Starting phenix.real_space_refine on Sat Mar 7 06:45:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yc5_33734/03_2026/7yc5_33734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yc5_33734/03_2026/7yc5_33734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yc5_33734/03_2026/7yc5_33734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yc5_33734/03_2026/7yc5_33734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yc5_33734/03_2026/7yc5_33734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yc5_33734/03_2026/7yc5_33734.map" } resolution = 3.1 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= 0.002 sd= 0.202 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 159 5.16 5 C 24808 2.51 5 N 6494 2.21 5 O 7696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39157 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8094 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Chain: "B" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8094 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Chain: "C" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8094 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Chain: "D" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3313 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 2 Chain: "E" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3313 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 2 Chain: "F" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3313 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 2 Chain: "G" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1496 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1496 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1496 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 9.48, per 1000 atoms: 0.24 Number of scatterers: 39157 At special positions: 0 Unit cell: (137.899, 144.208, 248.759, 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 159 16.00 O 7696 8.00 N 6494 7.00 C 24808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.02 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=2.02 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=2.03 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 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.02 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 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 350 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 458 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 158 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 283 " - pdb=" SG CYS E 350 " distance=2.03 Simple disulfide: pdb=" SG CYS E 398 " - pdb=" SG CYS E 458 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 158 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 283 " - pdb=" SG CYS F 350 " distance=2.03 Simple disulfide: pdb=" SG CYS F 398 " - pdb=" SG CYS F 458 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 165 " " NAG C1403 " - " ASN C 282 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 709 " " NAG C1406 " - " ASN C 801 " " NAG C1407 " - " ASN C1074 " " NAG C1408 " - " ASN C1098 " " NAG C1409 " - " ASN C1134 " Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 2.4 seconds 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9294 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 110 sheets defined 17.7% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.042A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.658A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.680A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.065A 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 919 removed outlier: 4.200A 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: 3.862A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.261A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1148 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.041A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.661A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.775A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.504A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.151A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.204A 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 964 removed outlier: 3.875A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.273A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1148 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.040A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.660A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 removed outlier: 3.538A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.226A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.598A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.265A 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 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.514A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 Processing helix chain 'C' and resid 1141 through 1148 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.553A pdb=" N ASP D 90 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.525A pdb=" N ASP D 219 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 220 " --> pdb=" O SER D 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 220' Processing helix chain 'D' and resid 385 through 392 removed outlier: 3.617A pdb=" N LEU D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 452 removed outlier: 4.223A pdb=" N GLU D 451 " --> pdb=" O LYS D 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.555A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.525A pdb=" N ASP E 219 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E 220 " --> pdb=" O SER E 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 220' Processing helix chain 'E' and resid 385 through 392 removed outlier: 3.615A pdb=" N LEU E 389 " --> pdb=" O SER E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 452 removed outlier: 4.222A pdb=" N GLU E 451 " --> pdb=" O LYS E 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.554A pdb=" N ASP F 90 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'F' and resid 216 through 220 removed outlier: 3.526A pdb=" N ASP F 219 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 220 " --> pdb=" O SER F 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 216 through 220' Processing helix chain 'F' and resid 385 through 392 removed outlier: 3.616A pdb=" N LEU F 389 " --> pdb=" O SER F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 452 removed outlier: 4.222A pdb=" N GLU F 451 " --> pdb=" O LYS F 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.680A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 170 through 172 No H-bonds generated for 'chain 'G' and resid 170 through 172' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.681A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 170 through 172 No H-bonds generated for 'chain 'I' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.167A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.580A 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: 6.243A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.828A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.535A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 105 through 106 removed outlier: 7.048A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.252A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 324 through 328 removed outlier: 7.090A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.618A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 659 through 660 removed outlier: 3.999A pdb=" N TYR A 660 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.677A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.155A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.265A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.471A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.035A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.851A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.605A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 101 through 103 removed outlier: 3.903A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.802A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.355A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.280A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.909A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.529A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 565 through 567 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.339A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.430A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.706A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.245A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.250A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.549A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.351A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.795A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE9, first strand: chain 'C' and resid 116 through 121 Processing sheet with id=AF1, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AF2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.314A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.811A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.373A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.196A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.267A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.466A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 145 through 148 removed outlier: 3.849A pdb=" N ALA D 146 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 153 through 157 Processing sheet with id=AG9, first strand: chain 'D' and resid 182 through 185 removed outlier: 6.333A pdb=" N TRP D 172 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 272 through 273 Processing sheet with id=AH2, first strand: chain 'D' and resid 278 through 284 Processing sheet with id=AH3, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.308A pdb=" N TRP D 297 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.308A pdb=" N TRP D 297 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.530A pdb=" N VAL D 397 " --> pdb=" O PHE D 382 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR D 437 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 440 " --> pdb=" O SER D 426 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 409 through 411 Processing sheet with id=AH7, first strand: chain 'D' and resid 455 through 456 removed outlier: 3.526A pdb=" N TYR D 456 " --> pdb=" O PHE D 473 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 473 " --> pdb=" O TYR D 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 145 through 148 removed outlier: 3.848A pdb=" N ALA E 146 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 153 through 157 Processing sheet with id=AI4, first strand: chain 'E' and resid 182 through 185 removed outlier: 6.333A pdb=" N TRP E 172 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 272 through 273 Processing sheet with id=AI6, first strand: chain 'E' and resid 278 through 284 Processing sheet with id=AI7, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.306A pdb=" N TRP E 297 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.306A pdb=" N TRP E 297 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 378 through 382 removed outlier: 3.530A pdb=" N VAL E 397 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR E 437 " --> pdb=" O ASN E 402 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 440 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 409 through 411 Processing sheet with id=AJ2, first strand: chain 'E' and resid 455 through 456 removed outlier: 3.526A pdb=" N TYR E 456 " --> pdb=" O PHE E 473 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 473 " --> pdb=" O TYR E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AJ4, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 145 through 148 removed outlier: 3.848A pdb=" N ALA F 146 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 153 through 157 Processing sheet with id=AJ8, first strand: chain 'F' and resid 182 through 185 removed outlier: 6.332A pdb=" N TRP F 172 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 272 through 273 Processing sheet with id=AK1, first strand: chain 'F' and resid 278 through 284 Processing sheet with id=AK2, first strand: chain 'F' and resid 307 through 310 removed outlier: 6.307A pdb=" N TRP F 297 " --> pdb=" O LEU F 309 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 378 through 382 removed outlier: 3.529A pdb=" N VAL F 397 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR F 437 " --> pdb=" O ASN F 402 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 440 " --> pdb=" O SER F 426 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 409 through 411 Processing sheet with id=AK5, first strand: chain 'F' and resid 455 through 456 removed outlier: 3.527A pdb=" N TYR F 456 " --> pdb=" O PHE F 473 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE F 473 " --> pdb=" O TYR F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AK7, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.848A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.677A pdb=" N VAL G 116 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 134 through 137 removed outlier: 3.828A pdb=" N LEU G 152 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR G 190 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 165 through 168 Processing sheet with id=AL2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AL3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.843A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.680A pdb=" N VAL H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'H' and resid 134 through 138 removed outlier: 4.308A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU H 152 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'H' and resid 165 through 168 Processing sheet with id=AL7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AL8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.847A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.680A pdb=" N VAL I 116 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'I' and resid 134 through 138 removed outlier: 4.310A pdb=" N GLY I 153 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU I 152 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR I 190 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'I' and resid 165 through 168 1559 hydrogen bonds defined for protein. 4095 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: 14.45 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11584 1.33 - 1.46: 8105 1.46 - 1.58: 20152 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 40039 Sorted by residual: bond pdb=" N ILE G 101 " pdb=" CA ILE G 101 " ideal model delta sigma weight residual 1.459 1.495 -0.037 9.10e-03 1.21e+04 1.61e+01 bond pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.58e+01 bond pdb=" N ILE H 101 " pdb=" CA ILE H 101 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.55e+01 bond pdb=" N ILE I 101 " pdb=" CA ILE I 101 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.30e-03 1.16e+04 1.49e+01 bond pdb=" N VAL C 213 " pdb=" CA VAL C 213 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.30e+01 ... (remaining 40034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 52180 2.02 - 4.03: 2067 4.03 - 6.05: 193 6.05 - 8.06: 38 8.06 - 10.08: 10 Bond angle restraints: 54488 Sorted by residual: angle pdb=" C ASN B 544 " pdb=" CA ASN B 544 " pdb=" CB ASN B 544 " ideal model delta sigma weight residual 116.54 109.82 6.72 1.15e+00 7.56e-01 3.41e+01 angle pdb=" C ASN A 331 " pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " ideal model delta sigma weight residual 109.84 118.28 -8.44 1.50e+00 4.44e-01 3.17e+01 angle pdb=" N MET G 114 " pdb=" CA MET G 114 " pdb=" C MET G 114 " ideal model delta sigma weight residual 109.15 101.69 7.46 1.44e+00 4.82e-01 2.68e+01 angle pdb=" N PHE B 456 " pdb=" CA PHE B 456 " pdb=" C PHE B 456 " ideal model delta sigma weight residual 108.02 117.05 -9.03 1.75e+00 3.27e-01 2.66e+01 angle pdb=" N MET H 114 " pdb=" CA MET H 114 " pdb=" C MET H 114 " ideal model delta sigma weight residual 109.15 101.82 7.33 1.44e+00 4.82e-01 2.59e+01 ... (remaining 54483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 21841 17.92 - 35.83: 1891 35.83 - 53.75: 360 53.75 - 71.66: 78 71.66 - 89.58: 43 Dihedral angle restraints: 24213 sinusoidal: 9705 harmonic: 14508 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.25 71.25 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.23 71.23 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.19 71.19 1 1.00e+01 1.00e-02 6.51e+01 ... (remaining 24210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 6222 0.237 - 0.473: 12 0.473 - 0.710: 4 0.710 - 0.947: 2 0.947 - 1.184: 1 Chirality restraints: 6241 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-01 2.50e+01 3.50e+01 chirality pdb=" C1 NAG C1405 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1405 " pdb=" O5 NAG C1405 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG C1402 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1402 " pdb=" O5 NAG C1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 6238 not shown) Planarity restraints: 7033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG B1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1402 " 0.354 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1402 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG C1402 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG C1402 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C1402 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1408 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C1408 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1408 " 0.064 2.00e-02 2.50e+03 pdb=" N2 NAG C1408 " -0.525 2.00e-02 2.50e+03 pdb=" O7 NAG C1408 " 0.196 2.00e-02 2.50e+03 ... (remaining 7030 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6083 2.76 - 3.29: 39350 3.29 - 3.83: 66571 3.83 - 4.36: 82445 4.36 - 4.90: 139124 Nonbonded interactions: 333573 Sorted by model distance: nonbonded pdb=" OH TYR E 173 " pdb=" OH TYR E 235 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR F 173 " pdb=" OH TYR F 235 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR D 173 " pdb=" OH TYR D 235 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR E 298 " pdb=" OH TYR E 360 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR D 298 " pdb=" OH TYR D 360 " model vdw 2.224 3.040 ... (remaining 333568 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 16 through 1310) selection = (chain 'B' and resid 16 through 1310) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 44.060 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4227 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 : 0.006 0.054 40125 Z= 0.386 Angle : 0.891 30.104 54689 Z= 0.526 Chirality : 0.061 1.184 6241 Planarity : 0.015 0.305 7004 Dihedral : 14.001 89.576 14748 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.78 % Allowed : 10.66 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.47 (0.12), residues: 4938 helix: 0.16 (0.19), residues: 733 sheet: -1.03 (0.14), residues: 1272 loop : -1.25 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1107 TYR 0.044 0.002 TYR B 904 PHE 0.029 0.002 PHE C 168 TRP 0.017 0.002 TRP A 886 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00611 (40039) covalent geometry : angle 0.83367 (54488) SS BOND : bond 0.00480 ( 57) SS BOND : angle 1.45811 ( 114) hydrogen bonds : bond 0.17234 ( 1481) hydrogen bonds : angle 8.19337 ( 4095) link_NAG-ASN : bond 0.03656 ( 29) link_NAG-ASN : angle 7.83364 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 586 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6694 (m-40) cc_final: 0.5803 (p0) REVERT: A 314 GLN cc_start: 0.8147 (tt0) cc_final: 0.7793 (tp40) REVERT: A 319 ARG cc_start: 0.7573 (ptp90) cc_final: 0.6232 (ptm-80) REVERT: A 554 GLU cc_start: 0.8154 (pt0) cc_final: 0.7779 (mt-10) REVERT: A 663 ASP cc_start: 0.7549 (t0) cc_final: 0.7322 (t0) REVERT: A 775 ASP cc_start: 0.7420 (m-30) cc_final: 0.6923 (m-30) REVERT: A 787 GLN cc_start: 0.7928 (mt0) cc_final: 0.7174 (mt0) REVERT: A 796 ASP cc_start: 0.7267 (p0) cc_final: 0.6708 (t70) REVERT: A 875 SER cc_start: 0.7780 (t) cc_final: 0.7366 (p) REVERT: A 886 TRP cc_start: 0.6844 (p90) cc_final: 0.6033 (p90) REVERT: A 919 ASN cc_start: 0.7083 (m-40) cc_final: 0.6870 (m110) REVERT: A 921 LYS cc_start: 0.6758 (mtpp) cc_final: 0.6484 (tttt) REVERT: A 985 ASP cc_start: 0.5820 (m-30) cc_final: 0.5442 (t0) REVERT: A 1017 GLU cc_start: 0.6657 (tt0) cc_final: 0.6437 (tt0) REVERT: A 1045 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7192 (tptp) REVERT: A 1136 THR cc_start: 0.8446 (m) cc_final: 0.8230 (t) REVERT: B 48 LEU cc_start: 0.8414 (mt) cc_final: 0.8109 (mt) REVERT: B 191 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7716 (mt-10) REVERT: B 271 GLN cc_start: 0.7096 (mt0) cc_final: 0.6709 (mt0) REVERT: B 314 GLN cc_start: 0.8065 (tt0) cc_final: 0.7532 (tm-30) REVERT: B 675 GLN cc_start: 0.7211 (mt0) cc_final: 0.6604 (mt0) REVERT: B 790 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8073 (mtpp) REVERT: B 804 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7913 (mm-40) REVERT: B 875 SER cc_start: 0.8039 (t) cc_final: 0.7376 (m) REVERT: B 964 LYS cc_start: 0.7543 (mmtp) cc_final: 0.6952 (mptt) REVERT: B 1138 TYR cc_start: 0.6970 (t80) cc_final: 0.6586 (t80) REVERT: C 202 LYS cc_start: 0.6633 (mttm) cc_final: 0.6319 (mttp) REVERT: C 314 GLN cc_start: 0.8430 (tt0) cc_final: 0.8226 (tt0) REVERT: C 554 GLU cc_start: 0.8099 (pt0) cc_final: 0.7853 (pt0) REVERT: C 583 GLU cc_start: 0.7182 (tt0) cc_final: 0.6954 (tt0) REVERT: C 661 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6680 (mm-30) REVERT: C 675 GLN cc_start: 0.7091 (mt0) cc_final: 0.6822 (mt0) REVERT: C 790 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7915 (mtpp) REVERT: C 796 ASP cc_start: 0.8118 (t70) cc_final: 0.7042 (p0) REVERT: C 825 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6966 (mptt) REVERT: C 867 ASP cc_start: 0.7478 (m-30) cc_final: 0.7212 (m-30) REVERT: C 875 SER cc_start: 0.7803 (t) cc_final: 0.7494 (p) REVERT: C 921 LYS cc_start: 0.6935 (mtpp) cc_final: 0.6410 (mmpt) REVERT: C 1045 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7596 (tmtt) REVERT: C 1107 ARG cc_start: 0.7201 (mmt180) cc_final: 0.6669 (mmt90) REVERT: C 1119 ASN cc_start: 0.6807 (m-40) cc_final: 0.6293 (m-40) REVERT: D 156 LEU cc_start: -0.1523 (OUTLIER) cc_final: -0.1758 (pt) REVERT: D 387 GLU cc_start: 0.2790 (OUTLIER) cc_final: 0.2377 (mt-10) REVERT: E 344 ASP cc_start: 0.1483 (m-30) cc_final: 0.1213 (t70) outliers start: 34 outliers final: 7 residues processed: 613 average time/residue: 0.2245 time to fit residues: 225.1171 Evaluate side-chains 347 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 338 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain I residue 156 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 40.0000 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 239 GLN A 354 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 616 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN A1108 ASN B 125 ASN B 196 ASN B 354 ASN B 506 GLN B 613 GLN B 616 ASN B 901 GLN B 955 ASN B 965 GLN B1054 GLN B1101 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 134 GLN C 196 ASN C 354 ASN C 544 ASN C 764 ASN C 856 ASN C 901 GLN C1101 HIS D 113 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN D 388 GLN D 416 ASN E 164 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN E 388 GLN F 277 GLN F 289 ASN F 388 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.274387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.235224 restraints weight = 44799.402| |-----------------------------------------------------------------------------| r_work (start): 0.4584 rms_B_bonded: 2.22 r_work: 0.4288 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 40125 Z= 0.237 Angle : 0.737 17.331 54689 Z= 0.363 Chirality : 0.049 0.375 6241 Planarity : 0.005 0.085 7004 Dihedral : 5.923 52.597 6076 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.63 % Allowed : 12.95 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.43 (0.12), residues: 4938 helix: -0.06 (0.18), residues: 734 sheet: -1.03 (0.13), residues: 1367 loop : -1.11 (0.12), residues: 2837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.037 0.002 TYR B 904 PHE 0.021 0.002 PHE C 86 TRP 0.017 0.002 TRP D 111 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00567 (40039) covalent geometry : angle 0.71292 (54488) SS BOND : bond 0.00480 ( 57) SS BOND : angle 1.66837 ( 114) hydrogen bonds : bond 0.03938 ( 1481) hydrogen bonds : angle 6.42776 ( 4095) link_NAG-ASN : bond 0.00686 ( 29) link_NAG-ASN : angle 4.45475 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 378 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 TRP cc_start: 0.7424 (p90) cc_final: 0.7166 (p90) REVERT: B 875 SER cc_start: 0.8918 (t) cc_final: 0.8420 (m) REVERT: B 886 TRP cc_start: 0.7273 (p90) cc_final: 0.6834 (p90) REVERT: C 875 SER cc_start: 0.8600 (t) cc_final: 0.8399 (p) REVERT: D 387 GLU cc_start: 0.3560 (OUTLIER) cc_final: 0.3313 (mt-10) REVERT: E 11 LEU cc_start: 0.6142 (pt) cc_final: 0.5927 (pt) REVERT: E 230 TYR cc_start: 0.2914 (p90) cc_final: 0.2272 (p90) REVERT: E 344 ASP cc_start: 0.2013 (m-30) cc_final: 0.1561 (t70) REVERT: F 153 ARG cc_start: 0.4179 (ttp80) cc_final: 0.3247 (mtt180) REVERT: F 314 ASN cc_start: 0.5238 (t0) cc_final: 0.4905 (m110) REVERT: F 440 SER cc_start: 0.1958 (OUTLIER) cc_final: 0.1721 (t) REVERT: H 114 MET cc_start: 0.1644 (tpt) cc_final: 0.1278 (tpp) REVERT: I 34 MET cc_start: 0.2340 (mmt) cc_final: 0.2113 (mmp) outliers start: 114 outliers final: 60 residues processed: 460 average time/residue: 0.2077 time to fit residues: 161.3941 Evaluate side-chains 341 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 440 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain I residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 298 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 435 optimal weight: 50.0000 chunk 116 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 206 optimal weight: 20.0000 chunk 417 optimal weight: 30.0000 chunk 233 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 chunk 378 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 207 HIS A 314 GLN A 506 GLN A 755 GLN A 762 GLN B 52 GLN B1135 ASN C 99 ASN C 121 ASN C 580 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN F 164 ASN F 422 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.275744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.239367 restraints weight = 44877.515| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 2.07 r_work: 0.4328 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4241 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40125 Z= 0.136 Angle : 0.610 13.413 54689 Z= 0.304 Chirality : 0.045 0.393 6241 Planarity : 0.004 0.048 7004 Dihedral : 5.453 56.770 6065 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.26 % Allowed : 14.52 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.17 (0.12), residues: 4938 helix: 0.26 (0.19), residues: 734 sheet: -0.77 (0.13), residues: 1355 loop : -1.02 (0.12), residues: 2849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.030 0.001 TYR B 904 PHE 0.026 0.002 PHE B 374 TRP 0.017 0.002 TRP E 36 HIS 0.003 0.001 HIS F 453 Details of bonding type rmsd covalent geometry : bond 0.00310 (40039) covalent geometry : angle 0.58978 (54488) SS BOND : bond 0.00388 ( 57) SS BOND : angle 1.31767 ( 114) hydrogen bonds : bond 0.03638 ( 1481) hydrogen bonds : angle 6.05310 ( 4095) link_NAG-ASN : bond 0.00738 ( 29) link_NAG-ASN : angle 3.66727 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 324 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7826 (mmt180) cc_final: 0.7564 (mmt180) REVERT: A 546 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6996 (tp) REVERT: A 565 PHE cc_start: 0.6680 (m-10) cc_final: 0.6409 (m-10) REVERT: A 584 ILE cc_start: 0.8438 (mm) cc_final: 0.8160 (mm) REVERT: A 886 TRP cc_start: 0.7391 (p90) cc_final: 0.6824 (p90) REVERT: B 875 SER cc_start: 0.8846 (t) cc_final: 0.8378 (m) REVERT: B 886 TRP cc_start: 0.7444 (p90) cc_final: 0.7185 (p90) REVERT: C 51 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7561 (t) REVERT: C 643 PHE cc_start: 0.8280 (t80) cc_final: 0.8068 (t80) REVERT: D 324 PHE cc_start: 0.1500 (m-80) cc_final: 0.0310 (t80) REVERT: D 349 TYR cc_start: 0.2394 (m-80) cc_final: 0.1963 (m-10) REVERT: D 387 GLU cc_start: 0.3522 (OUTLIER) cc_final: 0.2901 (pt0) REVERT: E 230 TYR cc_start: 0.2969 (p90) cc_final: 0.2387 (p90) REVERT: E 344 ASP cc_start: 0.2093 (m-30) cc_final: 0.1578 (t70) REVERT: F 153 ARG cc_start: 0.4262 (ttp80) cc_final: 0.3260 (mtt180) REVERT: F 451 GLU cc_start: 0.2430 (mp0) cc_final: 0.2196 (mt-10) REVERT: G 124 THR cc_start: 0.1246 (p) cc_final: 0.0570 (t) outliers start: 98 outliers final: 53 residues processed: 397 average time/residue: 0.2005 time to fit residues: 136.4224 Evaluate side-chains 333 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 65 optimal weight: 0.0000 chunk 105 optimal weight: 1.9990 chunk 354 optimal weight: 0.0470 chunk 389 optimal weight: 5.9990 chunk 382 optimal weight: 7.9990 chunk 310 optimal weight: 40.0000 chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 408 optimal weight: 6.9990 overall best weight: 0.7886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 271 GLN B 675 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 710 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.276269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.241324 restraints weight = 44775.391| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 2.02 r_work: 0.4320 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4214 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40125 Z= 0.138 Angle : 0.588 12.000 54689 Z= 0.293 Chirality : 0.044 0.470 6241 Planarity : 0.004 0.047 7004 Dihedral : 5.302 55.931 6063 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.00 % Allowed : 14.43 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.06 (0.12), residues: 4938 helix: 0.35 (0.19), residues: 734 sheet: -0.64 (0.13), residues: 1373 loop : -0.99 (0.12), residues: 2831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.026 0.001 TYR B 904 PHE 0.020 0.001 PHE B 898 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS F 453 Details of bonding type rmsd covalent geometry : bond 0.00316 (40039) covalent geometry : angle 0.57118 (54488) SS BOND : bond 0.00421 ( 57) SS BOND : angle 1.23715 ( 114) hydrogen bonds : bond 0.03453 ( 1481) hydrogen bonds : angle 5.81708 ( 4095) link_NAG-ASN : bond 0.00624 ( 29) link_NAG-ASN : angle 3.27641 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 302 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7894 (mmt180) cc_final: 0.7634 (mmt180) REVERT: A 546 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7008 (tp) REVERT: A 565 PHE cc_start: 0.6780 (m-10) cc_final: 0.6528 (m-10) REVERT: A 584 ILE cc_start: 0.8486 (mm) cc_final: 0.8223 (mm) REVERT: A 886 TRP cc_start: 0.7407 (p90) cc_final: 0.6914 (p90) REVERT: B 875 SER cc_start: 0.8836 (t) cc_final: 0.8366 (m) REVERT: B 886 TRP cc_start: 0.7519 (p90) cc_final: 0.7309 (p90) REVERT: C 293 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7662 (pt) REVERT: D 67 ARG cc_start: 0.1854 (ptp-170) cc_final: 0.1428 (mtt180) REVERT: D 324 PHE cc_start: 0.1481 (m-80) cc_final: 0.0414 (t80) REVERT: D 349 TYR cc_start: 0.2430 (m-80) cc_final: 0.1949 (m-10) REVERT: D 387 GLU cc_start: 0.3639 (OUTLIER) cc_final: 0.2915 (pt0) REVERT: E 230 TYR cc_start: 0.3080 (p90) cc_final: 0.2597 (p90) REVERT: E 344 ASP cc_start: 0.2200 (m-30) cc_final: 0.1729 (t70) REVERT: E 414 VAL cc_start: 0.2799 (OUTLIER) cc_final: 0.2445 (m) REVERT: F 34 MET cc_start: 0.4032 (mmp) cc_final: 0.3111 (mmm) REVERT: F 140 LEU cc_start: 0.1277 (mm) cc_final: 0.0643 (mt) REVERT: F 153 ARG cc_start: 0.4291 (ttp80) cc_final: 0.3236 (mmt180) REVERT: F 188 ASP cc_start: 0.1257 (m-30) cc_final: 0.0753 (t0) REVERT: F 451 GLU cc_start: 0.2521 (mp0) cc_final: 0.2135 (mt-10) REVERT: G 124 THR cc_start: 0.1071 (p) cc_final: 0.0424 (t) REVERT: H 81 LEU cc_start: 0.0776 (OUTLIER) cc_final: 0.0216 (mt) outliers start: 130 outliers final: 75 residues processed: 402 average time/residue: 0.1953 time to fit residues: 136.0177 Evaluate side-chains 353 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 273 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 343 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 337 optimal weight: 0.8980 chunk 288 optimal weight: 3.9990 chunk 399 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 338 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 90 optimal weight: 0.0970 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 52 GLN B 99 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 935 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.273550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.237345 restraints weight = 44589.446| |-----------------------------------------------------------------------------| r_work (start): 0.4609 rms_B_bonded: 2.02 r_work: 0.4332 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4253 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40125 Z= 0.179 Angle : 0.602 13.458 54689 Z= 0.299 Chirality : 0.046 0.677 6241 Planarity : 0.004 0.061 7004 Dihedral : 5.331 56.285 6063 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.21 % Allowed : 14.84 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.03 (0.12), residues: 4938 helix: 0.30 (0.19), residues: 740 sheet: -0.55 (0.13), residues: 1399 loop : -1.00 (0.12), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1107 TYR 0.045 0.001 TYR B 904 PHE 0.021 0.002 PHE C 541 TRP 0.014 0.001 TRP E 36 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00422 (40039) covalent geometry : angle 0.58421 (54488) SS BOND : bond 0.00400 ( 57) SS BOND : angle 1.34491 ( 114) hydrogen bonds : bond 0.03518 ( 1481) hydrogen bonds : angle 5.77043 ( 4095) link_NAG-ASN : bond 0.00636 ( 29) link_NAG-ASN : angle 3.37568 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 285 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7929 (mmt180) cc_final: 0.7679 (mmt180) REVERT: A 886 TRP cc_start: 0.7441 (p90) cc_final: 0.6963 (p90) REVERT: A 904 TYR cc_start: 0.6016 (t80) cc_final: 0.5602 (t80) REVERT: A 966 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8568 (mt) REVERT: B 92 PHE cc_start: 0.7633 (t80) cc_final: 0.7331 (t80) REVERT: B 875 SER cc_start: 0.8847 (t) cc_final: 0.8373 (m) REVERT: C 293 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7771 (pt) REVERT: C 318 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7503 (p90) REVERT: D 67 ARG cc_start: 0.1796 (ptp-170) cc_final: 0.1541 (mtt180) REVERT: D 324 PHE cc_start: 0.1417 (m-80) cc_final: 0.0396 (t80) REVERT: D 349 TYR cc_start: 0.2482 (m-80) cc_final: 0.1948 (m-80) REVERT: D 387 GLU cc_start: 0.3716 (OUTLIER) cc_final: 0.2969 (pt0) REVERT: E 36 TRP cc_start: 0.5374 (m100) cc_final: 0.4770 (m100) REVERT: E 190 GLN cc_start: 0.6233 (OUTLIER) cc_final: 0.5029 (mp10) REVERT: E 230 TYR cc_start: 0.2957 (p90) cc_final: 0.2444 (p90) REVERT: E 344 ASP cc_start: 0.2318 (m-30) cc_final: 0.1727 (t70) REVERT: E 414 VAL cc_start: 0.2869 (OUTLIER) cc_final: 0.2578 (m) REVERT: F 153 ARG cc_start: 0.4193 (ttp80) cc_final: 0.3189 (mmt180) REVERT: F 188 ASP cc_start: 0.1281 (m-30) cc_final: 0.0795 (t0) REVERT: F 451 GLU cc_start: 0.2608 (mp0) cc_final: 0.2126 (mt-10) REVERT: G 124 THR cc_start: 0.1241 (p) cc_final: 0.0581 (t) REVERT: H 34 MET cc_start: 0.1935 (mmm) cc_final: 0.1551 (mmm) outliers start: 139 outliers final: 87 residues processed: 385 average time/residue: 0.2033 time to fit residues: 134.7312 Evaluate side-chains 359 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 266 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 45 optimal weight: 6.9990 chunk 362 optimal weight: 30.0000 chunk 246 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 437 optimal weight: 40.0000 chunk 176 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 969 ASN C 121 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1071 GLN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN E 164 ASN E 402 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.271545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.235709 restraints weight = 44431.844| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 1.97 r_work: 0.4227 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 40125 Z= 0.260 Angle : 0.652 12.981 54689 Z= 0.327 Chirality : 0.048 0.646 6241 Planarity : 0.005 0.090 7004 Dihedral : 5.455 56.300 6063 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.39 % Allowed : 15.47 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.09 (0.12), residues: 4938 helix: 0.13 (0.19), residues: 729 sheet: -0.46 (0.13), residues: 1377 loop : -1.07 (0.12), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 316 TYR 0.044 0.002 TYR B 904 PHE 0.025 0.002 PHE C 541 TRP 0.015 0.002 TRP E 36 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00626 (40039) covalent geometry : angle 0.63713 (54488) SS BOND : bond 0.00526 ( 57) SS BOND : angle 1.64200 ( 114) hydrogen bonds : bond 0.03794 ( 1481) hydrogen bonds : angle 5.87750 ( 4095) link_NAG-ASN : bond 0.00494 ( 29) link_NAG-ASN : angle 3.12316 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 278 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6473 (t80) REVERT: A 886 TRP cc_start: 0.7447 (p90) cc_final: 0.7022 (p90) REVERT: A 904 TYR cc_start: 0.6079 (t80) cc_final: 0.5659 (t80) REVERT: A 966 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8640 (mt) REVERT: B 92 PHE cc_start: 0.7814 (t80) cc_final: 0.7488 (t80) REVERT: B 978 ASN cc_start: 0.7197 (m-40) cc_final: 0.6932 (t0) REVERT: C 293 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7809 (pt) REVERT: C 318 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7456 (p90) REVERT: C 886 TRP cc_start: 0.7498 (p90) cc_final: 0.7099 (p90) REVERT: D 67 ARG cc_start: 0.1870 (ptp-170) cc_final: 0.1633 (mtt180) REVERT: D 324 PHE cc_start: 0.1255 (m-80) cc_final: 0.0427 (t80) REVERT: D 387 GLU cc_start: 0.3783 (OUTLIER) cc_final: 0.2865 (pt0) REVERT: E 36 TRP cc_start: 0.5897 (m100) cc_final: 0.5317 (m100) REVERT: E 190 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.5286 (mp10) REVERT: E 230 TYR cc_start: 0.3236 (p90) cc_final: 0.2619 (p90) REVERT: E 414 VAL cc_start: 0.2861 (OUTLIER) cc_final: 0.2548 (m) REVERT: F 140 LEU cc_start: 0.0980 (mm) cc_final: 0.0324 (mt) REVERT: F 153 ARG cc_start: 0.4477 (ttp80) cc_final: 0.3337 (mmt90) REVERT: F 451 GLU cc_start: 0.2485 (mp0) cc_final: 0.1988 (mt-10) REVERT: H 81 LEU cc_start: 0.0149 (OUTLIER) cc_final: -0.0379 (mt) REVERT: H 114 MET cc_start: 0.1454 (tpp) cc_final: 0.1172 (tpp) outliers start: 147 outliers final: 100 residues processed: 388 average time/residue: 0.1984 time to fit residues: 132.2110 Evaluate side-chains 365 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 257 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 402 ASN Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 137 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 395 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 352 optimal weight: 0.0770 chunk 242 optimal weight: 0.7980 chunk 157 optimal weight: 0.3980 chunk 402 optimal weight: 9.9990 chunk 83 optimal weight: 0.0970 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 616 ASN A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 239 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1101 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN D 113 GLN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.275368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.239782 restraints weight = 44675.247| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 2.03 r_work: 0.4297 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4180 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40125 Z= 0.114 Angle : 0.567 10.622 54689 Z= 0.283 Chirality : 0.043 0.412 6241 Planarity : 0.004 0.067 7004 Dihedral : 5.238 56.164 6063 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.61 % Allowed : 16.46 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.89 (0.12), residues: 4938 helix: 0.50 (0.19), residues: 740 sheet: -0.37 (0.14), residues: 1358 loop : -0.98 (0.12), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1107 TYR 0.027 0.001 TYR B 904 PHE 0.029 0.001 PHE E 403 TRP 0.015 0.001 TRP B 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00257 (40039) covalent geometry : angle 0.55300 (54488) SS BOND : bond 0.00349 ( 57) SS BOND : angle 1.23649 ( 114) hydrogen bonds : bond 0.03298 ( 1481) hydrogen bonds : angle 5.55983 ( 4095) link_NAG-ASN : bond 0.00522 ( 29) link_NAG-ASN : angle 2.88255 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 294 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7225 (t70) cc_final: 0.6990 (t0) REVERT: A 740 MET cc_start: 0.7141 (tpp) cc_final: 0.6928 (ttt) REVERT: A 756 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6557 (t80) REVERT: A 886 TRP cc_start: 0.7324 (p90) cc_final: 0.6976 (p90) REVERT: B 92 PHE cc_start: 0.7703 (t80) cc_final: 0.7465 (t80) REVERT: B 875 SER cc_start: 0.8811 (t) cc_final: 0.8232 (m) REVERT: B 978 ASN cc_start: 0.7130 (m-40) cc_final: 0.6897 (t0) REVERT: C 318 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7386 (p90) REVERT: C 886 TRP cc_start: 0.7428 (p90) cc_final: 0.6872 (p90) REVERT: C 1005 GLN cc_start: 0.7656 (tp40) cc_final: 0.7382 (mm-40) REVERT: D 34 MET cc_start: 0.3500 (mmt) cc_final: 0.2956 (mmm) REVERT: D 113 GLN cc_start: 0.2307 (OUTLIER) cc_final: 0.2069 (pm20) REVERT: D 324 PHE cc_start: 0.1159 (m-80) cc_final: 0.0500 (t80) REVERT: E 36 TRP cc_start: 0.5905 (m100) cc_final: 0.5634 (m100) REVERT: E 190 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.5330 (mp10) REVERT: E 230 TYR cc_start: 0.3243 (p90) cc_final: 0.2652 (p90) REVERT: E 414 VAL cc_start: 0.2806 (OUTLIER) cc_final: 0.2520 (m) REVERT: F 34 MET cc_start: 0.4302 (mmp) cc_final: 0.3242 (mmm) REVERT: F 74 ASN cc_start: 0.2119 (OUTLIER) cc_final: 0.1914 (m-40) REVERT: F 153 ARG cc_start: 0.4509 (ttp80) cc_final: 0.3404 (mmt90) REVERT: F 188 ASP cc_start: 0.1341 (m-30) cc_final: 0.0848 (t0) REVERT: F 451 GLU cc_start: 0.2246 (mp0) cc_final: 0.2007 (mt-10) REVERT: G 124 THR cc_start: 0.1216 (p) cc_final: 0.0532 (t) REVERT: G 192 LEU cc_start: 0.2873 (OUTLIER) cc_final: 0.2516 (tp) REVERT: H 34 MET cc_start: 0.2281 (mmm) cc_final: 0.1877 (mmm) REVERT: H 81 LEU cc_start: -0.0082 (OUTLIER) cc_final: -0.0563 (mt) REVERT: H 114 MET cc_start: 0.1431 (tpp) cc_final: 0.1218 (tpp) outliers start: 113 outliers final: 73 residues processed: 374 average time/residue: 0.1981 time to fit residues: 128.7851 Evaluate side-chains 348 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 267 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 50 optimal weight: 2.9990 chunk 342 optimal weight: 7.9990 chunk 234 optimal weight: 0.6980 chunk 387 optimal weight: 0.5980 chunk 177 optimal weight: 0.3980 chunk 420 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 489 optimal weight: 40.0000 chunk 295 optimal weight: 1.9990 chunk 355 optimal weight: 5.9990 chunk 376 optimal weight: 30.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1101 HIS C 121 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.273864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.238072 restraints weight = 44488.225| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 2.02 r_work: 0.4234 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4113 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40125 Z= 0.163 Angle : 0.585 9.819 54689 Z= 0.291 Chirality : 0.044 0.433 6241 Planarity : 0.004 0.047 7004 Dihedral : 5.194 56.022 6063 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.68 % Allowed : 16.67 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.83 (0.12), residues: 4938 helix: 0.55 (0.19), residues: 726 sheet: -0.32 (0.13), residues: 1403 loop : -0.95 (0.12), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.034 0.001 TYR F 173 PHE 0.019 0.002 PHE A 898 TRP 0.013 0.001 TRP B 886 HIS 0.003 0.001 HIS F 453 Details of bonding type rmsd covalent geometry : bond 0.00384 (40039) covalent geometry : angle 0.57278 (54488) SS BOND : bond 0.00378 ( 57) SS BOND : angle 1.24073 ( 114) hydrogen bonds : bond 0.03392 ( 1481) hydrogen bonds : angle 5.53706 ( 4095) link_NAG-ASN : bond 0.00448 ( 29) link_NAG-ASN : angle 2.80738 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 274 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6611 (t80) REVERT: A 886 TRP cc_start: 0.7326 (p90) cc_final: 0.6999 (p90) REVERT: B 92 PHE cc_start: 0.7732 (t80) cc_final: 0.7465 (t80) REVERT: B 978 ASN cc_start: 0.7227 (m-40) cc_final: 0.6949 (t0) REVERT: C 318 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7352 (p90) REVERT: C 886 TRP cc_start: 0.7494 (p90) cc_final: 0.6899 (p90) REVERT: C 1005 GLN cc_start: 0.7688 (tp40) cc_final: 0.7409 (mm-40) REVERT: C 1145 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5480 (tt) REVERT: D 34 MET cc_start: 0.3614 (mmt) cc_final: 0.3049 (mmm) REVERT: D 324 PHE cc_start: 0.1197 (m-80) cc_final: 0.0513 (t80) REVERT: D 349 TYR cc_start: 0.2917 (m-80) cc_final: 0.2014 (m-10) REVERT: E 190 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.5329 (mp10) REVERT: E 230 TYR cc_start: 0.3331 (p90) cc_final: 0.2719 (p90) REVERT: E 414 VAL cc_start: 0.2788 (OUTLIER) cc_final: 0.2512 (m) REVERT: F 34 MET cc_start: 0.4385 (mmp) cc_final: 0.3365 (mmm) REVERT: F 74 ASN cc_start: 0.2176 (OUTLIER) cc_final: 0.1965 (m-40) REVERT: F 153 ARG cc_start: 0.4585 (ttp80) cc_final: 0.3430 (mmt90) REVERT: F 188 ASP cc_start: 0.1275 (m-30) cc_final: 0.0680 (t0) REVERT: F 451 GLU cc_start: 0.2412 (mp0) cc_final: 0.1888 (mt-10) REVERT: G 124 THR cc_start: 0.1239 (p) cc_final: 0.0535 (t) REVERT: G 192 LEU cc_start: 0.2902 (OUTLIER) cc_final: 0.2480 (tp) REVERT: H 34 MET cc_start: 0.2214 (mmm) cc_final: 0.1786 (mmm) REVERT: H 81 LEU cc_start: 0.0090 (OUTLIER) cc_final: -0.0443 (mt) REVERT: H 114 MET cc_start: 0.1445 (tpp) cc_final: 0.1239 (tpp) outliers start: 116 outliers final: 87 residues processed: 355 average time/residue: 0.1897 time to fit residues: 117.4249 Evaluate side-chains 358 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 263 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 22 optimal weight: 2.9990 chunk 390 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 427 optimal weight: 50.0000 chunk 170 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 580 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 121 ASN C1010 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 388 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.272627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.238046 restraints weight = 44441.243| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 2.02 r_work: 0.4288 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4175 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 40125 Z= 0.190 Angle : 0.598 9.687 54689 Z= 0.299 Chirality : 0.045 0.450 6241 Planarity : 0.004 0.047 7004 Dihedral : 5.213 56.134 6063 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.61 % Allowed : 16.78 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.86 (0.12), residues: 4938 helix: 0.45 (0.19), residues: 732 sheet: -0.31 (0.14), residues: 1364 loop : -0.96 (0.12), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 153 TYR 0.030 0.001 TYR C 369 PHE 0.029 0.002 PHE C 541 TRP 0.024 0.001 TRP E 36 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00452 (40039) covalent geometry : angle 0.58570 (54488) SS BOND : bond 0.00444 ( 57) SS BOND : angle 1.39371 ( 114) hydrogen bonds : bond 0.03468 ( 1481) hydrogen bonds : angle 5.55966 ( 4095) link_NAG-ASN : bond 0.00431 ( 29) link_NAG-ASN : angle 2.77720 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 267 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 GLU cc_start: 0.7373 (tp30) cc_final: 0.6974 (tp30) REVERT: A 756 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6860 (t80) REVERT: A 886 TRP cc_start: 0.7306 (p90) cc_final: 0.6976 (p90) REVERT: B 92 PHE cc_start: 0.7617 (t80) cc_final: 0.7360 (t80) REVERT: C 318 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7271 (p90) REVERT: C 886 TRP cc_start: 0.7490 (p90) cc_final: 0.6863 (p90) REVERT: C 1005 GLN cc_start: 0.7668 (tp40) cc_final: 0.7402 (mm-40) REVERT: C 1145 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5519 (tt) REVERT: D 34 MET cc_start: 0.3585 (mmt) cc_final: 0.3073 (mmm) REVERT: D 324 PHE cc_start: 0.1285 (m-80) cc_final: 0.0574 (t80) REVERT: D 349 TYR cc_start: 0.2834 (m-80) cc_final: 0.1944 (m-10) REVERT: E 36 TRP cc_start: 0.5999 (m100) cc_final: 0.5742 (m100) REVERT: E 190 GLN cc_start: 0.6256 (OUTLIER) cc_final: 0.5305 (mp10) REVERT: E 230 TYR cc_start: 0.3180 (p90) cc_final: 0.2634 (p90) REVERT: E 414 VAL cc_start: 0.2882 (OUTLIER) cc_final: 0.2579 (m) REVERT: F 34 MET cc_start: 0.4304 (mmp) cc_final: 0.3224 (ttm) REVERT: F 74 ASN cc_start: 0.2225 (OUTLIER) cc_final: 0.2013 (m-40) REVERT: F 144 PRO cc_start: 0.4041 (Cg_exo) cc_final: 0.3839 (Cg_endo) REVERT: F 153 ARG cc_start: 0.4503 (ttp80) cc_final: 0.3331 (mmt180) REVERT: F 188 ASP cc_start: 0.1302 (m-30) cc_final: 0.0768 (t0) REVERT: F 451 GLU cc_start: 0.2417 (mp0) cc_final: 0.1864 (mt-10) REVERT: G 192 LEU cc_start: 0.2783 (OUTLIER) cc_final: 0.2475 (tp) REVERT: H 34 MET cc_start: 0.2043 (mmm) cc_final: 0.1673 (mmm) REVERT: H 81 LEU cc_start: 0.0089 (OUTLIER) cc_final: -0.0570 (mp) outliers start: 113 outliers final: 91 residues processed: 349 average time/residue: 0.1958 time to fit residues: 119.0517 Evaluate side-chains 350 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 251 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 459 optimal weight: 40.0000 chunk 195 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 444 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 439 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 580 GLN A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 978 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 239 GLN C1010 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN F 101 ASN G 13 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.271635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.232968 restraints weight = 44230.946| |-----------------------------------------------------------------------------| r_work (start): 0.4572 rms_B_bonded: 2.13 r_work: 0.4286 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4202 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40125 Z= 0.179 Angle : 0.598 10.092 54689 Z= 0.297 Chirality : 0.045 0.431 6241 Planarity : 0.004 0.113 7004 Dihedral : 5.217 56.490 6063 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.52 % Allowed : 16.85 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.77 (0.12), residues: 4938 helix: 0.50 (0.19), residues: 724 sheet: -0.18 (0.14), residues: 1382 loop : -0.94 (0.12), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.037 0.001 TYR C 369 PHE 0.030 0.002 PHE C 541 TRP 0.034 0.001 TRP B1102 HIS 0.039 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00424 (40039) covalent geometry : angle 0.58504 (54488) SS BOND : bond 0.00406 ( 57) SS BOND : angle 1.39500 ( 114) hydrogen bonds : bond 0.03411 ( 1481) hydrogen bonds : angle 5.52196 ( 4095) link_NAG-ASN : bond 0.00429 ( 29) link_NAG-ASN : angle 2.78318 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 265 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 GLU cc_start: 0.7434 (tp30) cc_final: 0.7046 (tp30) REVERT: A 756 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6865 (t80) REVERT: A 886 TRP cc_start: 0.7285 (p90) cc_final: 0.6958 (p90) REVERT: B 92 PHE cc_start: 0.7653 (t80) cc_final: 0.7414 (t80) REVERT: C 318 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7290 (p90) REVERT: C 886 TRP cc_start: 0.7508 (p90) cc_final: 0.6919 (p90) REVERT: C 1005 GLN cc_start: 0.7721 (tp40) cc_final: 0.7451 (mm-40) REVERT: C 1145 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5528 (tt) REVERT: D 34 MET cc_start: 0.3495 (mmt) cc_final: 0.3008 (mmm) REVERT: D 324 PHE cc_start: 0.1301 (m-80) cc_final: 0.0604 (t80) REVERT: D 349 TYR cc_start: 0.2803 (m-80) cc_final: 0.1942 (m-10) REVERT: E 36 TRP cc_start: 0.5933 (m100) cc_final: 0.5693 (m100) REVERT: E 190 GLN cc_start: 0.6213 (OUTLIER) cc_final: 0.5280 (mp10) REVERT: E 230 TYR cc_start: 0.3010 (p90) cc_final: 0.2522 (p90) REVERT: E 414 VAL cc_start: 0.3111 (OUTLIER) cc_final: 0.2812 (m) REVERT: F 34 MET cc_start: 0.4180 (mmp) cc_final: 0.3239 (ttm) REVERT: F 144 PRO cc_start: 0.3926 (Cg_exo) cc_final: 0.3718 (Cg_endo) REVERT: F 153 ARG cc_start: 0.4507 (ttp80) cc_final: 0.3283 (mmt180) REVERT: F 451 GLU cc_start: 0.2352 (mp0) cc_final: 0.1772 (mt-10) REVERT: G 83 MET cc_start: 0.3181 (mtm) cc_final: 0.2887 (mtm) REVERT: G 192 LEU cc_start: 0.2803 (OUTLIER) cc_final: 0.2507 (tp) REVERT: H 34 MET cc_start: 0.1985 (mmm) cc_final: 0.1644 (mmm) REVERT: H 81 LEU cc_start: 0.0147 (OUTLIER) cc_final: -0.0486 (mp) outliers start: 109 outliers final: 93 residues processed: 345 average time/residue: 0.1942 time to fit residues: 116.4232 Evaluate side-chains 351 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 251 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 280 optimal weight: 6.9990 chunk 472 optimal weight: 40.0000 chunk 348 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 378 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 415 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 467 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 978 ASN B1101 HIS C 121 ASN C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.272703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.234240 restraints weight = 44563.700| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 2.15 r_work: 0.4274 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4193 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40125 Z= 0.140 Angle : 0.573 9.625 54689 Z= 0.285 Chirality : 0.044 0.393 6241 Planarity : 0.004 0.081 7004 Dihedral : 5.106 55.711 6063 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.42 % Allowed : 16.97 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.70 (0.12), residues: 4938 helix: 0.66 (0.19), residues: 724 sheet: -0.15 (0.14), residues: 1347 loop : -0.91 (0.12), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.035 0.001 TYR C 369 PHE 0.029 0.001 PHE C 541 TRP 0.017 0.001 TRP E 36 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00326 (40039) covalent geometry : angle 0.56064 (54488) SS BOND : bond 0.00383 ( 57) SS BOND : angle 1.28292 ( 114) hydrogen bonds : bond 0.03307 ( 1481) hydrogen bonds : angle 5.43192 ( 4095) link_NAG-ASN : bond 0.00436 ( 29) link_NAG-ASN : angle 2.67300 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9602.98 seconds wall clock time: 165 minutes 36.66 seconds (9936.66 seconds total)