028 0.001 TRP F 36 HIS 0.005 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (31473) covalent geometry : angle 0.58598 / 0.30 (42822) SS BOND : bond 0.00342 / 0.24 ( 48) SS BOND : angle 0.73228 / 0.52 ( 96) hydrogen bonds : bond 0.03812 / 2.59 ( 1262) hydrogen bonds : angle 5.45761 / 3.85 ( 3612) link_BETA1-4 : bond 0.00131 / 0.08 ( 12) link_BETA1-4 : angle 1.16013 / 0.80 ( 36) link_NAG-ASN : bond 0.00379 / 0.26 ( 42) link_NAG-ASN : angle 1.77085 / 1.28 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 102 time to evaluate : 1.097 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.8262 (p0) cc_final: 0.7965 (p0) REVERT: B 200 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8528 (t80) REVERT: B 737 MET cc_start: 0.9060 (ttt) cc_final: 0.8711 (ttt) REVERT: A 737 MET cc_start: 0.9462 (tpp) cc_final: 0.8692 (tpp) REVERT: A 897 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.8818 (mtm) REVERT: A 999 GLN cc_start: 0.9145 (tt0) cc_final: 0.8803 (tm-30) REVERT: A 1026 MET cc_start: 0.9400 (mmm) cc_final: 0.9154 (tpt) REVERT: C 694 MET cc_start: 0.9111 (pmm) cc_final: 0.8082 (pmm) REVERT: C 866 MET cc_start: 0.9079 (mtm) cc_final: 0.8827 (mtm) REVERT: H 83 MET cc_start: 0.6455 (mtp) cc_final: 0.6235 (mtp) REVERT: L 16 GLN cc_start: 0.8704 (pp30) cc_final: 0.8454 (pp30) REVERT: E 97 LYS cc_start: 0.9420 (pttt) cc_final: 0.9175 (tmtt) REVERT: F 34 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9157 (tp) REVERT: G 96 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8837 (t0) outliers start: 63 outliers final: 51 residues processed: 149 average time/residue: 0.1736 time to fit residues: 44.4585 Evaluate side-chains 152 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 97 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 35 HIS Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 275 optimal weight: 0.7980 chunk 112 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 366 optimal weight: 0.0870 chunk 249 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 201 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN B 318 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN A 610 GLN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.077411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047554 restraints weight = 165732.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.049247 restraints weight = 72468.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.050290 restraints weight = 44005.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050932 restraints weight = 32288.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051277 restraints weight = 26701.870| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31575 Z= 0.127 Angle : 0.532 11.399 43080 Z= 0.270 Chirality : 0.043 0.270 4965 Planarity : 0.003 0.045 5465 Dihedral : 4.070 34.500 4163 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.49 % Rotamer: Outliers : 1.32 % Allowed : 11.67 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3822 helix: 1.99 (0.20), residues: 716 sheet: 0.22 (0.15), residues: 1052 loop : -0.41 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 63 TYR 0.014 0.001 TYR A 262 PHE 0.015 0.001 PHE B 135 TRP 0.042 0.001 TRP F 36 HIS 0.004 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (31473) covalent geometry : angle 0.52575 / 0.27 (42822) SS BOND : bond 0.00209 / 0.14 ( 48) SS BOND : angle 0.59156 / 0.42 ( 96) hydrogen bonds : bond 0.03490 / 2.35 ( 1262) hydrogen bonds : angle 5.20801 / 3.68 ( 3612) link_BETA1-4 : bond 0.00282 / 0.19 ( 12) link_BETA1-4 : angle 0.94601 / 0.65 ( 36) link_NAG-ASN : bond 0.00218 / 0.14 ( 42) link_NAG-ASN : angle 1.55260 / 1.13 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 1.104 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8473 (t80) REVERT: B 737 MET cc_start: 0.8982 (ttt) cc_final: 0.8636 (ttt) REVERT: B 899 MET cc_start: 0.9590 (tpt) cc_final: 0.9312 (tpt) REVERT: A 737 MET cc_start: 0.9512 (tpp) cc_final: 0.8730 (tpp) REVERT: A 897 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8704 (mtm) REVERT: A 999 GLN cc_start: 0.9142 (tt0) cc_final: 0.8940 (tm-30) REVERT: A 1026 MET cc_start: 0.9329 (mmm) cc_final: 0.9085 (tpt) REVERT: C 198 ASP cc_start: 0.8654 (p0) cc_final: 0.8405 (p0) REVERT: C 694 MET cc_start: 0.9091 (pmm) cc_final: 0.8024 (pmm) REVERT: L 16 GLN cc_start: 0.8691 (pp30) cc_final: 0.8447 (pp30) REVERT: E 97 LYS cc_start: 0.9421 (pttt) cc_final: 0.9171 (tmtt) REVERT: G 96 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8814 (t0) outliers start: 44 outliers final: 39 residues processed: 139 average time/residue: 0.1743 time to fit residues: 41.4613 Evaluate side-chains 142 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain F residue 35 HIS Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 239 optimal weight: 1.9990 chunk 343 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 208 optimal weight: 0.9990 chunk 329 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 286 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.077370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.047451 restraints weight = 166981.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049162 restraints weight = 72805.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.050200 restraints weight = 44169.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050836 restraints weight = 32413.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.051196 restraints weight = 26817.525| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.170 31575 Z= 0.155 Angle : 0.655 59.116 43080 Z= 0.358 Chirality : 0.044 0.755 4965 Planarity : 0.003 0.044 5465 Dihedral : 4.066 34.500 4163 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.49 % Rotamer: Outliers : 1.41 % Allowed : 11.67 % Favored : 86.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3822 helix: 1.99 (0.20), residues: 716 sheet: 0.22 (0.15), residues: 1052 loop : -0.41 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 574 TYR 0.014 0.001 TYR A1064 PHE 0.039 0.001 PHE F 27 TRP 0.030 0.001 TRP F 36 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (31473) covalent geometry : angle 0.65014 / 0.36 (42822) SS BOND : bond 0.00177 / 0.11 ( 48) SS BOND : angle 0.57571 / 0.41 ( 96) hydrogen bonds : bond 0.03495 / 2.35 ( 1262) hydrogen bonds : angle 5.21179 / 3.68 ( 3612) link_BETA1-4 : bond 0.00176 / 0.11 ( 12) link_BETA1-4 : angle 0.86659 / 0.59 ( 36) link_NAG-ASN : bond 0.00221 / 0.15 ( 42) link_NAG-ASN : angle 1.55226 / 1.13 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6483.56 seconds wall clock time: 112 minutes 47.74 seconds (6767.74 seconds total)