Starting phenix.real_space_refine on Sun Jul 5 08:41:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ws4_32743/07_2026/7ws4_32743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws4_32743/07_2026/7ws4_32743.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/7ws4_32743/07_2026/7ws4_32743.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ws4_32743/07_2026/7ws4_32743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ws4_32743/07_2026/7ws4_32743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws4_32743/07_2026/7ws4_32743.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws4_32743/07_2026/7ws4_32743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws4_32743/07_2026/7ws4_32743.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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 16958 2.51 5 N 4371 2.21 5 O 5119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s 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: 26566 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8081 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8092 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8088 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "L" 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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.80, per 1000 atoms: 0.18 Number of scatterers: 26566 At special positions: 0 Unit cell: (138.944, 137.28, 211.328, 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 118 16.00 O 5119 8.00 N 4371 7.00 C 16958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG D 1 " - " ASN C 801 " " NAG E 1 " - " ASN C1074 " " NAG F 1 " - " ASN C1098 " " NAG G 1 " - " ASN C1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 801 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 957.7 milliseconds 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 51 sheets defined 23.9% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.602A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.240A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.735A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.038A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.138A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.145A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.553A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.566A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.506A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.076A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.963A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.536A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.536A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.627A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.041A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.187A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.504A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.587A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.012A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.117A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.898A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.616A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.103A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.137A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.566A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.051A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.409A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.933A pdb=" N ASP I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.144A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.276A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.999A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.769A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.107A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.799A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.602A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.960A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.623A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.778A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.427A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.674A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.778A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.457A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.374A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.875A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.972A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.721A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 13.102A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.620A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.584A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.656A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.029A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.636A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.557A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.948A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.776A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.032A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 135 through 141 removed outlier: 8.043A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 12.109A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.419A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.219A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.424A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.167A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.573A pdb=" N LEU H 105 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA H 84 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.830A pdb=" N THR I 69 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AF6, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.678A pdb=" N ASP I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY I 50 " --> pdb=" O ASP I 59 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR I 94 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR I 117 " --> pdb=" O TYR I 94 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 2937 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.28 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8377 1.34 - 1.46: 6218 1.46 - 1.58: 12435 1.58 - 1.70: 0 1.70 - 1.83: 148 Bond restraints: 27178 Sorted by residual: bond pdb=" N VAL B 534 " pdb=" CA VAL B 534 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.12e-02 7.97e+03 1.02e+01 bond pdb=" N VAL B 595 " pdb=" CA VAL B 595 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.27e+00 bond pdb=" C ALA B 264 " pdb=" N TYR B 265 " ideal model delta sigma weight residual 1.331 1.289 0.042 1.43e-02 4.89e+03 8.68e+00 bond pdb=" N VAL B 320 " pdb=" CA VAL B 320 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.29e-02 6.01e+03 8.23e+00 bond pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.65e+00 ... (remaining 27173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 35712 1.52 - 3.03: 1059 3.03 - 4.55: 167 4.55 - 6.06: 33 6.06 - 7.58: 3 Bond angle restraints: 36974 Sorted by residual: angle pdb=" CA ASN B 532 " pdb=" C ASN B 532 " pdb=" O ASN B 532 " ideal model delta sigma weight residual 121.55 117.81 3.74 1.06e+00 8.90e-01 1.25e+01 angle pdb=" CA LYS B 537 " pdb=" C LYS B 537 " pdb=" O LYS B 537 " ideal model delta sigma weight residual 121.38 117.67 3.71 1.06e+00 8.90e-01 1.23e+01 angle pdb=" CA CYS B 538 " pdb=" C CYS B 538 " pdb=" O CYS B 538 " ideal model delta sigma weight residual 122.41 118.22 4.19 1.21e+00 6.83e-01 1.20e+01 angle pdb=" C TYR B 265 " pdb=" N TYR B 266 " pdb=" CA TYR B 266 " ideal model delta sigma weight residual 122.94 128.07 -5.13 1.50e+00 4.44e-01 1.17e+01 angle pdb=" N THR C 19 " pdb=" CA THR C 19 " pdb=" C THR C 19 " ideal model delta sigma weight residual 113.89 108.56 5.33 1.58e+00 4.01e-01 1.14e+01 ... (remaining 36969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 14546 17.88 - 35.77: 1122 35.77 - 53.65: 172 53.65 - 71.53: 44 71.53 - 89.42: 33 Dihedral angle restraints: 15917 sinusoidal: 6229 harmonic: 9688 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 0.86 -86.86 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 177.59 -84.59 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.11 -60.89 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 15914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3988 0.094 - 0.188: 296 0.188 - 0.281: 5 0.281 - 0.375: 0 0.375 - 0.469: 1 Chirality restraints: 4290 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CG LEU H 33 " pdb=" CB LEU H 33 " pdb=" CD1 LEU H 33 " pdb=" CD2 LEU H 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4287 not shown) Planarity restraints: 4754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO C 987 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.019 2.00e-02 2.50e+03 1.81e-02 4.10e+00 pdb=" CG ASN C 709 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO C 986 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.028 5.00e-02 4.00e+02 ... (remaining 4751 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 483 2.67 - 3.23: 24936 3.23 - 3.78: 40318 3.78 - 4.34: 53877 4.34 - 4.90: 89970 Nonbonded interactions: 209584 Sorted by model distance: nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS C 378 " pdb=" OH TYR C 380 " model vdw 2.222 3.120 nonbonded pdb=" O THR C 747 " pdb=" OG SER C 750 " model vdw 2.224 3.040 ... (remaining 209579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 318 or (resid 319 and (name N or n \ ame CA or name C or name O or name CB )) or resid 320 through 1303)) selection = (chain 'B' and (resid 14 through 500 or (resid 501 and (name N or name CA or nam \ e C or name O or name CB )) or resid 502 through 518 or (resid 519 through 520 a \ nd (name N or name CA or name C or name O or name CB )) or resid 521 through 527 \ or (resid 528 through 529 and (name N or name CA or name C or name O or name CB \ )) or resid 530 through 1303)) selection = (chain 'C' and (resid 14 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 318 or (resid 319 and (name N or n \ ame CA or name C or name O or name CB )) or resid 320 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or resid 502 through 13 \ 03)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 8.780 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.140 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 0.069 27259 Z= 0.211 Angle : 0.633 12.710 37172 Z= 0.346 Chirality : 0.047 0.469 4290 Planarity : 0.004 0.053 4730 Dihedral : 13.410 89.415 9551 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3269 helix: 1.91 (0.21), residues: 658 sheet: 0.43 (0.18), residues: 759 loop : -0.80 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 19 TYR 0.033 0.001 TYR A 453 PHE 0.026 0.001 PHE A 906 TRP 0.023 0.001 TRP I 47 HIS 0.003 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.21 (27178) covalent geometry : angle 0.61900 / 0.34 (36974) SS BOND : bond 0.00330 / 0.19 ( 42) SS BOND : angle 1.22849 / 0.74 ( 84) hydrogen bonds : bond 0.12069 / 8.04 ( 1067) hydrogen bonds : angle 6.62521 / 4.60 ( 2937) Misc. bond : bond 0.06899 / 3.63 ( 1) link_BETA1-4 : bond 0.00356 / 0.22 ( 14) link_BETA1-4 : angle 0.84190 / 0.61 ( 42) link_NAG-ASN : bond 0.00370 / 0.21 ( 24) link_NAG-ASN : angle 2.84576 / 2.05 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8293 (m-80) cc_final: 0.7884 (m-80) REVERT: A 515 PHE cc_start: 0.7253 (m-80) cc_final: 0.6793 (m-80) REVERT: B 436 TRP cc_start: 0.7364 (p90) cc_final: 0.6827 (p90) REVERT: C 53 ASP cc_start: 0.7938 (t70) cc_final: 0.7561 (t70) REVERT: C 780 GLU cc_start: 0.8246 (tt0) cc_final: 0.8042 (tt0) REVERT: H 87 TYR cc_start: 0.7462 (m-10) cc_final: 0.7169 (m-10) REVERT: I 74 ASN cc_start: 0.8272 (m-40) cc_final: 0.7558 (m-40) REVERT: I 80 TYR cc_start: 0.7961 (m-80) cc_final: 0.7695 (m-80) REVERT: I 119 VAL cc_start: 0.6722 (m) cc_final: 0.5938 (m) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1496 time to fit residues: 40.0349 Evaluate side-chains 120 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 417 ASN B 804 GLN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 474 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058758 restraints weight = 81715.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.060922 restraints weight = 40480.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062329 restraints weight = 26796.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063225 restraints weight = 20834.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063704 restraints weight = 17893.146| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27259 Z= 0.122 Angle : 0.547 11.101 37172 Z= 0.278 Chirality : 0.044 0.429 4290 Planarity : 0.004 0.049 4730 Dihedral : 4.019 21.483 3568 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.28 % Allowed : 5.20 % Favored : 94.53 % 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 (0.15), residues: 3269 helix: 2.14 (0.21), residues: 662 sheet: 0.44 (0.17), residues: 788 loop : -0.78 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 493 TYR 0.020 0.001 TYR A 453 PHE 0.017 0.001 PHE I 29 TRP 0.009 0.001 TRP I 36 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (27178) covalent geometry : angle 0.53488 / 0.28 (36974) SS BOND : bond 0.00321 / 0.20 ( 42) SS BOND : angle 1.10068 / 0.72 ( 84) hydrogen bonds : bond 0.04441 / 2.93 ( 1067) hydrogen bonds : angle 5.35401 / 3.77 ( 2937) Misc. bond : bond 0.00079 / 0.04 ( 1) link_BETA1-4 : bond 0.00355 / 0.21 ( 14) link_BETA1-4 : angle 0.86607 / 0.63 ( 42) link_NAG-ASN : bond 0.00272 / 0.15 ( 24) link_NAG-ASN : angle 2.34074 / 1.67 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8271 (m-80) cc_final: 0.8041 (m-80) REVERT: A 455 LEU cc_start: 0.5193 (mm) cc_final: 0.4977 (mm) REVERT: A 571 ASP cc_start: 0.8251 (t0) cc_final: 0.7837 (t0) REVERT: B 342 PHE cc_start: 0.8699 (m-10) cc_final: 0.7940 (m-10) REVERT: B 436 TRP cc_start: 0.7485 (p90) cc_final: 0.7095 (p90) REVERT: B 1005 GLN cc_start: 0.8820 (tp40) cc_final: 0.8411 (tm-30) REVERT: C 53 ASP cc_start: 0.7945 (t70) cc_final: 0.7677 (t70) REVERT: C 525 CYS cc_start: 0.7692 (t) cc_final: 0.7357 (p) REVERT: C 740 MET cc_start: 0.9124 (tpt) cc_final: 0.8852 (tpp) REVERT: C 780 GLU cc_start: 0.8217 (tt0) cc_final: 0.8013 (tt0) REVERT: H 24 ARG cc_start: 0.8462 (mmm160) cc_final: 0.8262 (mmm160) REVERT: H 95 PRO cc_start: 0.6136 (Cg_exo) cc_final: 0.5811 (Cg_endo) REVERT: I 119 VAL cc_start: 0.5445 (OUTLIER) cc_final: 0.4980 (t) outliers start: 8 outliers final: 3 residues processed: 140 average time/residue: 0.1810 time to fit residues: 41.7290 Evaluate side-chains 119 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain I residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 110 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 300 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 247 optimal weight: 0.0980 chunk 318 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 935 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.091643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.058830 restraints weight = 81810.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061020 restraints weight = 40682.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.062457 restraints weight = 26943.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063299 restraints weight = 20907.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063873 restraints weight = 17984.558| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27259 Z= 0.108 Angle : 0.519 10.880 37172 Z= 0.262 Chirality : 0.044 0.409 4290 Planarity : 0.004 0.050 4730 Dihedral : 3.912 20.039 3568 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.58 % Allowed : 7.02 % Favored : 92.40 % 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: 0.26 (0.15), residues: 3269 helix: 2.18 (0.21), residues: 665 sheet: 0.50 (0.18), residues: 773 loop : -0.76 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.025 0.001 TYR H 49 PHE 0.020 0.001 PHE B 168 TRP 0.013 0.001 TRP H 35 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (27178) covalent geometry : angle 0.50789 / 0.26 (36974) SS BOND : bond 0.00259 / 0.16 ( 42) SS BOND : angle 1.03022 / 0.68 ( 84) hydrogen bonds : bond 0.04077 / 2.69 ( 1067) hydrogen bonds : angle 5.09356 / 3.60 ( 2937) Misc. bond : bond 0.00070 / 0.04 ( 1) link_BETA1-4 : bond 0.00332 / 0.20 ( 14) link_BETA1-4 : angle 0.82920 / 0.58 ( 42) link_NAG-ASN : bond 0.00267 / 0.15 ( 24) link_NAG-ASN : angle 2.22116 / 1.59 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7562 (m-10) cc_final: 0.7272 (m-80) REVERT: A 571 ASP cc_start: 0.8246 (t0) cc_final: 0.7816 (t0) REVERT: B 436 TRP cc_start: 0.7554 (p90) cc_final: 0.7108 (p90) REVERT: C 53 ASP cc_start: 0.8007 (t70) cc_final: 0.7724 (t70) REVERT: C 780 GLU cc_start: 0.8212 (tt0) cc_final: 0.7994 (tt0) REVERT: H 24 ARG cc_start: 0.8548 (mmm160) cc_final: 0.8212 (mmm160) REVERT: H 95 PRO cc_start: 0.6291 (Cg_exo) cc_final: 0.5976 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7843 (m-80) cc_final: 0.7308 (m-80) REVERT: H 104 LYS cc_start: 0.8585 (tptt) cc_final: 0.8358 (tppt) REVERT: H 106 GLU cc_start: 0.7877 (pm20) cc_final: 0.7595 (pm20) REVERT: I 104 ILE cc_start: 0.7636 (pt) cc_final: 0.6792 (mt) outliers start: 17 outliers final: 7 residues processed: 148 average time/residue: 0.1759 time to fit residues: 42.8306 Evaluate side-chains 129 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 200 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 326 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.092808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.061071 restraints weight = 81127.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063197 restraints weight = 41758.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.064594 restraints weight = 28093.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.065417 restraints weight = 22054.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065991 restraints weight = 19052.845| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27259 Z= 0.170 Angle : 0.541 10.347 37172 Z= 0.275 Chirality : 0.044 0.401 4290 Planarity : 0.004 0.050 4730 Dihedral : 3.984 19.168 3568 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.79 % Allowed : 8.91 % Favored : 90.30 % 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 (0.14), residues: 3269 helix: 2.07 (0.21), residues: 674 sheet: 0.34 (0.18), residues: 753 loop : -0.77 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 38 TYR 0.025 0.001 TYR B 265 PHE 0.017 0.001 PHE B 168 TRP 0.021 0.001 TRP H 35 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (27178) covalent geometry : angle 0.52949 / 0.27 (36974) SS BOND : bond 0.00303 / 0.19 ( 42) SS BOND : angle 1.17410 / 0.81 ( 84) hydrogen bonds : bond 0.04387 / 2.90 ( 1067) hydrogen bonds : angle 5.05625 / 3.58 ( 2937) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00258 / 0.17 ( 14) link_BETA1-4 : angle 0.89317 / 0.63 ( 42) link_NAG-ASN : bond 0.00337 / 0.19 ( 24) link_NAG-ASN : angle 2.26832 / 1.60 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6520 (m-10) REVERT: A 571 ASP cc_start: 0.8151 (t0) cc_final: 0.7722 (t0) REVERT: B 168 PHE cc_start: 0.7812 (t80) cc_final: 0.7381 (t80) REVERT: B 436 TRP cc_start: 0.7621 (p90) cc_final: 0.7336 (p90) REVERT: C 979 ASP cc_start: 0.8455 (m-30) cc_final: 0.8225 (t70) REVERT: H 24 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8296 (mmm160) REVERT: H 45 LYS cc_start: 0.8304 (tptm) cc_final: 0.8100 (mmmt) REVERT: H 95 PRO cc_start: 0.6537 (Cg_exo) cc_final: 0.6233 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7938 (m-80) cc_final: 0.7422 (m-80) REVERT: H 104 LYS cc_start: 0.8564 (tptt) cc_final: 0.8320 (tppt) REVERT: H 106 GLU cc_start: 0.7893 (pm20) cc_final: 0.7601 (pm20) REVERT: I 82 GLN cc_start: 0.8595 (tt0) cc_final: 0.8301 (tp40) REVERT: I 87 ARG cc_start: 0.8757 (mpp80) cc_final: 0.8517 (mpp80) REVERT: I 104 ILE cc_start: 0.7752 (pt) cc_final: 0.6949 (mt) outliers start: 23 outliers final: 16 residues processed: 153 average time/residue: 0.1609 time to fit residues: 40.5641 Evaluate side-chains 143 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 84 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 229 optimal weight: 0.9990 chunk 158 optimal weight: 0.0070 chunk 75 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.093190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.061614 restraints weight = 81240.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063773 restraints weight = 41670.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.065177 restraints weight = 27915.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066043 restraints weight = 21885.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066525 restraints weight = 18829.606| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27259 Z= 0.130 Angle : 0.522 10.337 37172 Z= 0.264 Chirality : 0.044 0.388 4290 Planarity : 0.004 0.053 4730 Dihedral : 3.921 17.705 3568 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.83 % Allowed : 10.36 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3269 helix: 2.15 (0.21), residues: 671 sheet: 0.39 (0.18), residues: 786 loop : -0.75 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 493 TYR 0.021 0.001 TYR A1067 PHE 0.027 0.001 PHE H 71 TRP 0.013 0.001 TRP H 35 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (27178) covalent geometry : angle 0.51174 / 0.26 (36974) SS BOND : bond 0.00256 / 0.16 ( 42) SS BOND : angle 1.07449 / 0.72 ( 84) hydrogen bonds : bond 0.04152 / 2.75 ( 1067) hydrogen bonds : angle 4.95552 / 3.52 ( 2937) Misc. bond : bond 0.00009 / 0.00 ( 1) link_BETA1-4 : bond 0.00302 / 0.19 ( 14) link_BETA1-4 : angle 0.83900 / 0.60 ( 42) link_NAG-ASN : bond 0.00273 / 0.15 ( 24) link_NAG-ASN : angle 2.15833 / 1.53 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6519 (m-10) REVERT: A 571 ASP cc_start: 0.8160 (t0) cc_final: 0.7733 (t0) REVERT: B 168 PHE cc_start: 0.7856 (t80) cc_final: 0.7470 (t80) REVERT: B 436 TRP cc_start: 0.7594 (p90) cc_final: 0.7384 (p90) REVERT: C 979 ASP cc_start: 0.8472 (m-30) cc_final: 0.8250 (t70) REVERT: H 24 ARG cc_start: 0.8648 (mmm160) cc_final: 0.8328 (mmm160) REVERT: H 88 CYS cc_start: 0.5523 (m) cc_final: 0.4889 (m) REVERT: H 95 PRO cc_start: 0.6542 (Cg_exo) cc_final: 0.6230 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7981 (m-80) cc_final: 0.7406 (m-80) REVERT: H 104 LYS cc_start: 0.8546 (tptt) cc_final: 0.8331 (tppt) REVERT: H 106 GLU cc_start: 0.7882 (pm20) cc_final: 0.7654 (pm20) REVERT: I 82 GLN cc_start: 0.8558 (tt0) cc_final: 0.8276 (tp40) REVERT: I 87 ARG cc_start: 0.8771 (mpp80) cc_final: 0.8546 (mpp80) REVERT: I 104 ILE cc_start: 0.7768 (pt) cc_final: 0.6961 (mt) outliers start: 24 outliers final: 16 residues processed: 157 average time/residue: 0.1726 time to fit residues: 45.3081 Evaluate side-chains 145 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 84 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 129 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 965 GLN A1083 HIS B 239 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 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 = 0.3767 r_free = 0.3767 target = 0.093515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.061985 restraints weight = 80851.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.064108 restraints weight = 42387.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065496 restraints weight = 28722.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.066304 restraints weight = 22592.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066877 restraints weight = 19603.495| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27259 Z= 0.195 Angle : 0.566 11.982 37172 Z= 0.287 Chirality : 0.044 0.377 4290 Planarity : 0.004 0.053 4730 Dihedral : 4.030 18.641 3568 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.96 % Allowed : 11.25 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3269 helix: 2.03 (0.21), residues: 670 sheet: 0.29 (0.18), residues: 747 loop : -0.78 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 61 TYR 0.026 0.001 TYR B 265 PHE 0.016 0.001 PHE H 71 TRP 0.012 0.001 TRP I 47 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (27178) covalent geometry : angle 0.55525 / 0.28 (36974) SS BOND : bond 0.00339 / 0.21 ( 42) SS BOND : angle 1.23256 / 0.83 ( 84) hydrogen bonds : bond 0.04523 / 2.99 ( 1067) hydrogen bonds : angle 5.02494 / 3.56 ( 2937) Misc. bond : bond 0.00007 / 0.00 ( 1) link_BETA1-4 : bond 0.00246 / 0.16 ( 14) link_BETA1-4 : angle 0.90665 / 0.64 ( 42) link_NAG-ASN : bond 0.00374 / 0.22 ( 24) link_NAG-ASN : angle 2.25138 / 1.58 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6659 (m-10) REVERT: A 571 ASP cc_start: 0.8142 (t0) cc_final: 0.7700 (t0) REVERT: A 1083 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7461 (t-90) REVERT: B 436 TRP cc_start: 0.7638 (p90) cc_final: 0.7150 (p90) REVERT: C 988 GLU cc_start: 0.8232 (pm20) cc_final: 0.7963 (pm20) REVERT: H 24 ARG cc_start: 0.8607 (mmm160) cc_final: 0.8325 (mmm160) REVERT: H 95 PRO cc_start: 0.6521 (Cg_exo) cc_final: 0.6208 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7924 (m-80) cc_final: 0.7339 (m-80) REVERT: H 104 LYS cc_start: 0.8498 (tptt) cc_final: 0.8288 (tppt) REVERT: H 106 GLU cc_start: 0.7909 (pm20) cc_final: 0.7705 (pm20) REVERT: I 82 GLN cc_start: 0.8561 (tt0) cc_final: 0.8275 (tp40) REVERT: I 87 ARG cc_start: 0.8801 (mpp80) cc_final: 0.8570 (mpp80) REVERT: I 104 ILE cc_start: 0.7878 (pt) cc_final: 0.7044 (mt) outliers start: 28 outliers final: 20 residues processed: 154 average time/residue: 0.1747 time to fit residues: 44.3568 Evaluate side-chains 144 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 84 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 74 optimal weight: 0.0970 chunk 296 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1083 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.093581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.062355 restraints weight = 80996.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.064510 restraints weight = 42075.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065934 restraints weight = 28363.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066762 restraints weight = 22202.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067322 restraints weight = 19160.540| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27259 Z= 0.147 Angle : 0.542 12.754 37172 Z= 0.273 Chirality : 0.044 0.373 4290 Planarity : 0.004 0.054 4730 Dihedral : 3.978 18.288 3568 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.10 % Allowed : 11.67 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3269 helix: 2.18 (0.21), residues: 664 sheet: 0.37 (0.18), residues: 779 loop : -0.74 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 38 TYR 0.021 0.001 TYR B 265 PHE 0.014 0.001 PHE C 562 TRP 0.014 0.001 TRP H 35 HIS 0.009 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (27178) covalent geometry : angle 0.53102 / 0.27 (36974) SS BOND : bond 0.00280 / 0.18 ( 42) SS BOND : angle 1.13593 / 0.75 ( 84) hydrogen bonds : bond 0.04319 / 2.86 ( 1067) hydrogen bonds : angle 4.95620 / 3.52 ( 2937) Misc. bond : bond 0.00016 / 0.01 ( 1) link_BETA1-4 : bond 0.00279 / 0.18 ( 14) link_BETA1-4 : angle 0.85804 / 0.61 ( 42) link_NAG-ASN : bond 0.00305 / 0.18 ( 24) link_NAG-ASN : angle 2.17252 / 1.53 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6665 (m-10) REVERT: A 571 ASP cc_start: 0.8143 (t0) cc_final: 0.7696 (t0) REVERT: B 168 PHE cc_start: 0.8011 (t80) cc_final: 0.7766 (t80) REVERT: B 1005 GLN cc_start: 0.8801 (tp40) cc_final: 0.8478 (tm-30) REVERT: C 478 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7354 (pptt) REVERT: C 988 GLU cc_start: 0.8190 (pm20) cc_final: 0.7873 (pm20) REVERT: H 24 ARG cc_start: 0.8712 (mmm160) cc_final: 0.8487 (mmm160) REVERT: H 95 PRO cc_start: 0.6586 (Cg_exo) cc_final: 0.6270 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7922 (m-80) cc_final: 0.7338 (m-80) REVERT: H 104 LYS cc_start: 0.8497 (tptt) cc_final: 0.8287 (tppt) REVERT: H 106 GLU cc_start: 0.7913 (pm20) cc_final: 0.7711 (pm20) REVERT: I 87 ARG cc_start: 0.8811 (mpp80) cc_final: 0.8575 (mpp80) REVERT: I 104 ILE cc_start: 0.7843 (pt) cc_final: 0.7027 (mt) outliers start: 32 outliers final: 21 residues processed: 159 average time/residue: 0.1638 time to fit residues: 42.9685 Evaluate side-chains 148 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 185 optimal weight: 8.9990 chunk 324 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN B 121 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.092099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.061195 restraints weight = 83358.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063466 restraints weight = 41621.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.064984 restraints weight = 27338.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065909 restraints weight = 21195.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066440 restraints weight = 18126.202| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 27259 Z= 0.257 Angle : 0.636 11.863 37172 Z= 0.321 Chirality : 0.046 0.359 4290 Planarity : 0.004 0.052 4730 Dihedral : 4.270 20.628 3568 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.10 % Allowed : 12.35 % Favored : 86.55 % 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: -0.03 (0.15), residues: 3269 helix: 1.97 (0.21), residues: 669 sheet: 0.09 (0.18), residues: 755 loop : -0.82 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 19 TYR 0.029 0.001 TYR B 265 PHE 0.030 0.002 PHE I 29 TRP 0.027 0.002 TRP H 35 HIS 0.008 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 (27178) covalent geometry : angle 0.62414 / 0.32 (36974) SS BOND : bond 0.00364 / 0.25 ( 42) SS BOND : angle 1.58908 / 1.00 ( 84) hydrogen bonds : bond 0.05027 / 3.32 ( 1067) hydrogen bonds : angle 5.17564 / 3.67 ( 2937) Misc. bond : bond 0.00003 / 0.00 ( 1) link_BETA1-4 : bond 0.00216 / 0.14 ( 14) link_BETA1-4 : angle 0.96111 / 0.68 ( 42) link_NAG-ASN : bond 0.00493 / 0.30 ( 24) link_NAG-ASN : angle 2.36612 / 1.65 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6798 (m-10) REVERT: C 478 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7386 (pptt) REVERT: C 988 GLU cc_start: 0.8223 (pm20) cc_final: 0.7979 (pm20) REVERT: H 24 ARG cc_start: 0.8698 (mmm160) cc_final: 0.8381 (mmm160) REVERT: H 46 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7588 (tp) REVERT: H 55 GLN cc_start: 0.8166 (tp40) cc_final: 0.7942 (tp-100) REVERT: H 95 PRO cc_start: 0.6787 (Cg_exo) cc_final: 0.6474 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7975 (m-80) cc_final: 0.7272 (m-80) REVERT: H 104 LYS cc_start: 0.8458 (tptt) cc_final: 0.8234 (tppt) REVERT: H 106 GLU cc_start: 0.7873 (pm20) cc_final: 0.7672 (pm20) REVERT: I 87 ARG cc_start: 0.8802 (mpp80) cc_final: 0.8542 (mpp80) REVERT: I 99 ASP cc_start: 0.8931 (t0) cc_final: 0.8712 (t0) REVERT: I 104 ILE cc_start: 0.7943 (pt) cc_final: 0.7137 (mt) outliers start: 32 outliers final: 23 residues processed: 153 average time/residue: 0.1590 time to fit residues: 40.4141 Evaluate side-chains 147 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 171 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 295 optimal weight: 0.5980 chunk 226 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.092964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.062624 restraints weight = 82897.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066080 restraints weight = 42909.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066387 restraints weight = 23525.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066890 restraints weight = 20499.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.067018 restraints weight = 19638.966| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27259 Z= 0.172 Angle : 0.585 11.475 37172 Z= 0.294 Chirality : 0.045 0.358 4290 Planarity : 0.004 0.054 4730 Dihedral : 4.223 28.479 3568 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.00 % Allowed : 12.42 % Favored : 86.58 % 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: 0.11 (0.15), residues: 3269 helix: 2.12 (0.21), residues: 663 sheet: 0.30 (0.18), residues: 765 loop : -0.81 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 19 TYR 0.022 0.001 TYR B 265 PHE 0.029 0.001 PHE I 29 TRP 0.032 0.002 TRP B 436 HIS 0.007 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (27178) covalent geometry : angle 0.57136 / 0.29 (36974) SS BOND : bond 0.00307 / 0.20 ( 42) SS BOND : angle 1.81569 / 1.10 ( 84) hydrogen bonds : bond 0.04550 / 3.02 ( 1067) hydrogen bonds : angle 5.05022 / 3.58 ( 2937) Misc. bond : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : bond 0.00298 / 0.18 ( 14) link_BETA1-4 : angle 0.86387 / 0.62 ( 42) link_NAG-ASN : bond 0.00349 / 0.21 ( 24) link_NAG-ASN : angle 2.22220 / 1.56 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6836 (m-10) REVERT: A 571 ASP cc_start: 0.8109 (t0) cc_final: 0.7630 (t0) REVERT: C 478 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7166 (pptt) REVERT: C 988 GLU cc_start: 0.8350 (pm20) cc_final: 0.7963 (pm20) REVERT: H 24 ARG cc_start: 0.8753 (mmm160) cc_final: 0.8448 (mmm160) REVERT: H 95 PRO cc_start: 0.6572 (Cg_exo) cc_final: 0.6249 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7957 (m-80) cc_final: 0.7261 (m-80) REVERT: H 104 LYS cc_start: 0.8418 (tptt) cc_final: 0.8210 (tppt) REVERT: I 74 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8135 (t0) REVERT: I 87 ARG cc_start: 0.8848 (mpp80) cc_final: 0.8574 (mpp80) REVERT: I 99 ASP cc_start: 0.8926 (t0) cc_final: 0.8633 (t0) REVERT: I 104 ILE cc_start: 0.7867 (pt) cc_final: 0.7065 (mt) outliers start: 29 outliers final: 19 residues processed: 152 average time/residue: 0.1736 time to fit residues: 43.0735 Evaluate side-chains 146 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 282 optimal weight: 0.7980 chunk 243 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 325 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 279 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.093864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063682 restraints weight = 82435.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067131 restraints weight = 41981.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067488 restraints weight = 23244.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068679 restraints weight = 19809.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068457 restraints weight = 18397.593| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27259 Z= 0.126 Angle : 0.575 17.242 37172 Z= 0.287 Chirality : 0.044 0.359 4290 Planarity : 0.004 0.055 4730 Dihedral : 4.145 26.377 3568 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.89 % Allowed : 12.84 % Favored : 86.27 % 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 (0.15), residues: 3269 helix: 2.24 (0.21), residues: 657 sheet: 0.35 (0.18), residues: 775 loop : -0.75 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 61 TYR 0.021 0.001 TYR A1067 PHE 0.029 0.001 PHE I 29 TRP 0.038 0.002 TRP H 35 HIS 0.007 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (27178) covalent geometry : angle 0.56285 / 0.28 (36974) SS BOND : bond 0.00275 / 0.17 ( 42) SS BOND : angle 1.62942 / 0.98 ( 84) hydrogen bonds : bond 0.04274 / 2.84 ( 1067) hydrogen bonds : angle 4.96370 / 3.52 ( 2937) Misc. bond : bond 0.00020 / 0.01 ( 1) link_BETA1-4 : bond 0.00304 / 0.19 ( 14) link_BETA1-4 : angle 0.83995 / 0.60 ( 42) link_NAG-ASN : bond 0.00289 / 0.16 ( 24) link_NAG-ASN : angle 2.12167 / 1.49 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6837 (m-10) REVERT: A 571 ASP cc_start: 0.8086 (t0) cc_final: 0.7621 (t0) REVERT: C 478 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7325 (pptt) REVERT: C 988 GLU cc_start: 0.8274 (pm20) cc_final: 0.7955 (pm20) REVERT: H 24 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8470 (mmm160) REVERT: H 89 GLN cc_start: 0.7312 (tm-30) cc_final: 0.7024 (tm-30) REVERT: H 95 PRO cc_start: 0.6579 (Cg_exo) cc_final: 0.6254 (Cg_endo) REVERT: H 97 TYR cc_start: 0.8013 (m-80) cc_final: 0.7278 (m-80) REVERT: H 106 GLU cc_start: 0.8231 (pm20) cc_final: 0.7927 (pm20) REVERT: I 74 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8176 (t0) REVERT: I 87 ARG cc_start: 0.8825 (mpp80) cc_final: 0.8559 (mpp80) REVERT: I 99 ASP cc_start: 0.8915 (t0) cc_final: 0.8605 (t0) REVERT: I 104 ILE cc_start: 0.7796 (pt) cc_final: 0.7033 (mt) outliers start: 26 outliers final: 19 residues processed: 149 average time/residue: 0.1624 time to fit residues: 39.6781 Evaluate side-chains 146 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 316 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 324 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.093794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.063689 restraints weight = 82130.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067159 restraints weight = 42605.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067403 restraints weight = 24073.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.067895 restraints weight = 20345.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068067 restraints weight = 19439.113| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27259 Z= 0.141 Angle : 0.575 16.917 37172 Z= 0.288 Chirality : 0.044 0.354 4290 Planarity : 0.004 0.055 4730 Dihedral : 4.081 24.041 3568 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.79 % Allowed : 13.25 % Favored : 85.96 % 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 (0.15), residues: 3269 helix: 2.23 (0.21), residues: 657 sheet: 0.35 (0.18), residues: 779 loop : -0.75 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 493 TYR 0.027 0.001 TYR C 904 PHE 0.029 0.001 PHE I 29 TRP 0.036 0.001 TRP H 35 HIS 0.008 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (27178) covalent geometry : angle 0.56358 / 0.28 (36974) SS BOND : bond 0.00279 / 0.17 ( 42) SS BOND : angle 1.57597 / 0.94 ( 84) hydrogen bonds : bond 0.04232 / 2.81 ( 1067) hydrogen bonds : angle 4.93279 / 3.50 ( 2937) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : bond 0.00291 / 0.18 ( 14) link_BETA1-4 : angle 0.83701 / 0.59 ( 42) link_NAG-ASN : bond 0.00299 / 0.17 ( 24) link_NAG-ASN : angle 2.10166 / 1.48 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4815.10 seconds wall clock time: 99 minutes 53.76 seconds (5993.76 seconds total)