Starting phenix.real_space_refine on Mon Jun 23 13:51:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz5_26879/06_2025/7uz5_26879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz5_26879/06_2025/7uz5_26879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz5_26879/06_2025/7uz5_26879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz5_26879/06_2025/7uz5_26879.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz5_26879/06_2025/7uz5_26879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz5_26879/06_2025/7uz5_26879.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 120 5.16 5 C 17209 2.51 5 N 4433 2.21 5 O 5289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 1.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27051 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8204 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8204 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8204 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 15.44, per 1000 atoms: 0.57 Number of scatterers: 27051 At special positions: 0 Unit cell: (160.576, 170.56, 197.184, 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 120 16.00 O 5289 8.00 N 4433 7.00 C 17209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " 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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A 801 " " NAG A1314 " - " ASN A1074 " " NAG A1315 " - " ASN A1098 " " NAG A1316 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B 801 " " NAG B1314 " - " ASN B1074 " " NAG B1315 " - " ASN B1098 " " NAG B1316 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1312 " - " ASN C 717 " " NAG C1313 " - " ASN C 801 " " NAG C1314 " - " ASN C1074 " " NAG C1315 " - " ASN C1098 " " NAG C1316 " - " ASN C1134 " Time building additional restraints: 7.22 Conformation dependent library (CDL) restraints added in 3.7 seconds 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6346 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 62 sheets defined 23.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 removed outlier: 4.318A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.521A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.009A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.949A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.695A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.949A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.616A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (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 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.645A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.645A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.510A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1147' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.639A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.687A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.637A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.832A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.552A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.503A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.552A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.715A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.671A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (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 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.557A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.814A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.714A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1147' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.832A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.513A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.889A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.649A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (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 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: 3.722A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.507A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 4.204A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1142 through 1147' Processing helix chain 'H' and resid 69 through 72 removed outlier: 3.522A pdb=" N LYS H 72 " --> pdb=" O GLN H 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 69 through 72' Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'L' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.387A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.990A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 164 removed outlier: 4.365A pdb=" N TRP A 152 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR A 144 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 13.947A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 13.541A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.578A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.329A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.639A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.558A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.666A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.631A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.631A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.671A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 30 removed outlier: 8.607A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.077A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC6, first strand: chain 'B' and resid 151 through 172 removed outlier: 4.762A pdb=" N TRP B 152 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR B 144 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 13.122A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.994A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.041A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.728A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.167A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.748A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.813A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.639A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.904A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.128A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE2, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AE3, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.722A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.934A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.668A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 12.410A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.690A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 13.187A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 13.338A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.389A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 12.410A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.188A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 324 through 327 removed outlier: 7.507A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.569A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.809A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.545A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.716A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG2, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AG3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AG4, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.607A pdb=" N MET H 39 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.560A pdb=" N TYR H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.739A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.520A pdb=" N GLN L 106 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR L 117 " --> pdb=" O GLN L 106 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 2883 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: 14.80 Time building geometry restraints manager: 8.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8594 1.34 - 1.46: 6037 1.46 - 1.58: 12894 1.58 - 1.70: 0 1.70 - 1.82: 155 Bond restraints: 27680 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CA GLN C 913 " pdb=" C GLN C 913 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.38e-02 5.25e+03 6.49e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" CA GLN A 913 " pdb=" C GLN A 913 " ideal model delta sigma weight residual 1.522 1.490 0.033 1.38e-02 5.25e+03 5.56e+00 bond pdb=" CA GLN B 913 " pdb=" C GLN B 913 " ideal model delta sigma weight residual 1.522 1.490 0.032 1.38e-02 5.25e+03 5.43e+00 ... (remaining 27675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 36841 1.81 - 3.61: 791 3.61 - 5.42: 60 5.42 - 7.22: 14 7.22 - 9.03: 1 Bond angle restraints: 37707 Sorted by residual: angle pdb=" N ASN A1074 " pdb=" CA ASN A1074 " pdb=" C ASN A1074 " ideal model delta sigma weight residual 110.48 104.86 5.62 1.48e+00 4.57e-01 1.44e+01 angle pdb=" C ASN A 121 " pdb=" N ASN A 122 " pdb=" CA ASN A 122 " ideal model delta sigma weight residual 121.86 116.37 5.49 1.65e+00 3.67e-01 1.11e+01 angle pdb=" N ILE A 666 " pdb=" CA ILE A 666 " pdb=" C ILE A 666 " ideal model delta sigma weight residual 111.62 109.02 2.60 7.90e-01 1.60e+00 1.08e+01 angle pdb=" CB ASN A1074 " pdb=" CG ASN A1074 " pdb=" ND2 ASN A1074 " ideal model delta sigma weight residual 116.40 121.28 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" CA GLN C 173 " pdb=" CB GLN C 173 " pdb=" CG GLN C 173 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.83e+00 ... (remaining 37702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.03: 16223 25.03 - 50.06: 684 50.06 - 75.09: 96 75.09 - 100.11: 33 100.11 - 125.14: 13 Dihedral angle restraints: 17049 sinusoidal: 7166 harmonic: 9883 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -37.71 -48.29 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -39.75 -46.25 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -40.41 -45.59 1 1.00e+01 1.00e-02 2.88e+01 ... (remaining 17046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4165 0.098 - 0.196: 225 0.196 - 0.294: 5 0.294 - 0.392: 2 0.392 - 0.490: 3 Chirality restraints: 4400 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C1 NAG B1314 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1314 " pdb=" O5 NAG B1314 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 4397 not shown) Planarity restraints: 4874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.058 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO B 987 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1078 " -0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO B1079 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B1079 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B1079 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.023 2.00e-02 2.50e+03 2.15e-02 5.77e+00 pdb=" CG ASN A1074 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.011 2.00e-02 2.50e+03 pdb=" C1 NAG A1314 " -0.019 2.00e-02 2.50e+03 ... (remaining 4871 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 523 2.68 - 3.24: 26134 3.24 - 3.79: 41928 3.79 - 4.35: 56714 4.35 - 4.90: 93737 Nonbonded interactions: 219036 Sorted by model distance: nonbonded pdb=" O GLU B1031 " pdb=" OG SER B1037 " model vdw 2.126 3.040 nonbonded pdb=" O GLY L 36 " pdb=" OH TYR L 87 " model vdw 2.187 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.196 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.204 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.228 3.040 ... (remaining 219031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.010 Normalize map: mean=0, sd=1: 45.200 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: 0.040 Extract box with map and model: 1.180 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 67.740 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.140 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27766 Z= 0.200 Angle : 0.654 16.073 37927 Z= 0.339 Chirality : 0.047 0.490 4400 Planarity : 0.004 0.087 4826 Dihedral : 14.162 125.142 10589 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.07 % Allowed : 0.69 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3357 helix: 1.45 (0.20), residues: 638 sheet: 0.55 (0.18), residues: 838 loop : -0.35 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 56 HIS 0.010 0.001 HIS A1064 PHE 0.025 0.002 PHE C 906 TYR 0.021 0.001 TYR C 170 ARG 0.005 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 48) link_NAG-ASN : angle 3.70270 ( 144) hydrogen bonds : bond 0.21372 ( 1021) hydrogen bonds : angle 8.75830 ( 2883) SS BOND : bond 0.00286 ( 38) SS BOND : angle 0.68672 ( 76) covalent geometry : bond 0.00426 (27680) covalent geometry : angle 0.61345 (37707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 2.840 Fit side-chains REVERT: A 65 PHE cc_start: 0.7277 (m-80) cc_final: 0.6872 (m-80) REVERT: A 663 ASP cc_start: 0.8168 (m-30) cc_final: 0.7786 (m-30) REVERT: A 752 LEU cc_start: 0.8852 (tt) cc_final: 0.8626 (tt) REVERT: A 997 ILE cc_start: 0.9000 (mt) cc_final: 0.8792 (mt) REVERT: B 206 LYS cc_start: 0.7980 (tptp) cc_final: 0.7492 (tptp) REVERT: B 957 GLN cc_start: 0.7997 (tm130) cc_final: 0.7488 (tm-30) REVERT: C 140 PHE cc_start: 0.7164 (p90) cc_final: 0.6845 (p90) REVERT: C 160 TYR cc_start: 0.7772 (p90) cc_final: 0.7428 (p90) REVERT: C 529 LYS cc_start: 0.6964 (tmtt) cc_final: 0.6744 (tmtt) REVERT: C 974 SER cc_start: 0.9130 (t) cc_final: 0.8897 (t) REVERT: H 14 MET cc_start: 0.6561 (ttt) cc_final: 0.5476 (pmm) outliers start: 2 outliers final: 0 residues processed: 229 average time/residue: 0.3342 time to fit residues: 130.2849 Evaluate side-chains 168 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 1.9990 chunk 255 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 87 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 264 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 306 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 370 ASN A1036 GLN A1142 GLN B 239 GLN B 907 ASN B 949 GLN B 957 GLN B 965 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.238081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.172759 restraints weight = 43967.880| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.18 r_work: 0.3615 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27766 Z= 0.137 Angle : 0.617 15.047 37927 Z= 0.298 Chirality : 0.048 0.402 4400 Planarity : 0.004 0.065 4826 Dihedral : 9.017 108.150 4653 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.93 % Allowed : 6.00 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3357 helix: 1.78 (0.20), residues: 643 sheet: 0.59 (0.18), residues: 820 loop : -0.31 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.005 0.001 HIS C1064 PHE 0.022 0.001 PHE B 168 TYR 0.022 0.001 TYR B1067 ARG 0.007 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 48) link_NAG-ASN : angle 3.68192 ( 144) hydrogen bonds : bond 0.04374 ( 1021) hydrogen bonds : angle 6.40454 ( 2883) SS BOND : bond 0.00314 ( 38) SS BOND : angle 0.83656 ( 76) covalent geometry : bond 0.00309 (27680) covalent geometry : angle 0.57402 (37707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7799 (m-80) cc_final: 0.7547 (m-80) REVERT: A 584 ILE cc_start: 0.8919 (mm) cc_final: 0.8597 (mp) REVERT: A 663 ASP cc_start: 0.8461 (m-30) cc_final: 0.8026 (m-30) REVERT: A 752 LEU cc_start: 0.8834 (tt) cc_final: 0.8567 (tt) REVERT: A 868 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7444 (tp30) REVERT: B 931 ILE cc_start: 0.7607 (mm) cc_final: 0.7331 (tp) REVERT: B 957 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 979 ASP cc_start: 0.7588 (t70) cc_final: 0.7299 (t0) REVERT: B 1002 GLN cc_start: 0.8518 (tp40) cc_final: 0.8211 (tp-100) REVERT: C 160 TYR cc_start: 0.7595 (p90) cc_final: 0.7362 (p90) REVERT: C 536 ASN cc_start: 0.8286 (m-40) cc_final: 0.7952 (m-40) REVERT: C 574 ASP cc_start: 0.7135 (t0) cc_final: 0.6918 (t0) REVERT: C 902 MET cc_start: 0.8430 (tpt) cc_final: 0.8214 (tpt) REVERT: H 103 PHE cc_start: 0.5255 (m-80) cc_final: 0.4993 (m-80) outliers start: 27 outliers final: 18 residues processed: 213 average time/residue: 0.3202 time to fit residues: 118.3016 Evaluate side-chains 186 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 336 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 334 optimal weight: 50.0000 chunk 66 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 ASN A 955 ASN A 965 GLN A1054 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 239 GLN B 481 ASN B 804 GLN B 949 GLN B1088 HIS C 146 HIS C 334 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.231518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.166194 restraints weight = 43796.461| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 4.55 r_work: 0.3447 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 27766 Z= 0.369 Angle : 0.776 14.441 37927 Z= 0.378 Chirality : 0.053 0.392 4400 Planarity : 0.005 0.059 4826 Dihedral : 7.687 94.473 4653 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.40 % Allowed : 8.30 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3357 helix: 1.00 (0.19), residues: 644 sheet: 0.16 (0.18), residues: 873 loop : -0.43 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 886 HIS 0.012 0.002 HIS C1064 PHE 0.046 0.003 PHE C 782 TYR 0.038 0.002 TYR A1067 ARG 0.006 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 48) link_NAG-ASN : angle 3.71830 ( 144) hydrogen bonds : bond 0.04784 ( 1021) hydrogen bonds : angle 6.41795 ( 2883) SS BOND : bond 0.00730 ( 38) SS BOND : angle 1.05686 ( 76) covalent geometry : bond 0.00893 (27680) covalent geometry : angle 0.74197 (37707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 191 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7158 (tm-30) REVERT: A 584 ILE cc_start: 0.8884 (mm) cc_final: 0.8536 (mp) REVERT: A 661 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 663 ASP cc_start: 0.8764 (m-30) cc_final: 0.8328 (m-30) REVERT: A 988 GLU cc_start: 0.8355 (mp0) cc_final: 0.8094 (mp0) REVERT: B 52 GLN cc_start: 0.7600 (tp40) cc_final: 0.7304 (tp40) REVERT: B 104 TRP cc_start: 0.6756 (m-90) cc_final: 0.6490 (m-90) REVERT: B 271 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: B 577 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6963 (ttm170) REVERT: B 723 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8566 (p) REVERT: B 904 TYR cc_start: 0.8213 (m-10) cc_final: 0.7331 (m-10) REVERT: B 957 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 979 ASP cc_start: 0.8030 (t70) cc_final: 0.7667 (t0) REVERT: B 1002 GLN cc_start: 0.8690 (tp40) cc_final: 0.8408 (tp-100) REVERT: B 1029 MET cc_start: 0.8410 (tpp) cc_final: 0.7961 (ttm) REVERT: C 160 TYR cc_start: 0.7695 (p90) cc_final: 0.7411 (p90) REVERT: C 536 ASN cc_start: 0.8446 (m-40) cc_final: 0.8090 (m110) REVERT: C 745 ASP cc_start: 0.8378 (m-30) cc_final: 0.7689 (t0) REVERT: H 103 PHE cc_start: 0.5354 (m-80) cc_final: 0.5089 (m-80) REVERT: L 11 MET cc_start: 0.2573 (ppp) cc_final: 0.2143 (ppp) outliers start: 70 outliers final: 49 residues processed: 239 average time/residue: 0.3197 time to fit residues: 131.0664 Evaluate side-chains 222 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 8 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 289 optimal weight: 0.6980 chunk 315 optimal weight: 50.0000 chunk 78 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 641 ASN B 762 GLN B 913 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.217526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.131361 restraints weight = 42937.563| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.89 r_work: 0.3581 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27766 Z= 0.122 Angle : 0.594 14.158 37927 Z= 0.285 Chirality : 0.047 0.428 4400 Planarity : 0.004 0.054 4826 Dihedral : 6.917 84.851 4653 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.71 % Allowed : 10.73 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3357 helix: 1.76 (0.20), residues: 647 sheet: 0.25 (0.18), residues: 834 loop : -0.37 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP L 56 HIS 0.005 0.001 HIS B1083 PHE 0.023 0.002 PHE A 65 TYR 0.019 0.001 TYR C 170 ARG 0.003 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 48) link_NAG-ASN : angle 3.46194 ( 144) hydrogen bonds : bond 0.03730 ( 1021) hydrogen bonds : angle 5.78595 ( 2883) SS BOND : bond 0.00258 ( 38) SS BOND : angle 0.93282 ( 76) covalent geometry : bond 0.00276 (27680) covalent geometry : angle 0.55463 (37707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8575 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 584 ILE cc_start: 0.8831 (mm) cc_final: 0.8499 (mp) REVERT: A 663 ASP cc_start: 0.8639 (m-30) cc_final: 0.8127 (m-30) REVERT: A 804 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: A 868 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7355 (tp30) REVERT: A 988 GLU cc_start: 0.8505 (mp0) cc_final: 0.8171 (mp0) REVERT: B 104 TRP cc_start: 0.6691 (m-90) cc_final: 0.6314 (m-90) REVERT: B 170 TYR cc_start: 0.8066 (t80) cc_final: 0.7822 (t80) REVERT: B 202 LYS cc_start: 0.7204 (mtmt) cc_final: 0.6854 (mtpp) REVERT: B 957 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 979 ASP cc_start: 0.8118 (t70) cc_final: 0.7785 (t0) REVERT: B 1002 GLN cc_start: 0.8660 (tp40) cc_final: 0.8335 (tp-100) REVERT: B 1029 MET cc_start: 0.8347 (tpp) cc_final: 0.8013 (ttm) REVERT: C 84 LEU cc_start: 0.7291 (mt) cc_final: 0.7064 (mp) REVERT: C 129 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7541 (tppp) REVERT: C 160 TYR cc_start: 0.7703 (p90) cc_final: 0.7372 (p90) REVERT: C 536 ASN cc_start: 0.8491 (m-40) cc_final: 0.8090 (m110) REVERT: C 723 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8358 (p) REVERT: C 745 ASP cc_start: 0.8408 (m-30) cc_final: 0.7628 (t0) REVERT: H 103 PHE cc_start: 0.5399 (m-80) cc_final: 0.5093 (m-80) REVERT: L 11 MET cc_start: 0.2581 (ppp) cc_final: 0.2251 (ppp) outliers start: 50 outliers final: 24 residues processed: 226 average time/residue: 0.3328 time to fit residues: 129.7068 Evaluate side-chains 197 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 265 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 160 optimal weight: 7.9990 chunk 280 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 152 optimal weight: 30.0000 chunk 199 optimal weight: 3.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 762 GLN B 856 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.214880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.142135 restraints weight = 42569.931| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 4.42 r_work: 0.3469 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27766 Z= 0.223 Angle : 0.643 13.520 37927 Z= 0.309 Chirality : 0.049 0.413 4400 Planarity : 0.004 0.054 4826 Dihedral : 6.706 76.537 4653 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.19 % Allowed : 11.32 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3357 helix: 1.61 (0.20), residues: 646 sheet: 0.18 (0.18), residues: 827 loop : -0.41 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP L 56 HIS 0.005 0.001 HIS A1064 PHE 0.026 0.002 PHE C1089 TYR 0.025 0.001 TYR A1067 ARG 0.004 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 48) link_NAG-ASN : angle 3.46887 ( 144) hydrogen bonds : bond 0.03911 ( 1021) hydrogen bonds : angle 5.83393 ( 2883) SS BOND : bond 0.00429 ( 38) SS BOND : angle 1.22498 ( 76) covalent geometry : bond 0.00538 (27680) covalent geometry : angle 0.60609 (37707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 182 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7220 (tm-30) REVERT: A 314 GLN cc_start: 0.8528 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 584 ILE cc_start: 0.8832 (mm) cc_final: 0.8509 (mp) REVERT: A 661 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 663 ASP cc_start: 0.8705 (m-30) cc_final: 0.8165 (m-30) REVERT: A 988 GLU cc_start: 0.8437 (mp0) cc_final: 0.8131 (mp0) REVERT: B 52 GLN cc_start: 0.7545 (tp40) cc_final: 0.7244 (tp40) REVERT: B 58 PHE cc_start: 0.8854 (m-10) cc_final: 0.8636 (m-10) REVERT: B 104 TRP cc_start: 0.6723 (m-90) cc_final: 0.6366 (m-90) REVERT: B 957 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 979 ASP cc_start: 0.8122 (t70) cc_final: 0.7791 (t0) REVERT: B 1002 GLN cc_start: 0.8591 (tp40) cc_final: 0.8241 (tp-100) REVERT: B 1029 MET cc_start: 0.8314 (tpp) cc_final: 0.7901 (ttm) REVERT: C 129 LYS cc_start: 0.7590 (ttmt) cc_final: 0.7355 (tppp) REVERT: C 160 TYR cc_start: 0.7784 (p90) cc_final: 0.7446 (p90) REVERT: C 536 ASN cc_start: 0.8451 (m-40) cc_final: 0.8072 (m110) REVERT: C 692 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8499 (mm) REVERT: C 745 ASP cc_start: 0.8437 (m-30) cc_final: 0.7635 (t0) REVERT: H 55 GLU cc_start: 0.8031 (pt0) cc_final: 0.7735 (pp20) REVERT: H 103 PHE cc_start: 0.5563 (m-80) cc_final: 0.5261 (m-80) REVERT: L 11 MET cc_start: 0.2442 (ppp) cc_final: 0.2033 (ppp) outliers start: 64 outliers final: 46 residues processed: 227 average time/residue: 0.3217 time to fit residues: 127.7289 Evaluate side-chains 220 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 56 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 336 optimal weight: 40.0000 chunk 173 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 40.0000 chunk 102 optimal weight: 0.9990 chunk 330 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 269 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 762 GLN B 856 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.217183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.130556 restraints weight = 42568.128| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.88 r_work: 0.3591 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27766 Z= 0.132 Angle : 0.582 13.447 37927 Z= 0.278 Chirality : 0.047 0.421 4400 Planarity : 0.004 0.052 4826 Dihedral : 6.295 70.956 4653 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.13 % Allowed : 11.76 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3357 helix: 1.84 (0.20), residues: 640 sheet: 0.21 (0.17), residues: 829 loop : -0.42 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP L 56 HIS 0.005 0.001 HIS A1048 PHE 0.024 0.001 PHE C 140 TYR 0.020 0.001 TYR C 170 ARG 0.003 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 48) link_NAG-ASN : angle 3.44913 ( 144) hydrogen bonds : bond 0.03523 ( 1021) hydrogen bonds : angle 5.56800 ( 2883) SS BOND : bond 0.00405 ( 38) SS BOND : angle 1.18517 ( 76) covalent geometry : bond 0.00310 (27680) covalent geometry : angle 0.54096 (37707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 443 SER cc_start: 0.4809 (OUTLIER) cc_final: 0.4493 (t) REVERT: A 584 ILE cc_start: 0.8823 (mm) cc_final: 0.8501 (mp) REVERT: A 661 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7920 (mt-10) REVERT: A 663 ASP cc_start: 0.8708 (m-30) cc_final: 0.8199 (m-30) REVERT: A 868 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7310 (tp30) REVERT: A 988 GLU cc_start: 0.8454 (mp0) cc_final: 0.8164 (mp0) REVERT: B 52 GLN cc_start: 0.7595 (tp40) cc_final: 0.7216 (tp40) REVERT: B 104 TRP cc_start: 0.6642 (m-90) cc_final: 0.6203 (m-90) REVERT: B 170 TYR cc_start: 0.7912 (t80) cc_final: 0.7652 (t80) REVERT: B 202 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6695 (mtpp) REVERT: B 726 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8529 (mm) REVERT: B 957 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8098 (tm-30) REVERT: B 979 ASP cc_start: 0.8216 (t70) cc_final: 0.7901 (t0) REVERT: B 1002 GLN cc_start: 0.8657 (tp40) cc_final: 0.8325 (tp-100) REVERT: B 1029 MET cc_start: 0.8415 (tpp) cc_final: 0.7992 (ttm) REVERT: C 129 LYS cc_start: 0.7633 (ttmt) cc_final: 0.7389 (tppp) REVERT: C 160 TYR cc_start: 0.7776 (p90) cc_final: 0.7401 (p90) REVERT: C 536 ASN cc_start: 0.8498 (m-40) cc_final: 0.8142 (m110) REVERT: C 723 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8353 (p) REVERT: C 752 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8800 (tt) REVERT: C 767 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8377 (mm) REVERT: C 855 PHE cc_start: 0.7420 (m-80) cc_final: 0.7207 (m-80) REVERT: H 103 PHE cc_start: 0.5457 (m-80) cc_final: 0.5144 (m-80) REVERT: L 11 MET cc_start: 0.2296 (ppp) cc_final: 0.1986 (ppp) outliers start: 62 outliers final: 36 residues processed: 237 average time/residue: 0.3258 time to fit residues: 134.2761 Evaluate side-chains 216 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 56 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 251 optimal weight: 50.0000 chunk 13 optimal weight: 0.9980 chunk 277 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 308 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.217222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.130628 restraints weight = 42599.895| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.86 r_work: 0.3569 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27766 Z= 0.134 Angle : 0.585 13.496 37927 Z= 0.280 Chirality : 0.047 0.415 4400 Planarity : 0.003 0.052 4826 Dihedral : 6.186 67.372 4653 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.13 % Allowed : 12.24 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3357 helix: 1.82 (0.20), residues: 645 sheet: 0.20 (0.17), residues: 839 loop : -0.40 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP L 56 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.001 PHE C 140 TYR 0.018 0.001 TYR A1067 ARG 0.002 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 48) link_NAG-ASN : angle 3.38595 ( 144) hydrogen bonds : bond 0.03524 ( 1021) hydrogen bonds : angle 5.50297 ( 2883) SS BOND : bond 0.00274 ( 38) SS BOND : angle 1.29441 ( 76) covalent geometry : bond 0.00317 (27680) covalent geometry : angle 0.54492 (37707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8115 (tm-30) REVERT: A 443 SER cc_start: 0.4864 (OUTLIER) cc_final: 0.4534 (t) REVERT: A 584 ILE cc_start: 0.8827 (mm) cc_final: 0.8510 (mp) REVERT: A 661 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7918 (mt-10) REVERT: A 663 ASP cc_start: 0.8728 (m-30) cc_final: 0.8236 (m-30) REVERT: A 868 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7303 (tp30) REVERT: B 52 GLN cc_start: 0.7598 (tp40) cc_final: 0.7199 (tp40) REVERT: B 104 TRP cc_start: 0.6650 (m-90) cc_final: 0.6225 (m-90) REVERT: B 170 TYR cc_start: 0.7975 (t80) cc_final: 0.7681 (t80) REVERT: B 202 LYS cc_start: 0.7186 (mtmt) cc_final: 0.6806 (mtpp) REVERT: B 726 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8532 (mm) REVERT: B 957 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 979 ASP cc_start: 0.8223 (t70) cc_final: 0.7963 (t0) REVERT: B 1002 GLN cc_start: 0.8660 (tp40) cc_final: 0.8330 (tp-100) REVERT: B 1029 MET cc_start: 0.8371 (tpp) cc_final: 0.7961 (ttm) REVERT: C 160 TYR cc_start: 0.7723 (p90) cc_final: 0.7394 (p90) REVERT: C 536 ASN cc_start: 0.8466 (m-40) cc_final: 0.8094 (m110) REVERT: C 723 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8339 (p) REVERT: C 752 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8788 (tt) REVERT: C 767 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8357 (mm) REVERT: H 55 GLU cc_start: 0.8099 (pt0) cc_final: 0.7732 (pp20) REVERT: H 103 PHE cc_start: 0.5465 (m-80) cc_final: 0.5126 (m-80) REVERT: L 11 MET cc_start: 0.2394 (ppp) cc_final: 0.2168 (ppp) REVERT: L 56 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.7056 (m-90) outliers start: 62 outliers final: 44 residues processed: 225 average time/residue: 0.3146 time to fit residues: 123.4214 Evaluate side-chains 221 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 56 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 321 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 138 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 965 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 856 ASN B 901 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN L 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.215931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.128780 restraints weight = 42375.111| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.85 r_work: 0.3537 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27766 Z= 0.182 Angle : 0.609 13.721 37927 Z= 0.292 Chirality : 0.048 0.406 4400 Planarity : 0.004 0.052 4826 Dihedral : 6.178 64.866 4653 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.33 % Allowed : 12.38 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3357 helix: 1.75 (0.20), residues: 650 sheet: 0.18 (0.18), residues: 829 loop : -0.40 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP L 56 HIS 0.004 0.001 HIS B1083 PHE 0.026 0.002 PHE B 168 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 48) link_NAG-ASN : angle 3.41143 ( 144) hydrogen bonds : bond 0.03626 ( 1021) hydrogen bonds : angle 5.54011 ( 2883) SS BOND : bond 0.00321 ( 38) SS BOND : angle 1.11896 ( 76) covalent geometry : bond 0.00440 (27680) covalent geometry : angle 0.57094 (37707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 443 SER cc_start: 0.4845 (OUTLIER) cc_final: 0.4519 (t) REVERT: A 661 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7944 (mt-10) REVERT: A 663 ASP cc_start: 0.8736 (m-30) cc_final: 0.8223 (m-30) REVERT: A 868 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7316 (tp30) REVERT: A 965 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.9109 (tp40) REVERT: A 988 GLU cc_start: 0.8500 (mp0) cc_final: 0.8176 (mp0) REVERT: B 52 GLN cc_start: 0.7552 (tp40) cc_final: 0.7141 (tp40) REVERT: B 83 VAL cc_start: 0.6779 (OUTLIER) cc_final: 0.6474 (p) REVERT: B 104 TRP cc_start: 0.6752 (m-90) cc_final: 0.6382 (m-90) REVERT: B 170 TYR cc_start: 0.8048 (t80) cc_final: 0.7808 (t80) REVERT: B 202 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6912 (mtpp) REVERT: B 592 PHE cc_start: 0.8398 (p90) cc_final: 0.8154 (p90) REVERT: B 726 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8556 (mm) REVERT: B 957 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8152 (tm-30) REVERT: B 979 ASP cc_start: 0.8283 (t70) cc_final: 0.8024 (t0) REVERT: B 1002 GLN cc_start: 0.8688 (tp40) cc_final: 0.8357 (tp-100) REVERT: B 1029 MET cc_start: 0.8372 (tpp) cc_final: 0.7970 (ttm) REVERT: C 129 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7571 (tppp) REVERT: C 160 TYR cc_start: 0.7729 (p90) cc_final: 0.7408 (p90) REVERT: C 536 ASN cc_start: 0.8491 (m-40) cc_final: 0.8130 (m110) REVERT: C 692 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8543 (mm) REVERT: C 723 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8355 (p) REVERT: C 752 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8807 (tt) REVERT: C 767 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8417 (mm) REVERT: C 913 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: C 1089 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: H 55 GLU cc_start: 0.8077 (pt0) cc_final: 0.7737 (pp20) REVERT: H 103 PHE cc_start: 0.5626 (m-80) cc_final: 0.5345 (m-80) REVERT: L 11 MET cc_start: 0.2253 (ppp) cc_final: 0.2037 (ppp) outliers start: 68 outliers final: 51 residues processed: 228 average time/residue: 0.3326 time to fit residues: 131.7895 Evaluate side-chains 232 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 56 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 154 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 170 optimal weight: 0.5980 chunk 331 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 901 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.217622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.131228 restraints weight = 42651.346| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.87 r_work: 0.3587 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27766 Z= 0.119 Angle : 0.575 13.705 37927 Z= 0.275 Chirality : 0.046 0.413 4400 Planarity : 0.003 0.051 4826 Dihedral : 6.052 62.868 4653 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.09 % Allowed : 12.69 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3357 helix: 1.84 (0.20), residues: 653 sheet: 0.18 (0.17), residues: 830 loop : -0.36 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP L 56 HIS 0.005 0.001 HIS A1048 PHE 0.022 0.001 PHE A 92 TYR 0.017 0.001 TYR A1067 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 48) link_NAG-ASN : angle 3.35477 ( 144) hydrogen bonds : bond 0.03418 ( 1021) hydrogen bonds : angle 5.39228 ( 2883) SS BOND : bond 0.00229 ( 38) SS BOND : angle 1.01584 ( 76) covalent geometry : bond 0.00276 (27680) covalent geometry : angle 0.53579 (37707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8125 (tm-30) REVERT: A 443 SER cc_start: 0.4870 (OUTLIER) cc_final: 0.4542 (t) REVERT: A 661 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7914 (mt-10) REVERT: A 663 ASP cc_start: 0.8717 (m-30) cc_final: 0.8225 (m-30) REVERT: A 868 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7364 (tp30) REVERT: B 52 GLN cc_start: 0.7511 (tp40) cc_final: 0.7189 (tp40) REVERT: B 104 TRP cc_start: 0.6679 (m-90) cc_final: 0.6239 (m-90) REVERT: B 168 PHE cc_start: 0.8580 (t80) cc_final: 0.8082 (t80) REVERT: B 170 TYR cc_start: 0.8010 (t80) cc_final: 0.7783 (t80) REVERT: B 202 LYS cc_start: 0.7116 (mtmt) cc_final: 0.6754 (mtpp) REVERT: B 592 PHE cc_start: 0.8334 (p90) cc_final: 0.8121 (p90) REVERT: B 619 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8249 (tp30) REVERT: B 726 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8560 (mm) REVERT: B 901 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7928 (tm130) REVERT: B 957 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8062 (tm-30) REVERT: B 979 ASP cc_start: 0.8274 (t70) cc_final: 0.8024 (t0) REVERT: B 1002 GLN cc_start: 0.8638 (tp40) cc_final: 0.8288 (tp-100) REVERT: B 1029 MET cc_start: 0.8353 (tpp) cc_final: 0.7973 (ttm) REVERT: C 129 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7560 (tppp) REVERT: C 160 TYR cc_start: 0.7727 (p90) cc_final: 0.7436 (p90) REVERT: C 536 ASN cc_start: 0.8476 (m-40) cc_final: 0.8092 (m110) REVERT: C 723 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8330 (p) REVERT: C 752 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8748 (tt) REVERT: C 767 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8294 (mm) REVERT: C 913 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: H 55 GLU cc_start: 0.8057 (pt0) cc_final: 0.7717 (pp20) REVERT: H 64 TYR cc_start: 0.5409 (t80) cc_final: 0.4894 (t80) REVERT: H 103 PHE cc_start: 0.5629 (m-80) cc_final: 0.5337 (m-80) REVERT: L 11 MET cc_start: 0.2300 (ppp) cc_final: 0.1880 (ppp) outliers start: 61 outliers final: 46 residues processed: 222 average time/residue: 0.3247 time to fit residues: 126.2443 Evaluate side-chains 221 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 56 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 283 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 112 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 965 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 856 ASN B 901 GLN B1011 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** 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 = 0.4727 r_free = 0.4727 target = 0.215141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.127559 restraints weight = 42412.503| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.85 r_work: 0.3517 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 27766 Z= 0.213 Angle : 0.627 13.648 37927 Z= 0.303 Chirality : 0.048 0.396 4400 Planarity : 0.004 0.052 4826 Dihedral : 6.148 62.079 4653 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 12.79 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3357 helix: 1.68 (0.20), residues: 647 sheet: 0.15 (0.18), residues: 831 loop : -0.42 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 56 HIS 0.005 0.001 HIS B1064 PHE 0.037 0.002 PHE B 238 TYR 0.025 0.001 TYR A1067 ARG 0.003 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 48) link_NAG-ASN : angle 3.39783 ( 144) hydrogen bonds : bond 0.03669 ( 1021) hydrogen bonds : angle 5.55745 ( 2883) SS BOND : bond 0.00349 ( 38) SS BOND : angle 1.18005 ( 76) covalent geometry : bond 0.00519 (27680) covalent geometry : angle 0.59087 (37707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 443 SER cc_start: 0.4819 (OUTLIER) cc_final: 0.4497 (t) REVERT: A 661 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7987 (mt-10) REVERT: A 663 ASP cc_start: 0.8807 (m-30) cc_final: 0.8284 (m-30) REVERT: A 868 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7328 (tp30) REVERT: B 52 GLN cc_start: 0.7536 (tp40) cc_final: 0.7208 (tp40) REVERT: B 104 TRP cc_start: 0.6644 (m-90) cc_final: 0.6277 (m-90) REVERT: B 170 TYR cc_start: 0.8014 (t80) cc_final: 0.7772 (t80) REVERT: B 202 LYS cc_start: 0.7304 (mtmt) cc_final: 0.6908 (mtpp) REVERT: B 592 PHE cc_start: 0.8371 (p90) cc_final: 0.8170 (p90) REVERT: B 619 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8389 (tp30) REVERT: B 726 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8565 (mm) REVERT: B 957 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 979 ASP cc_start: 0.8343 (t70) cc_final: 0.8097 (t0) REVERT: B 1002 GLN cc_start: 0.8715 (tp40) cc_final: 0.8374 (tp-100) REVERT: B 1029 MET cc_start: 0.8361 (tpp) cc_final: 0.7928 (ttm) REVERT: C 129 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7641 (tppp) REVERT: C 160 TYR cc_start: 0.7651 (p90) cc_final: 0.7358 (p90) REVERT: C 536 ASN cc_start: 0.8520 (m-40) cc_final: 0.8166 (m110) REVERT: C 752 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8830 (tt) REVERT: C 767 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8470 (mm) REVERT: C 913 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: H 55 GLU cc_start: 0.8038 (pt0) cc_final: 0.7677 (pp20) REVERT: H 64 TYR cc_start: 0.5307 (t80) cc_final: 0.4802 (t80) REVERT: H 103 PHE cc_start: 0.5673 (m-80) cc_final: 0.5381 (m-80) REVERT: L 4 MET cc_start: 0.5129 (mmp) cc_final: 0.4855 (tpp) REVERT: L 11 MET cc_start: 0.2293 (ppp) cc_final: 0.1997 (ppp) REVERT: L 56 TRP cc_start: 0.7525 (OUTLIER) cc_final: 0.7301 (m-90) outliers start: 65 outliers final: 51 residues processed: 228 average time/residue: 0.3141 time to fit residues: 124.7756 Evaluate side-chains 231 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 173 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 56 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 0.4980 chunk 334 optimal weight: 8.9990 chunk 136 optimal weight: 40.0000 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 321 optimal weight: 5.9990 chunk 257 optimal weight: 40.0000 chunk 75 optimal weight: 0.9990 chunk 252 optimal weight: 30.0000 chunk 187 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 856 ASN B 901 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.216740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.130217 restraints weight = 42537.909| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.85 r_work: 0.3572 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27766 Z= 0.135 Angle : 0.584 13.575 37927 Z= 0.279 Chirality : 0.047 0.404 4400 Planarity : 0.004 0.051 4826 Dihedral : 6.015 59.845 4653 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.92 % Allowed : 13.20 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3357 helix: 1.77 (0.20), residues: 653 sheet: 0.17 (0.18), residues: 823 loop : -0.36 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 56 HIS 0.005 0.001 HIS A1048 PHE 0.033 0.001 PHE B 238 TYR 0.019 0.001 TYR A1067 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 48) link_NAG-ASN : angle 3.41247 ( 144) hydrogen bonds : bond 0.03414 ( 1021) hydrogen bonds : angle 5.38885 ( 2883) SS BOND : bond 0.00242 ( 38) SS BOND : angle 1.07857 ( 76) covalent geometry : bond 0.00321 (27680) covalent geometry : angle 0.54381 (37707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24183.53 seconds wall clock time: 418 minutes 0.44 seconds (25080.44 seconds total)