Starting phenix.real_space_refine on Fri Mar 6 02:00:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz5_26879/03_2026/7uz5_26879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz5_26879/03_2026/7uz5_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_26879/03_2026/7uz5_26879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz5_26879/03_2026/7uz5_26879.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz5_26879/03_2026/7uz5_26879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz5_26879/03_2026/7uz5_26879.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} 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, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} 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, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} 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: 6.01, per 1000 atoms: 0.22 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 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: 1.23 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: 6.85 Time building geometry restraints manager: 2.97 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: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.090 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- 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 : 9.51 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 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 ARG 0.005 0.000 ARG C 815 TYR 0.021 0.001 TYR C 170 PHE 0.025 0.002 PHE C 906 TRP 0.027 0.001 TRP L 56 HIS 0.010 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00426 (27680) covalent geometry : angle 0.61345 (37707) SS BOND : bond 0.00286 ( 38) SS BOND : angle 0.68672 ( 76) hydrogen bonds : bond 0.21372 ( 1021) hydrogen bonds : angle 8.75830 ( 2883) link_NAG-ASN : bond 0.00849 ( 48) link_NAG-ASN : angle 3.70270 ( 144) *********************** 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 : 1.185 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: 0.6942 (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: 0.1588 time to fit residues: 62.4123 Evaluate side-chains 167 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0270 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.6242 ------------------------------------------------------------------------------- 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 ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 239 GLN B 856 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.238938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.173193 restraints weight = 44200.477| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.10 r_work: 0.3641 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27766 Z= 0.122 Angle : 0.605 15.043 37927 Z= 0.292 Chirality : 0.047 0.411 4400 Planarity : 0.004 0.065 4826 Dihedral : 8.957 108.619 4653 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.79 % Allowed : 5.83 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3357 helix: 1.82 (0.20), residues: 648 sheet: 0.59 (0.18), residues: 820 loop : -0.29 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.001 PHE B 168 TRP 0.021 0.001 TRP C 104 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00266 (27680) covalent geometry : angle 0.56135 (37707) SS BOND : bond 0.00218 ( 38) SS BOND : angle 0.83441 ( 76) hydrogen bonds : bond 0.04555 ( 1021) hydrogen bonds : angle 6.38683 ( 2883) link_NAG-ASN : bond 0.00688 ( 48) link_NAG-ASN : angle 3.66398 ( 144) *********************** 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 224 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7830 (m-80) cc_final: 0.7598 (m-80) REVERT: A 584 ILE cc_start: 0.8911 (mm) cc_final: 0.8587 (mp) REVERT: A 663 ASP cc_start: 0.8439 (m-30) cc_final: 0.8023 (m-30) REVERT: A 752 LEU cc_start: 0.8834 (tt) cc_final: 0.8579 (tt) REVERT: A 868 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7388 (tp30) REVERT: A 950 ASP cc_start: 0.8579 (t0) cc_final: 0.8197 (t0) REVERT: B 931 ILE cc_start: 0.7566 (mm) cc_final: 0.7245 (tp) REVERT: B 957 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 979 ASP cc_start: 0.7552 (t70) cc_final: 0.7259 (t0) REVERT: B 1002 GLN cc_start: 0.8488 (tp40) cc_final: 0.8175 (tp-100) REVERT: C 160 TYR cc_start: 0.7570 (p90) cc_final: 0.7342 (p90) REVERT: C 536 ASN cc_start: 0.8224 (m-40) cc_final: 0.7886 (m-40) REVERT: H 103 PHE cc_start: 0.5257 (m-80) cc_final: 0.4864 (m-80) outliers start: 23 outliers final: 15 residues processed: 212 average time/residue: 0.1538 time to fit residues: 56.8446 Evaluate side-chains 186 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 152 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 31 optimal weight: 20.0000 chunk 200 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 334 optimal weight: 50.0000 chunk 138 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 A1054 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 481 ASN B 804 GLN B 856 ASN C 146 HIS ** 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** L 8 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.237074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.173308 restraints weight = 44057.542| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.43 r_work: 0.3571 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27766 Z= 0.156 Angle : 0.591 14.387 37927 Z= 0.285 Chirality : 0.047 0.418 4400 Planarity : 0.004 0.059 4826 Dihedral : 7.372 101.064 4653 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.27 % Allowed : 8.37 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3357 helix: 1.84 (0.20), residues: 654 sheet: 0.55 (0.18), residues: 813 loop : -0.28 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.021 0.001 TYR A1067 PHE 0.022 0.001 PHE C 140 TRP 0.009 0.001 TRP B 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00371 (27680) covalent geometry : angle 0.55239 (37707) SS BOND : bond 0.00297 ( 38) SS BOND : angle 0.70653 ( 76) hydrogen bonds : bond 0.03959 ( 1021) hydrogen bonds : angle 5.93472 ( 2883) link_NAG-ASN : bond 0.00614 ( 48) link_NAG-ASN : angle 3.42187 ( 144) *********************** 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 223 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8872 (mm) cc_final: 0.8551 (mp) REVERT: A 614 ASP cc_start: 0.7784 (m-30) cc_final: 0.7530 (p0) REVERT: A 663 ASP cc_start: 0.8542 (m-30) cc_final: 0.8068 (m-30) REVERT: A 752 LEU cc_start: 0.8800 (tt) cc_final: 0.8511 (tt) REVERT: A 868 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7337 (tp30) REVERT: B 52 GLN cc_start: 0.7619 (tp40) cc_final: 0.7381 (tp40) REVERT: B 957 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 979 ASP cc_start: 0.7724 (t70) cc_final: 0.7356 (t0) REVERT: B 994 ASP cc_start: 0.8838 (t0) cc_final: 0.8578 (t70) REVERT: B 1002 GLN cc_start: 0.8533 (tp40) cc_final: 0.8213 (tp-100) REVERT: C 160 TYR cc_start: 0.7604 (p90) cc_final: 0.7384 (p90) REVERT: C 536 ASN cc_start: 0.8305 (m-40) cc_final: 0.7980 (m-40) REVERT: C 895 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: H 103 PHE cc_start: 0.5389 (m-80) cc_final: 0.5095 (m-80) outliers start: 37 outliers final: 27 residues processed: 206 average time/residue: 0.1446 time to fit residues: 52.0242 Evaluate side-chains 191 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 911 VAL 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 911 VAL 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 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 747 THR 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 L residue 8 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 168 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 255 optimal weight: 40.0000 chunk 309 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 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 370 ASN A 965 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 856 ASN B 949 GLN B1088 HIS C 334 ASN ** 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 926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.231509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.168868 restraints weight = 43734.141| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 3.81 r_work: 0.3458 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 27766 Z= 0.360 Angle : 0.765 14.721 37927 Z= 0.373 Chirality : 0.053 0.398 4400 Planarity : 0.005 0.056 4826 Dihedral : 7.329 85.551 4653 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.71 % Allowed : 9.53 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.14), residues: 3357 helix: 1.14 (0.19), residues: 645 sheet: 0.10 (0.17), residues: 867 loop : -0.41 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 408 TYR 0.038 0.002 TYR A1067 PHE 0.041 0.003 PHE C1089 TRP 0.054 0.002 TRP L 56 HIS 0.010 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00865 (27680) covalent geometry : angle 0.73039 (37707) SS BOND : bond 0.01079 ( 38) SS BOND : angle 1.29573 ( 76) hydrogen bonds : bond 0.04559 ( 1021) hydrogen bonds : angle 6.22253 ( 2883) link_NAG-ASN : bond 0.00634 ( 48) link_NAG-ASN : angle 3.67001 ( 144) *********************** 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 260 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 181 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 584 ILE cc_start: 0.8843 (mm) cc_final: 0.8499 (mp) REVERT: A 661 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 663 ASP cc_start: 0.8746 (m-30) cc_final: 0.8238 (m-30) REVERT: A 988 GLU cc_start: 0.8384 (mp0) cc_final: 0.8121 (mp0) REVERT: B 52 GLN cc_start: 0.7536 (tp40) cc_final: 0.7287 (tp40) REVERT: B 104 TRP cc_start: 0.6824 (m-90) cc_final: 0.6564 (m-90) REVERT: B 577 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.7019 (ttm170) REVERT: B 957 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8183 (tm-30) REVERT: B 979 ASP cc_start: 0.8092 (t70) cc_final: 0.7717 (t0) REVERT: B 994 ASP cc_start: 0.9082 (t0) cc_final: 0.8863 (t0) REVERT: B 1002 GLN cc_start: 0.8672 (tp40) cc_final: 0.8370 (tp-100) REVERT: B 1029 MET cc_start: 0.8380 (tpp) cc_final: 0.7952 (ttm) REVERT: C 160 TYR cc_start: 0.7654 (p90) cc_final: 0.7369 (p90) REVERT: C 536 ASN cc_start: 0.8462 (m-40) cc_final: 0.8119 (m110) REVERT: C 745 ASP cc_start: 0.8344 (m-30) cc_final: 0.7678 (t0) REVERT: C 957 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8499 (tm-30) REVERT: H 103 PHE cc_start: 0.5364 (m-80) cc_final: 0.5080 (m-80) REVERT: L 11 MET cc_start: 0.2739 (ppp) cc_final: 0.2407 (ppp) REVERT: L 56 TRP cc_start: 0.7514 (OUTLIER) cc_final: 0.6822 (m-90) outliers start: 79 outliers final: 58 residues processed: 240 average time/residue: 0.1529 time to fit residues: 63.6872 Evaluate side-chains 228 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 153 MET 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 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 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 577 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 859 THR 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 934 ILE 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 1040 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 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL 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 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 974 SER 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 56 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 312 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 321 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 170 optimal weight: 0.6980 chunk 313 optimal weight: 0.8980 chunk 224 optimal weight: 7.9990 chunk 291 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 913 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 317 ASN B 762 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** ** 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 = 0.4748 r_free = 0.4748 target = 0.217271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.131058 restraints weight = 42471.359| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.86 r_work: 0.3569 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27766 Z= 0.124 Angle : 0.598 14.131 37927 Z= 0.286 Chirality : 0.047 0.432 4400 Planarity : 0.004 0.053 4826 Dihedral : 6.685 73.959 4653 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.51 % Allowed : 11.42 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3357 helix: 1.73 (0.20), residues: 654 sheet: 0.23 (0.18), residues: 830 loop : -0.36 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.018 0.001 TYR A1067 PHE 0.024 0.001 PHE C 140 TRP 0.038 0.001 TRP L 56 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00284 (27680) covalent geometry : angle 0.55853 (37707) SS BOND : bond 0.00332 ( 38) SS BOND : angle 1.04989 ( 76) hydrogen bonds : bond 0.03647 ( 1021) hydrogen bonds : angle 5.68365 ( 2883) link_NAG-ASN : bond 0.00629 ( 48) link_NAG-ASN : angle 3.46650 ( 144) *********************** 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 244 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8554 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 584 ILE cc_start: 0.8814 (mm) cc_final: 0.8490 (mp) REVERT: A 663 ASP cc_start: 0.8647 (m-30) cc_final: 0.8132 (m-30) REVERT: A 804 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: A 868 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7443 (tp30) REVERT: A 902 MET cc_start: 0.8459 (tpp) cc_final: 0.8053 (tpp) REVERT: A 988 GLU cc_start: 0.8486 (mp0) cc_final: 0.8171 (mp0) REVERT: B 52 GLN cc_start: 0.7599 (tp40) cc_final: 0.7238 (tp40) REVERT: B 104 TRP cc_start: 0.6705 (m-90) cc_final: 0.6311 (m-90) REVERT: B 202 LYS cc_start: 0.7219 (mtmt) cc_final: 0.6868 (mtpp) REVERT: B 913 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: B 957 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 979 ASP cc_start: 0.8167 (t70) cc_final: 0.7820 (t0) REVERT: B 994 ASP cc_start: 0.8953 (t0) cc_final: 0.8752 (t0) REVERT: B 1002 GLN cc_start: 0.8673 (tp40) cc_final: 0.8350 (tp-100) REVERT: B 1029 MET cc_start: 0.8337 (tpp) cc_final: 0.8041 (ttm) REVERT: C 129 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7518 (tppp) REVERT: C 160 TYR cc_start: 0.7698 (p90) cc_final: 0.7352 (p90) REVERT: C 536 ASN cc_start: 0.8490 (m-40) cc_final: 0.8116 (m110) REVERT: C 723 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8384 (p) REVERT: C 745 ASP cc_start: 0.8421 (m-30) cc_final: 0.7627 (t0) REVERT: H 55 GLU cc_start: 0.8105 (pt0) cc_final: 0.7825 (pp20) REVERT: H 89 MET cc_start: -0.2142 (tpp) cc_final: -0.2371 (tpp) REVERT: H 103 PHE cc_start: 0.5442 (m-80) cc_final: 0.5132 (m-80) REVERT: L 11 MET cc_start: 0.2427 (ppp) cc_final: 0.2174 (ppp) outliers start: 44 outliers final: 29 residues processed: 228 average time/residue: 0.1560 time to fit residues: 61.4238 Evaluate side-chains 212 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 996 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS 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 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 913 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 617 CYS Chi-restraints excluded: chain C residue 723 THR 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 911 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 53 ILE Chi-restraints excluded: chain L residue 8 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 13 optimal weight: 20.0000 chunk 286 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ** 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** C 965 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.215795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.128594 restraints weight = 42522.775| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.87 r_work: 0.3534 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27766 Z= 0.187 Angle : 0.622 13.891 37927 Z= 0.299 Chirality : 0.048 0.413 4400 Planarity : 0.004 0.053 4826 Dihedral : 6.475 70.972 4653 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.99 % Allowed : 12.04 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3357 helix: 1.69 (0.20), residues: 647 sheet: 0.17 (0.18), residues: 839 loop : -0.39 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.023 0.001 TYR A1067 PHE 0.023 0.002 PHE C 140 TRP 0.052 0.001 TRP L 56 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00452 (27680) covalent geometry : angle 0.58304 (37707) SS BOND : bond 0.00334 ( 38) SS BOND : angle 1.34224 ( 76) hydrogen bonds : bond 0.03769 ( 1021) hydrogen bonds : angle 5.69145 ( 2883) link_NAG-ASN : bond 0.00599 ( 48) link_NAG-ASN : angle 3.47247 ( 144) *********************** 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 244 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8228 (mp) cc_final: 0.8024 (mp) REVERT: A 314 GLN cc_start: 0.8589 (tm-30) cc_final: 0.7888 (tm-30) REVERT: A 443 SER cc_start: 0.4795 (OUTLIER) cc_final: 0.4478 (t) REVERT: A 584 ILE cc_start: 0.8820 (mm) cc_final: 0.8499 (mp) REVERT: A 661 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7939 (mt-10) REVERT: A 663 ASP cc_start: 0.8742 (m-30) cc_final: 0.8241 (m-30) REVERT: A 804 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8485 (mp10) REVERT: A 868 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7410 (tp30) REVERT: A 988 GLU cc_start: 0.8438 (mp0) cc_final: 0.8144 (mp0) REVERT: B 52 GLN cc_start: 0.7599 (tp40) cc_final: 0.7207 (tp40) REVERT: B 104 TRP cc_start: 0.6684 (m-90) cc_final: 0.6324 (m-90) REVERT: B 170 TYR cc_start: 0.7889 (t80) cc_final: 0.7596 (t80) REVERT: B 202 LYS cc_start: 0.7141 (mtmt) cc_final: 0.6778 (mtpp) REVERT: B 913 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: B 957 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 979 ASP cc_start: 0.8217 (t70) cc_final: 0.7888 (t0) REVERT: B 994 ASP cc_start: 0.9056 (t0) cc_final: 0.8805 (t0) REVERT: B 1002 GLN cc_start: 0.8705 (tp40) cc_final: 0.8381 (tp-100) REVERT: B 1029 MET cc_start: 0.8375 (tpp) cc_final: 0.7954 (ttm) REVERT: C 84 LEU cc_start: 0.7335 (mt) cc_final: 0.7126 (mp) REVERT: C 129 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7420 (tppp) REVERT: C 160 TYR cc_start: 0.7767 (p90) cc_final: 0.7417 (p90) REVERT: C 536 ASN cc_start: 0.8520 (m-40) cc_final: 0.8154 (m110) REVERT: C 692 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8561 (mm) REVERT: C 723 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8392 (p) REVERT: C 745 ASP cc_start: 0.8447 (m-30) cc_final: 0.7642 (t0) REVERT: C 752 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8833 (tt) REVERT: H 103 PHE cc_start: 0.5392 (m-80) cc_final: 0.5070 (m-80) REVERT: L 11 MET cc_start: 0.2347 (ppp) cc_final: 0.1791 (ppp) REVERT: L 56 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.7152 (m-90) outliers start: 58 outliers final: 37 residues processed: 229 average time/residue: 0.1550 time to fit residues: 61.8573 Evaluate side-chains 219 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 931 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1074 ASN 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 551 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 974 SER 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 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1001 LEU 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 L residue 56 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 158 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 141 optimal weight: 40.0000 chunk 204 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** 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 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 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** ** 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 = 0.4745 r_free = 0.4745 target = 0.216930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.130361 restraints weight = 42322.750| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.85 r_work: 0.3561 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27766 Z= 0.143 Angle : 0.591 13.880 37927 Z= 0.284 Chirality : 0.047 0.414 4400 Planarity : 0.003 0.053 4826 Dihedral : 6.234 67.145 4653 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.95 % Allowed : 12.31 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3357 helix: 1.79 (0.20), residues: 648 sheet: 0.17 (0.17), residues: 841 loop : -0.38 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.019 0.001 TYR A1067 PHE 0.023 0.001 PHE C 140 TRP 0.049 0.001 TRP L 56 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00338 (27680) covalent geometry : angle 0.55132 (37707) SS BOND : bond 0.00284 ( 38) SS BOND : angle 1.29383 ( 76) hydrogen bonds : bond 0.03570 ( 1021) hydrogen bonds : angle 5.53002 ( 2883) link_NAG-ASN : bond 0.00606 ( 48) link_NAG-ASN : angle 3.41215 ( 144) *********************** 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 243 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 443 SER cc_start: 0.4783 (OUTLIER) cc_final: 0.4464 (t) REVERT: A 584 ILE cc_start: 0.8842 (mm) cc_final: 0.8529 (mp) REVERT: A 661 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7915 (mt-10) REVERT: A 663 ASP cc_start: 0.8697 (m-30) cc_final: 0.8150 (m-30) REVERT: A 868 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7432 (tp30) REVERT: A 988 GLU cc_start: 0.8517 (mp0) cc_final: 0.8195 (mp0) REVERT: B 52 GLN cc_start: 0.7598 (tp40) cc_final: 0.7191 (tp40) REVERT: B 104 TRP cc_start: 0.6678 (m-90) cc_final: 0.6259 (m-90) REVERT: B 170 TYR cc_start: 0.7935 (t80) cc_final: 0.7638 (t80) REVERT: B 202 LYS cc_start: 0.7212 (mtmt) cc_final: 0.6844 (mtpp) REVERT: B 726 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8614 (mm) REVERT: B 913 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: B 957 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 979 ASP cc_start: 0.8215 (t70) cc_final: 0.7954 (t0) REVERT: B 994 ASP cc_start: 0.8998 (t0) cc_final: 0.8742 (t0) REVERT: B 1002 GLN cc_start: 0.8672 (tp40) cc_final: 0.8341 (tp-100) REVERT: B 1029 MET cc_start: 0.8369 (tpp) cc_final: 0.7968 (ttm) REVERT: C 84 LEU cc_start: 0.7308 (mt) cc_final: 0.7105 (mp) REVERT: C 160 TYR cc_start: 0.7685 (p90) cc_final: 0.7329 (p90) REVERT: C 536 ASN cc_start: 0.8479 (m-40) cc_final: 0.8131 (m110) REVERT: C 692 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8527 (mm) REVERT: C 723 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8387 (p) REVERT: C 745 ASP cc_start: 0.8397 (m-30) cc_final: 0.7596 (t0) REVERT: C 752 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8802 (tt) REVERT: H 55 GLU cc_start: 0.8057 (pt0) cc_final: 0.7769 (pp20) REVERT: H 103 PHE cc_start: 0.5462 (m-80) cc_final: 0.5155 (m-80) REVERT: L 11 MET cc_start: 0.2382 (ppp) cc_final: 0.2071 (ppp) REVERT: L 56 TRP cc_start: 0.7664 (OUTLIER) cc_final: 0.7093 (m-90) outliers start: 57 outliers final: 37 residues processed: 229 average time/residue: 0.1613 time to fit residues: 64.3499 Evaluate side-chains 216 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 996 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1074 ASN 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 551 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1094 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 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 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 911 VAL Chi-restraints excluded: chain C residue 1001 LEU 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 L residue 56 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 277 optimal weight: 0.9980 chunk 317 optimal weight: 20.0000 chunk 315 optimal weight: 6.9990 chunk 331 optimal weight: 0.9980 chunk 335 optimal weight: 30.0000 chunk 171 optimal weight: 0.9990 chunk 222 optimal weight: 30.0000 chunk 142 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 228 optimal weight: 0.0670 chunk 193 optimal weight: 9.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- 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 ** 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 762 GLN B 856 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN 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** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.218420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133458 restraints weight = 42761.117| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.44 r_work: 0.3567 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27766 Z= 0.114 Angle : 0.568 13.532 37927 Z= 0.272 Chirality : 0.046 0.410 4400 Planarity : 0.003 0.053 4826 Dihedral : 5.983 62.947 4653 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.54 % Allowed : 12.89 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3357 helix: 1.94 (0.21), residues: 646 sheet: 0.20 (0.17), residues: 843 loop : -0.35 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 102 TYR 0.021 0.001 TYR C 170 PHE 0.026 0.001 PHE B 168 TRP 0.043 0.001 TRP L 56 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00265 (27680) covalent geometry : angle 0.52937 (37707) SS BOND : bond 0.00215 ( 38) SS BOND : angle 1.15186 ( 76) hydrogen bonds : bond 0.03358 ( 1021) hydrogen bonds : angle 5.33581 ( 2883) link_NAG-ASN : bond 0.00623 ( 48) link_NAG-ASN : angle 3.30776 ( 144) *********************** 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 231 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 443 SER cc_start: 0.4813 (OUTLIER) cc_final: 0.4487 (t) REVERT: A 584 ILE cc_start: 0.8822 (mm) cc_final: 0.8615 (mp) REVERT: A 661 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7823 (mt-10) REVERT: A 663 ASP cc_start: 0.8548 (m-30) cc_final: 0.8056 (m-30) REVERT: A 868 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7263 (tp30) REVERT: B 52 GLN cc_start: 0.7578 (tp40) cc_final: 0.7174 (tp40) REVERT: B 168 PHE cc_start: 0.8446 (t80) cc_final: 0.8061 (t80) REVERT: B 170 TYR cc_start: 0.8027 (t80) cc_final: 0.7802 (t80) REVERT: B 202 LYS cc_start: 0.6967 (mtmt) cc_final: 0.6631 (mtpp) REVERT: B 239 GLN cc_start: 0.5784 (mm110) cc_final: 0.5563 (mm110) REVERT: B 913 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: B 957 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 979 ASP cc_start: 0.8204 (t70) cc_final: 0.7960 (t0) REVERT: B 994 ASP cc_start: 0.8850 (t0) cc_final: 0.8597 (t0) REVERT: B 1002 GLN cc_start: 0.8526 (tp40) cc_final: 0.8174 (tp-100) REVERT: B 1029 MET cc_start: 0.8218 (tpp) cc_final: 0.7797 (ttm) REVERT: C 84 LEU cc_start: 0.7225 (mt) cc_final: 0.7003 (mp) REVERT: C 129 LYS cc_start: 0.7573 (ttmt) cc_final: 0.7311 (tppp) REVERT: C 160 TYR cc_start: 0.7773 (p90) cc_final: 0.7426 (p90) REVERT: C 203 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7379 (mt) REVERT: C 536 ASN cc_start: 0.8355 (m-40) cc_final: 0.7956 (m110) REVERT: C 723 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8250 (p) REVERT: H 55 GLU cc_start: 0.8116 (pt0) cc_final: 0.7738 (pp20) REVERT: H 64 TYR cc_start: 0.5445 (t80) cc_final: 0.4918 (t80) REVERT: H 103 PHE cc_start: 0.5547 (m-80) cc_final: 0.5261 (m-80) REVERT: L 11 MET cc_start: 0.2306 (ppp) cc_final: 0.2050 (ppp) REVERT: L 56 TRP cc_start: 0.7634 (OUTLIER) cc_final: 0.7148 (m-90) outliers start: 45 outliers final: 35 residues processed: 220 average time/residue: 0.1586 time to fit residues: 60.6558 Evaluate side-chains 215 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 750 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 911 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 551 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 913 GLN 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 203 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 723 THR 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 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 L residue 56 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 54 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 311 optimal weight: 0.0980 chunk 131 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 271 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 913 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B1011 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.232422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.168953 restraints weight = 43473.175| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.59 r_work: 0.3490 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 27766 Z= 0.285 Angle : 0.683 13.479 37927 Z= 0.331 Chirality : 0.050 0.388 4400 Planarity : 0.004 0.054 4826 Dihedral : 6.306 64.018 4653 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.16 % Allowed : 12.93 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3357 helix: 1.50 (0.20), residues: 643 sheet: 0.05 (0.18), residues: 849 loop : -0.38 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 328 TYR 0.031 0.001 TYR A1067 PHE 0.032 0.002 PHE B 238 TRP 0.040 0.002 TRP L 56 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00692 (27680) covalent geometry : angle 0.64706 (37707) SS BOND : bond 0.00415 ( 38) SS BOND : angle 1.36049 ( 76) hydrogen bonds : bond 0.03984 ( 1021) hydrogen bonds : angle 5.74013 ( 2883) link_NAG-ASN : bond 0.00610 ( 48) link_NAG-ASN : angle 3.48092 ( 144) *********************** 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 238 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 175 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 314 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 443 SER cc_start: 0.4953 (OUTLIER) cc_final: 0.4603 (t) REVERT: A 584 ILE cc_start: 0.8846 (mm) cc_final: 0.8640 (mp) REVERT: A 661 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7981 (mt-10) REVERT: A 663 ASP cc_start: 0.8742 (m-30) cc_final: 0.8220 (m-30) REVERT: B 52 GLN cc_start: 0.7567 (tp40) cc_final: 0.7246 (tp40) REVERT: B 104 TRP cc_start: 0.6729 (m-90) cc_final: 0.6405 (m-90) REVERT: B 170 TYR cc_start: 0.8080 (t80) cc_final: 0.7844 (t80) REVERT: B 202 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6920 (mtpp) REVERT: B 723 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8540 (p) REVERT: B 913 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7863 (pm20) REVERT: B 957 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8149 (tm-30) REVERT: B 979 ASP cc_start: 0.8291 (t70) cc_final: 0.8039 (t0) REVERT: B 994 ASP cc_start: 0.9101 (t0) cc_final: 0.8800 (t0) REVERT: B 1002 GLN cc_start: 0.8625 (tp40) cc_final: 0.8255 (tp-100) REVERT: B 1029 MET cc_start: 0.8297 (tpp) cc_final: 0.7762 (ttm) REVERT: C 84 LEU cc_start: 0.7516 (mt) cc_final: 0.7294 (mp) REVERT: C 160 TYR cc_start: 0.7622 (p90) cc_final: 0.7300 (p90) REVERT: C 536 ASN cc_start: 0.8487 (m-40) cc_final: 0.8137 (m110) REVERT: C 692 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8545 (mm) REVERT: C 745 ASP cc_start: 0.8295 (m-30) cc_final: 0.7598 (t0) REVERT: C 752 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8856 (tt) REVERT: C 895 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: H 55 GLU cc_start: 0.8042 (pt0) cc_final: 0.7769 (pp20) REVERT: H 103 PHE cc_start: 0.5535 (m-80) cc_final: 0.5237 (m-80) REVERT: L 11 MET cc_start: 0.2427 (ppp) cc_final: 0.2109 (ppp) outliers start: 63 outliers final: 46 residues processed: 227 average time/residue: 0.1480 time to fit residues: 59.1271 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 : 0.965 ------------------------------------------------------------------------------- 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 931 ILE 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 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 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 803 SER 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 913 GLN Chi-restraints excluded: chain B residue 931 ILE 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 203 ILE 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 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 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 1001 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 262 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 317 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 209 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 913 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.217127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.130785 restraints weight = 42312.771| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.85 r_work: 0.3579 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27766 Z= 0.121 Angle : 0.582 13.376 37927 Z= 0.280 Chirality : 0.047 0.408 4400 Planarity : 0.004 0.052 4826 Dihedral : 6.047 61.828 4653 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.51 % Allowed : 13.37 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3357 helix: 1.74 (0.20), residues: 655 sheet: 0.16 (0.18), residues: 823 loop : -0.36 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 102 TYR 0.024 0.001 TYR C 170 PHE 0.031 0.001 PHE B 238 TRP 0.022 0.001 TRP A 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00283 (27680) covalent geometry : angle 0.54202 (37707) SS BOND : bond 0.00241 ( 38) SS BOND : angle 1.06197 ( 76) hydrogen bonds : bond 0.03448 ( 1021) hydrogen bonds : angle 5.41645 ( 2883) link_NAG-ASN : bond 0.00635 ( 48) link_NAG-ASN : angle 3.42491 ( 144) ********************** 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 225 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 443 SER cc_start: 0.4835 (OUTLIER) cc_final: 0.4502 (t) REVERT: A 584 ILE cc_start: 0.8840 (mm) cc_final: 0.8633 (mp) REVERT: A 661 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7942 (mt-10) REVERT: A 663 ASP cc_start: 0.8665 (m-30) cc_final: 0.8145 (m-30) REVERT: A 868 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7438 (tp30) REVERT: B 52 GLN cc_start: 0.7587 (tp40) cc_final: 0.7246 (tp40) REVERT: B 104 TRP cc_start: 0.6671 (m-90) cc_final: 0.6242 (m-90) REVERT: B 168 PHE cc_start: 0.8505 (t80) cc_final: 0.8034 (t80) REVERT: B 170 TYR cc_start: 0.7916 (t80) cc_final: 0.7681 (t80) REVERT: B 202 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6859 (mtpp) REVERT: B 592 PHE cc_start: 0.8345 (p90) cc_final: 0.8063 (p90) REVERT: B 913 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: B 957 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 979 ASP cc_start: 0.8308 (t70) cc_final: 0.8047 (t0) REVERT: B 994 ASP cc_start: 0.9029 (t0) cc_final: 0.8753 (t0) REVERT: B 1002 GLN cc_start: 0.8666 (tp40) cc_final: 0.8309 (tp-100) REVERT: B 1029 MET cc_start: 0.8343 (tpp) cc_final: 0.7929 (ttm) REVERT: C 84 LEU cc_start: 0.7378 (mt) cc_final: 0.7155 (mp) REVERT: C 129 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7527 (tppp) REVERT: C 160 TYR cc_start: 0.7652 (p90) cc_final: 0.7285 (p90) REVERT: C 536 ASN cc_start: 0.8491 (m-40) cc_final: 0.8133 (m110) REVERT: C 692 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8508 (mm) REVERT: C 723 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8352 (p) REVERT: C 745 ASP cc_start: 0.8422 (m-30) cc_final: 0.7604 (t0) REVERT: C 752 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8776 (tt) REVERT: C 895 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: H 55 GLU cc_start: 0.7918 (pt0) cc_final: 0.7374 (pm20) REVERT: H 103 PHE cc_start: 0.5596 (m-80) cc_final: 0.5282 (m-80) REVERT: L 11 MET cc_start: 0.2288 (ppp) cc_final: 0.1990 (ppp) outliers start: 44 outliers final: 37 residues processed: 214 average time/residue: 0.1492 time to fit residues: 55.5628 Evaluate side-chains 214 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 940 SER 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 551 VAL 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 913 GLN 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 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 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 1001 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 126 optimal weight: 30.0000 chunk 160 optimal weight: 0.4980 chunk 318 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 188 optimal weight: 2.9990 chunk 330 optimal weight: 30.0000 chunk 38 optimal weight: 40.0000 chunk 129 optimal weight: 1.9990 chunk 319 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.216235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.129431 restraints weight = 42298.698| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.85 r_work: 0.3546 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27766 Z= 0.151 Angle : 0.588 12.819 37927 Z= 0.282 Chirality : 0.047 0.398 4400 Planarity : 0.004 0.053 4826 Dihedral : 6.008 59.616 4653 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.58 % Allowed : 13.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3357 helix: 1.75 (0.20), residues: 654 sheet: 0.15 (0.18), residues: 827 loop : -0.34 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 273 TYR 0.020 0.001 TYR A1067 PHE 0.031 0.001 PHE B 238 TRP 0.021 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00364 (27680) covalent geometry : angle 0.54961 (37707) SS BOND : bond 0.00268 ( 38) SS BOND : angle 1.05501 ( 76) hydrogen bonds : bond 0.03468 ( 1021) hydrogen bonds : angle 5.40183 ( 2883) link_NAG-ASN : bond 0.00601 ( 48) link_NAG-ASN : angle 3.36325 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10783.49 seconds wall clock time: 184 minutes 5.88 seconds (11045.88 seconds total)