Starting phenix.real_space_refine on Fri Mar 6 22:52:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v26_31637/03_2026/7v26_31637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v26_31637/03_2026/7v26_31637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v26_31637/03_2026/7v26_31637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v26_31637/03_2026/7v26_31637.map" model { file = "/net/cci-nas-00/data/ceres_data/7v26_31637/03_2026/7v26_31637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v26_31637/03_2026/7v26_31637.cif" } resolution = 3.85 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= 0.002 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 153 5.16 5 C 22299 2.51 5 N 5799 2.21 5 O 6906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s 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: 35157 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8342 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8342 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8342 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "a" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "c" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "d" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "e" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "f" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 6.30, per 1000 atoms: 0.18 Number of scatterers: 35157 At special positions: 0 Unit cell: (207.108, 192.464, 234.304, 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 153 16.00 O 6906 8.00 N 5799 7.00 C 22299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=1.93 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 97 " distance=2.03 Simple disulfide: pdb=" SG CYS a 147 " - pdb=" SG CYS a 203 " distance=2.03 Simple disulfide: pdb=" SG CYS b 22 " - pdb=" SG CYS b 90 " distance=2.03 Simple disulfide: pdb=" SG CYS b 137 " - pdb=" SG CYS b 196 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 97 " distance=2.03 Simple disulfide: pdb=" SG CYS c 147 " - pdb=" SG CYS c 203 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 90 " distance=2.04 Simple disulfide: pdb=" SG CYS d 137 " - pdb=" SG CYS d 196 " distance=2.03 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 97 " distance=2.03 Simple disulfide: pdb=" SG CYS e 147 " - pdb=" SG CYS e 203 " distance=2.03 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 90 " distance=2.03 Simple disulfide: pdb=" SG CYS f 137 " - pdb=" SG CYS f 196 " 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 282 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 17 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 331 " " NAG A1314 " - " ASN A 234 " " NAG A1315 " - " ASN A 149 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 17 " " NAG C1314 " - " ASN C1074 " " NAG C1315 " - " ASN C 149 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 165 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 616 " " NAG E1307 " - " ASN E 709 " " NAG E1308 " - " ASN E 717 " " NAG E1309 " - " ASN E 801 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E1098 " " NAG E1312 " - " ASN E1134 " " NAG E1313 " - " ASN E 17 " " NAG E1314 " - " ASN E 149 " " NAG E1315 " - " ASN E 343 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8406 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 77 sheets defined 15.8% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.529A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.610A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.659A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.550A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.536A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.703A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.923A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.179A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.604A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.242A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.636A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.107A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.811A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.356A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.388A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 removed outlier: 3.560A pdb=" N GLU E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 364 through 370 removed outlier: 3.754A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.683A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.658A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 755 removed outlier: 3.936A pdb=" N GLN E 755 " --> pdb=" O ASN E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 782 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.615A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 918 removed outlier: 3.546A pdb=" N GLU E 918 " --> pdb=" O ASN E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 946 through 967 removed outlier: 3.581A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 983 removed outlier: 3.682A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 Processing helix chain 'E' and resid 1140 through 1145 removed outlier: 3.822A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 92 removed outlier: 3.884A pdb=" N THR c 92 " --> pdb=" O PRO c 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 92 removed outlier: 3.952A pdb=" N THR e 92 " --> pdb=" O PRO e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 193 through 197 removed outlier: 3.843A pdb=" N LEU e 196 " --> pdb=" O SER e 193 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY e 197 " --> pdb=" O SER e 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 193 through 197' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.315A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 removed outlier: 4.507A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.610A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.800A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.800A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.822A pdb=" N HIS A 146 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 4.110A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 598 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.909A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.122A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 670 through 675 removed outlier: 3.560A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 727 removed outlier: 7.373A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.240A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.997A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.546A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.628A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C 286 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AC4, first strand: chain 'C' and resid 131 through 135 removed outlier: 7.956A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 154 through 156 removed outlier: 6.282A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 205 removed outlier: 5.917A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 312 removed outlier: 3.856A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 312 removed outlier: 3.856A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.865A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 396 through 397 removed outlier: 3.550A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 396 through 397 removed outlier: 3.550A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.836A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD6, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AD7, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.577A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.504A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'E' and resid 28 through 30 removed outlier: 3.726A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 263 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 50 through 53 removed outlier: 3.613A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.712A pdb=" N VAL E 193 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 195 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 197 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AE6, first strand: chain 'E' and resid 127 through 131 removed outlier: 6.904A pdb=" N ILE E 128 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU E 169 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL E 130 " --> pdb=" O THR E 167 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 134 through 135 removed outlier: 3.913A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 151 through 156 removed outlier: 4.271A pdb=" N SER E 151 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS E 146 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET E 153 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER E 155 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLY E 142 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL E 143 " --> pdb=" O ARG E 246 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 311 through 319 removed outlier: 3.897A pdb=" N GLY E 311 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR E 599 " --> pdb=" O GLY E 311 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 315 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN E 613 " --> pdb=" O GLY E 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR E 612 " --> pdb=" O CYS E 649 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS E 649 " --> pdb=" O TYR E 612 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 648 " --> pdb=" O THR E 645 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 325 through 327 removed outlier: 6.379A pdb=" N ILE E 326 " --> pdb=" O ASN E 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 539 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY E 548 " --> pdb=" O PHE E 541 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.021A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE E 358 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AF4, first strand: chain 'E' and resid 452 through 453 removed outlier: 3.595A pdb=" N GLN E 493 " --> pdb=" O TYR E 453 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.535A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 673 " --> pdb=" O ILE E 693 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 664 " --> pdb=" O ALA E 672 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 711 through 727 removed outlier: 6.487A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E1068 " --> pdb=" O THR E 719 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 725 " --> pdb=" O PHE E1062 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 711 through 727 removed outlier: 6.487A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E1068 " --> pdb=" O THR E 719 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 725 " --> pdb=" O PHE E1062 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'E' and resid 1120 through 1122 removed outlier: 3.524A pdb=" N ILE E1081 " --> pdb=" O HIS E1088 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS E1082 " --> pdb=" O VAL E1133 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AG2, first strand: chain 'a' and resid 5 through 7 removed outlier: 3.791A pdb=" N VAL a 80 " --> pdb=" O CYS a 22 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 11 through 12 removed outlier: 3.918A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR a 114 " --> pdb=" O TYR a 95 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA a 93 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA a 51 " --> pdb=" O TRP a 38 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG a 40 " --> pdb=" O TRP a 49 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TRP a 49 " --> pdb=" O ARG a 40 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG a 60 " --> pdb=" O LEU a 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 149 through 150 Processing sheet with id=AG5, first strand: chain 'a' and resid 157 through 161 removed outlier: 3.945A pdb=" N THR a 158 " --> pdb=" O ASN a 206 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN a 206 " --> pdb=" O THR a 158 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 18 through 20 removed outlier: 3.712A pdb=" N ILE b 77 " --> pdb=" O ILE b 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU b 75 " --> pdb=" O ILE b 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER b 65 " --> pdb=" O THR b 76 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 48 through 50 removed outlier: 7.050A pdb=" N TRP b 37 " --> pdb=" O MET b 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 117 through 121 removed outlier: 3.543A pdb=" N SER b 140 " --> pdb=" O SER b 117 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'c' and resid 5 through 6 Processing sheet with id=AH1, first strand: chain 'c' and resid 11 through 12 removed outlier: 3.561A pdb=" N ALA c 51 " --> pdb=" O TRP c 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG c 40 " --> pdb=" O TRP c 49 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP c 49 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU c 52 " --> pdb=" O ARG c 60 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG c 60 " --> pdb=" O LEU c 52 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'c' and resid 11 through 12 removed outlier: 3.561A pdb=" N ARG c 99 " --> pdb=" O CYS c 109 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS c 109 " --> pdb=" O ARG c 99 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'c' and resid 129 through 130 removed outlier: 3.680A pdb=" N ASP c 151 " --> pdb=" O TYR c 183 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR c 183 " --> pdb=" O ASP c 151 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'c' and resid 157 through 161 removed outlier: 3.576A pdb=" N THR c 158 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR c 201 " --> pdb=" O VAL c 218 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 46 through 48 removed outlier: 3.684A pdb=" N SER d 92 " --> pdb=" O VAL d 99 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL d 99 " --> pdb=" O SER d 92 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 46 through 48 removed outlier: 3.591A pdb=" N ALA d 86 " --> pdb=" O LEU d 106 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 64 through 68 removed outlier: 3.611A pdb=" N SER d 67 " --> pdb=" O SER d 74 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER d 74 " --> pdb=" O SER d 67 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 117 through 121 removed outlier: 3.571A pdb=" N SER d 140 " --> pdb=" O SER d 117 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL d 136 " --> pdb=" O PHE d 121 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 11 through 12 removed outlier: 9.138A pdb=" N VAL e 12 " --> pdb=" O LEU e 115 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR e 117 " --> pdb=" O VAL e 12 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL e 36 " --> pdb=" O LEU e 52 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU e 52 " --> pdb=" O VAL e 36 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TRP e 38 " --> pdb=" O LEU e 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 18 through 21 Processing sheet with id=AI2, first strand: chain 'f' and resid 21 through 22 removed outlier: 4.271A pdb=" N CYS f 22 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA f 73 " --> pdb=" O CYS f 22 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'f' and resid 47 through 50 removed outlier: 6.445A pdb=" N TRP f 37 " --> pdb=" O MET f 49 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR f 89 " --> pdb=" O TYR f 38 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER f 92 " --> pdb=" O VAL f 99 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL f 99 " --> pdb=" O SER f 92 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'f' and resid 47 through 50 removed outlier: 6.445A pdb=" N TRP f 37 " --> pdb=" O MET f 49 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR f 89 " --> pdb=" O TYR f 38 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'f' and resid 119 through 121 removed outlier: 3.784A pdb=" N THR f 119 " --> pdb=" O LEU f 138 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU f 138 " --> pdb=" O THR f 119 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL f 136 " --> pdb=" O PHE f 121 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2535 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: 7.94 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11192 1.35 - 1.47: 9112 1.47 - 1.59: 15477 1.59 - 1.71: 0 1.71 - 1.83: 192 Bond restraints: 35973 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.55e+00 bond pdb=" C1 NAG A1315 " pdb=" O5 NAG A1315 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" C1 NAG C1314 " pdb=" O5 NAG C1314 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 NAG E1301 " pdb=" O5 NAG E1301 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 35968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 47072 1.20 - 2.40: 1481 2.40 - 3.60: 420 3.60 - 4.79: 56 4.79 - 5.99: 24 Bond angle restraints: 49053 Sorted by residual: angle pdb=" N VAL a 90 " pdb=" CA VAL a 90 " pdb=" C VAL a 90 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.78e+01 angle pdb=" N VAL b 60 " pdb=" CA VAL b 60 " pdb=" C VAL b 60 " ideal model delta sigma weight residual 106.21 109.88 -3.67 1.07e+00 8.73e-01 1.18e+01 angle pdb=" C ASN C 616 " pdb=" N CYS C 617 " pdb=" CA CYS C 617 " ideal model delta sigma weight residual 122.08 126.97 -4.89 1.47e+00 4.63e-01 1.11e+01 angle pdb=" C CYS A 336 " pdb=" N PRO A 337 " pdb=" CA PRO A 337 " ideal model delta sigma weight residual 119.84 123.68 -3.84 1.25e+00 6.40e-01 9.45e+00 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 111.90 109.45 2.45 8.10e-01 1.52e+00 9.17e+00 ... (remaining 49048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 20578 17.99 - 35.98: 1193 35.98 - 53.98: 201 53.98 - 71.97: 40 71.97 - 89.96: 17 Dihedral angle restraints: 22029 sinusoidal: 8940 harmonic: 13089 Sorted by residual: dihedral pdb=" CB CYS f 137 " pdb=" SG CYS f 137 " pdb=" SG CYS f 196 " pdb=" CB CYS f 196 " ideal model delta sinusoidal sigma weight residual -86.00 -175.71 89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 760 " pdb=" CB CYS E 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.16 88.84 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -169.91 83.91 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 22026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4883 0.056 - 0.111: 791 0.111 - 0.167: 83 0.167 - 0.222: 2 0.222 - 0.278: 1 Chirality restraints: 5760 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C1 NAG C1314 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1314 " pdb=" O5 NAG C1314 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" C2 NAG E1312 " pdb=" C1 NAG E1312 " pdb=" C3 NAG E1312 " pdb=" N2 NAG E1312 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 5757 not shown) Planarity restraints: 6303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 431 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C GLY A 431 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY A 431 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS A 432 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR f 184 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO f 185 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO f 185 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO f 185 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR d 184 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO d 185 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO d 185 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO d 185 " -0.027 5.00e-02 4.00e+02 ... (remaining 6300 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5919 2.77 - 3.30: 32692 3.30 - 3.83: 57619 3.83 - 4.37: 64768 4.37 - 4.90: 112098 Nonbonded interactions: 273096 Sorted by model distance: nonbonded pdb=" O ASN E 501 " pdb=" ND2 ASN f 33 " model vdw 2.234 3.120 nonbonded pdb=" O VAL C1040 " pdb=" OG SER E1030 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR d 19 " pdb=" OG SER d 74 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR e 101 " pdb=" OG1 THR e 105 " model vdw 2.274 3.040 ... (remaining 273091 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 29.420 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.003 0.101 36072 Z= 0.141 Angle : 0.556 24.649 49296 Z= 0.302 Chirality : 0.042 0.278 5760 Planarity : 0.003 0.050 6258 Dihedral : 11.199 89.962 13461 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.16 % Allowed : 3.60 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.11), residues: 4470 helix: 0.63 (0.20), residues: 629 sheet: -2.82 (0.14), residues: 966 loop : -3.41 (0.09), residues: 2875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.009 0.000 TYR C 495 PHE 0.014 0.001 PHE E 377 TRP 0.003 0.000 TRP e 110 HIS 0.002 0.000 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00262 (35973) covalent geometry : angle 0.53353 (49053) SS BOND : bond 0.01391 ( 54) SS BOND : angle 2.78838 ( 108) hydrogen bonds : bond 0.23088 ( 902) hydrogen bonds : angle 8.80738 ( 2535) link_NAG-ASN : bond 0.00371 ( 45) link_NAG-ASN : angle 1.82260 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 674 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.7206 (tp) cc_final: 0.6970 (tp) REVERT: A 157 PHE cc_start: 0.7392 (t80) cc_final: 0.5841 (t80) REVERT: A 160 TYR cc_start: 0.6390 (p90) cc_final: 0.5788 (p90) REVERT: A 203 ILE cc_start: 0.8461 (mt) cc_final: 0.8253 (tt) REVERT: A 408 ARG cc_start: 0.8585 (ppt170) cc_final: 0.8304 (ppt170) REVERT: A 729 VAL cc_start: 0.9078 (m) cc_final: 0.8807 (t) REVERT: A 762 GLN cc_start: 0.8870 (mt0) cc_final: 0.8611 (mt0) REVERT: A 777 ASN cc_start: 0.7214 (m-40) cc_final: 0.6978 (m110) REVERT: A 1029 MET cc_start: 0.8113 (tpp) cc_final: 0.7640 (ttm) REVERT: C 153 MET cc_start: 0.6314 (ptp) cc_final: 0.5976 (pmm) REVERT: C 307 THR cc_start: 0.7022 (m) cc_final: 0.6783 (t) REVERT: C 365 TYR cc_start: 0.7460 (m-80) cc_final: 0.7138 (m-10) REVERT: C 384 PRO cc_start: 0.6666 (Cg_exo) cc_final: 0.6435 (Cg_endo) REVERT: C 441 LEU cc_start: 0.7228 (mm) cc_final: 0.6898 (mm) REVERT: C 451 TYR cc_start: 0.7720 (m-80) cc_final: 0.7511 (m-80) REVERT: C 658 ASN cc_start: 0.7698 (p0) cc_final: 0.7002 (p0) REVERT: C 773 GLU cc_start: 0.7481 (tp30) cc_final: 0.5861 (tp30) REVERT: C 777 ASN cc_start: 0.6160 (m-40) cc_final: 0.5363 (m-40) REVERT: E 258 TRP cc_start: 0.6613 (p-90) cc_final: 0.6386 (p-90) REVERT: E 353 TRP cc_start: 0.7308 (p-90) cc_final: 0.6602 (p-90) REVERT: E 380 TYR cc_start: 0.6310 (m-80) cc_final: 0.6084 (m-80) REVERT: E 714 ILE cc_start: 0.8720 (mm) cc_final: 0.8517 (mt) REVERT: E 763 LEU cc_start: 0.8372 (mt) cc_final: 0.8100 (mt) REVERT: E 776 LYS cc_start: 0.8857 (tmtt) cc_final: 0.8602 (tttp) REVERT: E 978 ASN cc_start: 0.7831 (m-40) cc_final: 0.7589 (p0) REVERT: E 1031 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7040 (mt-10) REVERT: a 74 ASP cc_start: 0.7330 (t0) cc_final: 0.6746 (t0) REVERT: a 79 GLN cc_start: 0.8441 (tt0) cc_final: 0.8179 (tp-100) REVERT: a 91 ASP cc_start: 0.6979 (m-30) cc_final: 0.6715 (m-30) REVERT: a 106 ILE cc_start: 0.8143 (mt) cc_final: 0.7834 (mt) REVERT: b 18 ILE cc_start: 0.7216 (pt) cc_final: 0.6938 (mt) REVERT: b 87 ASP cc_start: 0.6395 (t0) cc_final: 0.5508 (t70) REVERT: c 57 ASP cc_start: 0.7773 (m-30) cc_final: 0.7445 (t0) REVERT: d 52 ASP cc_start: 0.8915 (t0) cc_final: 0.8438 (m-30) REVERT: d 55 LYS cc_start: 0.9034 (tppt) cc_final: 0.8753 (tppt) REVERT: e 88 ASP cc_start: 0.8356 (t70) cc_final: 0.7728 (t0) REVERT: f 44 GLN cc_start: 0.8204 (mp-120) cc_final: 0.7970 (mp10) REVERT: f 88 TYR cc_start: 0.7564 (m-80) cc_final: 0.7216 (m-10) outliers start: 6 outliers final: 2 residues processed: 680 average time/residue: 0.2353 time to fit residues: 252.2648 Evaluate side-chains 368 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 366 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 178 SER Chi-restraints excluded: chain f residue 166 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 146 HIS A 173 GLN A 239 GLN A 314 GLN A 334 ASN A 498 GLN A 501 ASN A 536 ASN A 564 GLN A 762 GLN A 784 GLN A 856 ASN A 872 GLN A 901 GLN A 926 GLN A 954 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN C 23 GLN C 69 HIS C 134 GLN C 185 ASN C 188 ASN C 196 ASN C 271 GLN C 394 ASN C 409 GLN C 414 GLN C 498 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 580 GLN C 690 GLN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 935 GLN C 954 GLN C 965 GLN C1002 GLN C1036 GLN C1101 HIS C1135 ASN E 137 ASN E 196 ASN E 218 GLN E 388 ASN E 460 ASN E 580 GLN E 603 ASN E 655 HIS E 658 ASN E 690 GLN E 777 ASN E 787 GLN ** E 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 935 GLN E 949 GLN E 953 ASN E 954 GLN E1011 GLN ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1101 HIS E1106 GLN E1135 ASN a 86 ASN ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 178 GLN a 204 ASN ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 81 GLN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 79 GLN c 178 GLN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 178 GLN e 211 ASN f 41 HIS f 170 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.086503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066062 restraints weight = 144481.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.065364 restraints weight = 92420.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.065889 restraints weight = 81067.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.066160 restraints weight = 64174.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.066385 restraints weight = 58983.783| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 36072 Z= 0.288 Angle : 0.749 16.136 49296 Z= 0.375 Chirality : 0.047 0.299 5760 Planarity : 0.005 0.067 6258 Dihedral : 6.645 59.688 5759 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.94 % Allowed : 13.88 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.12), residues: 4470 helix: 1.17 (0.21), residues: 638 sheet: -2.44 (0.15), residues: 1050 loop : -3.04 (0.10), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 408 TYR 0.020 0.002 TYR d 89 PHE 0.025 0.002 PHE A 429 TRP 0.019 0.002 TRP A 436 HIS 0.013 0.002 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00664 (35973) covalent geometry : angle 0.73590 (49053) SS BOND : bond 0.00559 ( 54) SS BOND : angle 2.00443 ( 108) hydrogen bonds : bond 0.04728 ( 902) hydrogen bonds : angle 6.25017 ( 2535) link_NAG-ASN : bond 0.00406 ( 45) link_NAG-ASN : angle 2.14510 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 367 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8150 (pp) REVERT: A 340 GLU cc_start: 0.8164 (pt0) cc_final: 0.7781 (tm-30) REVERT: A 392 PHE cc_start: 0.7965 (m-80) cc_final: 0.7642 (m-80) REVERT: A 697 MET cc_start: 0.8149 (ttp) cc_final: 0.7739 (mtm) REVERT: A 707 TYR cc_start: 0.8766 (t80) cc_final: 0.8508 (t80) REVERT: A 762 GLN cc_start: 0.9164 (mt0) cc_final: 0.8903 (mt0) REVERT: A 1029 MET cc_start: 0.8418 (tpp) cc_final: 0.8014 (ttm) REVERT: C 441 LEU cc_start: 0.7344 (mm) cc_final: 0.7046 (mm) REVERT: C 658 ASN cc_start: 0.7698 (p0) cc_final: 0.7405 (p0) REVERT: C 773 GLU cc_start: 0.7912 (tp30) cc_final: 0.6907 (tp30) REVERT: C 902 MET cc_start: 0.9093 (tpt) cc_final: 0.8347 (tpt) REVERT: C 997 ILE cc_start: 0.9232 (mt) cc_final: 0.8979 (mm) REVERT: C 1050 MET cc_start: 0.7433 (ptm) cc_final: 0.6876 (ptm) REVERT: E 55 PHE cc_start: 0.6674 (m-80) cc_final: 0.6138 (m-80) REVERT: E 353 TRP cc_start: 0.7695 (p-90) cc_final: 0.6735 (p-90) REVERT: E 856 ASN cc_start: 0.8511 (p0) cc_final: 0.8231 (t0) REVERT: E 900 MET cc_start: 0.8509 (mtp) cc_final: 0.8138 (ttm) REVERT: E 902 MET cc_start: 0.9056 (tpp) cc_final: 0.8507 (tpp) REVERT: E 1050 MET cc_start: 0.8446 (ptm) cc_final: 0.8081 (ptm) REVERT: a 74 ASP cc_start: 0.7678 (t0) cc_final: 0.7055 (t0) REVERT: a 84 MET cc_start: 0.6240 (pmm) cc_final: 0.5954 (pmm) REVERT: a 106 ILE cc_start: 0.8133 (mt) cc_final: 0.7899 (mt) REVERT: b 152 LYS cc_start: 0.6865 (mptt) cc_final: 0.6618 (pttt) REVERT: b 188 TRP cc_start: 0.5674 (OUTLIER) cc_final: 0.5388 (t-100) REVERT: d 52 ASP cc_start: 0.8614 (t0) cc_final: 0.8125 (m-30) REVERT: e 59 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7754 (mmpt) REVERT: e 71 ILE cc_start: 0.8345 (mm) cc_final: 0.7920 (tt) REVERT: e 87 MET cc_start: 0.8100 (tpp) cc_final: 0.7834 (tpp) REVERT: e 155 GLU cc_start: 0.7997 (tp30) cc_final: 0.7579 (mt-10) REVERT: f 28 ASP cc_start: 0.7590 (p0) cc_final: 0.7367 (t0) REVERT: f 44 GLN cc_start: 0.8268 (mp-120) cc_final: 0.7962 (mp10) outliers start: 75 outliers final: 35 residues processed: 424 average time/residue: 0.1998 time to fit residues: 142.1113 Evaluate side-chains 326 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 289 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 874 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 49 MET Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 188 TRP Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 109 CYS Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 199 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 302 optimal weight: 4.9990 chunk 346 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 417 optimal weight: 5.9990 chunk 258 optimal weight: 0.8980 chunk 177 optimal weight: 0.5980 chunk 196 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 361 optimal weight: 0.0050 chunk 292 optimal weight: 3.9990 chunk 436 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 334 ASN A 690 GLN A 787 GLN A 856 ASN A 935 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C1005 GLN E 450 ASN a 86 ASN ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 81 GLN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 171 HIS f 172 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.087900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068135 restraints weight = 143756.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066740 restraints weight = 92175.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067268 restraints weight = 74214.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.067616 restraints weight = 60218.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067861 restraints weight = 53443.645| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 36072 Z= 0.121 Angle : 0.591 13.881 49296 Z= 0.292 Chirality : 0.044 0.296 5760 Planarity : 0.004 0.048 6258 Dihedral : 5.796 56.068 5757 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.05 % Allowed : 16.19 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.88 (0.12), residues: 4470 helix: 1.77 (0.21), residues: 633 sheet: -2.29 (0.15), residues: 1056 loop : -2.81 (0.11), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 99 TYR 0.033 0.001 TYR d 32 PHE 0.020 0.001 PHE C 106 TRP 0.029 0.001 TRP b 37 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00281 (35973) covalent geometry : angle 0.57943 (49053) SS BOND : bond 0.00350 ( 54) SS BOND : angle 1.65245 ( 108) hydrogen bonds : bond 0.03927 ( 902) hydrogen bonds : angle 5.74646 ( 2535) link_NAG-ASN : bond 0.00339 ( 45) link_NAG-ASN : angle 1.87419 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 333 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.7424 (t80) cc_final: 0.6658 (t80) REVERT: A 160 TYR cc_start: 0.6933 (p90) cc_final: 0.6167 (p90) REVERT: A 244 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8162 (pp) REVERT: A 340 GLU cc_start: 0.7952 (pt0) cc_final: 0.7735 (tm-30) REVERT: A 651 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8832 (pt) REVERT: A 762 GLN cc_start: 0.9155 (mt0) cc_final: 0.8905 (mt0) REVERT: A 1029 MET cc_start: 0.8335 (tpp) cc_final: 0.8034 (ttm) REVERT: A 1050 MET cc_start: 0.7987 (ptm) cc_final: 0.7673 (ptt) REVERT: C 153 MET cc_start: 0.6202 (ptp) cc_final: 0.5393 (pmm) REVERT: C 198 ASP cc_start: 0.5211 (t0) cc_final: 0.4812 (t0) REVERT: C 369 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7085 (m-10) REVERT: C 441 LEU cc_start: 0.7310 (mm) cc_final: 0.6998 (mm) REVERT: C 658 ASN cc_start: 0.7653 (p0) cc_final: 0.7429 (p0) REVERT: C 697 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7490 (ttt) REVERT: C 773 GLU cc_start: 0.7716 (tp30) cc_final: 0.6380 (tp30) REVERT: C 777 ASN cc_start: 0.7638 (m-40) cc_final: 0.6756 (m-40) REVERT: C 873 TYR cc_start: 0.8599 (m-80) cc_final: 0.8366 (m-80) REVERT: C 902 MET cc_start: 0.8892 (tpt) cc_final: 0.8413 (tpt) REVERT: C 997 ILE cc_start: 0.9222 (mt) cc_final: 0.8945 (mm) REVERT: C 1050 MET cc_start: 0.7508 (ptm) cc_final: 0.7208 (ptm) REVERT: E 55 PHE cc_start: 0.6633 (m-80) cc_final: 0.6036 (m-80) REVERT: E 258 TRP cc_start: 0.6532 (p-90) cc_final: 0.6144 (p-90) REVERT: E 353 TRP cc_start: 0.7637 (p-90) cc_final: 0.6087 (p-90) REVERT: E 392 PHE cc_start: 0.7271 (m-10) cc_final: 0.6981 (m-80) REVERT: E 856 ASN cc_start: 0.8346 (p0) cc_final: 0.8060 (t0) REVERT: E 869 MET cc_start: 0.8823 (mmm) cc_final: 0.8166 (mmm) REVERT: E 900 MET cc_start: 0.8260 (mtp) cc_final: 0.7749 (ttm) REVERT: E 1050 MET cc_start: 0.8296 (ptm) cc_final: 0.8090 (ptm) REVERT: a 56 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7649 (t0) REVERT: a 74 ASP cc_start: 0.7767 (t0) cc_final: 0.7160 (t0) REVERT: a 84 MET cc_start: 0.6336 (pmm) cc_final: 0.6115 (pmm) REVERT: a 104 ASP cc_start: 0.8015 (p0) cc_final: 0.7776 (p0) REVERT: a 105 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6326 (p) REVERT: a 106 ILE cc_start: 0.8006 (mt) cc_final: 0.7747 (mt) REVERT: c 79 GLN cc_start: 0.7513 (pm20) cc_final: 0.6870 (mp10) REVERT: d 52 ASP cc_start: 0.8714 (t0) cc_final: 0.8227 (m-30) REVERT: e 71 ILE cc_start: 0.8097 (mm) cc_final: 0.7546 (tt) REVERT: e 87 MET cc_start: 0.8009 (tpp) cc_final: 0.7380 (tpp) REVERT: e 91 ASP cc_start: 0.6097 (t0) cc_final: 0.5266 (t70) REVERT: f 44 GLN cc_start: 0.8319 (mp-120) cc_final: 0.7983 (mp10) outliers start: 79 outliers final: 38 residues processed: 393 average time/residue: 0.1948 time to fit residues: 130.2537 Evaluate side-chains 335 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain E residue 733 LYS Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 966 LEU Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 105 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain b residue 32 TYR Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 164 THR Chi-restraints excluded: chain c residue 151 ASP Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain f residue 60 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 280 optimal weight: 0.9980 chunk 427 optimal weight: 8.9990 chunk 351 optimal weight: 2.9990 chunk 418 optimal weight: 6.9990 chunk 430 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 342 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 352 optimal weight: 0.9980 chunk 274 optimal weight: 0.0570 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 957 GLN C1048 HIS E1048 HIS ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 78 ASN f 172 ASN f 191 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.086483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066739 restraints weight = 144062.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.065339 restraints weight = 92563.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065884 restraints weight = 76905.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.066187 restraints weight = 62543.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066380 restraints weight = 55940.960| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36072 Z= 0.162 Angle : 0.595 12.463 49296 Z= 0.294 Chirality : 0.044 0.288 5760 Planarity : 0.004 0.048 6258 Dihedral : 5.555 56.648 5757 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.38 % Allowed : 17.07 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.12), residues: 4470 helix: 1.87 (0.21), residues: 631 sheet: -2.21 (0.15), residues: 1019 loop : -2.65 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 355 TYR 0.036 0.002 TYR e 183 PHE 0.021 0.001 PHE C 497 TRP 0.020 0.001 TRP b 37 HIS 0.006 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00375 (35973) covalent geometry : angle 0.58256 (49053) SS BOND : bond 0.00538 ( 54) SS BOND : angle 1.67567 ( 108) hydrogen bonds : bond 0.03809 ( 902) hydrogen bonds : angle 5.54235 ( 2535) link_NAG-ASN : bond 0.00307 ( 45) link_NAG-ASN : angle 1.88879 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 301 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8215 (pp) REVERT: A 651 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8793 (pt) REVERT: A 707 TYR cc_start: 0.8788 (t80) cc_final: 0.8529 (t80) REVERT: A 756 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7965 (t80) REVERT: A 762 GLN cc_start: 0.9184 (mt0) cc_final: 0.8902 (mt0) REVERT: A 1029 MET cc_start: 0.8411 (tpp) cc_final: 0.8053 (ttm) REVERT: C 153 MET cc_start: 0.6416 (ptp) cc_final: 0.5593 (pmm) REVERT: C 369 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7109 (m-10) REVERT: C 441 LEU cc_start: 0.7354 (mm) cc_final: 0.7010 (mm) REVERT: C 571 ASP cc_start: 0.7301 (t0) cc_final: 0.6976 (t0) REVERT: C 658 ASN cc_start: 0.7554 (p0) cc_final: 0.7303 (p0) REVERT: C 697 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7568 (ttt) REVERT: C 773 GLU cc_start: 0.7937 (tp30) cc_final: 0.6967 (tp30) REVERT: C 902 MET cc_start: 0.8854 (tpt) cc_final: 0.8345 (tpt) REVERT: C 1050 MET cc_start: 0.7541 (ptm) cc_final: 0.7177 (ptm) REVERT: E 55 PHE cc_start: 0.6722 (m-80) cc_final: 0.6109 (m-80) REVERT: E 177 MET cc_start: 0.5926 (pmm) cc_final: 0.5702 (pmm) REVERT: E 869 MET cc_start: 0.8870 (mmm) cc_final: 0.8196 (mmm) REVERT: E 900 MET cc_start: 0.8407 (mtp) cc_final: 0.7948 (ttm) REVERT: E 902 MET cc_start: 0.9004 (tpp) cc_final: 0.8689 (tpt) REVERT: E 1050 MET cc_start: 0.8372 (ptm) cc_final: 0.8117 (ptm) REVERT: a 40 ARG cc_start: 0.7646 (ptt180) cc_final: 0.6923 (ttm170) REVERT: a 74 ASP cc_start: 0.7873 (t0) cc_final: 0.7314 (t0) REVERT: a 105 THR cc_start: 0.6901 (OUTLIER) cc_final: 0.6369 (p) REVERT: a 106 ILE cc_start: 0.8029 (mt) cc_final: 0.7799 (mt) REVERT: b 87 ASP cc_start: 0.7667 (t70) cc_final: 0.7261 (t0) REVERT: b 152 LYS cc_start: 0.6998 (mptt) cc_final: 0.6616 (pttt) REVERT: d 52 ASP cc_start: 0.8730 (t0) cc_final: 0.8184 (m-30) REVERT: e 71 ILE cc_start: 0.8068 (mm) cc_final: 0.7637 (tt) REVERT: e 87 MET cc_start: 0.8046 (tpp) cc_final: 0.7690 (tpp) REVERT: e 118 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8251 (p) REVERT: f 38 TYR cc_start: 0.7045 (m-10) cc_final: 0.6775 (m-10) REVERT: f 44 GLN cc_start: 0.8436 (mp-120) cc_final: 0.8070 (mp10) outliers start: 92 outliers final: 55 residues processed: 373 average time/residue: 0.2009 time to fit residues: 128.8477 Evaluate side-chains 334 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 272 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 733 LYS Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 966 LEU Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain a residue 105 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 32 TYR Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 164 THR Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 188 VAL Chi-restraints excluded: chain e residue 190 THR Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 199 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 171 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 326 optimal weight: 8.9990 chunk 363 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 281 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 388 ASN A 655 HIS A 784 GLN A 919 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN E 271 GLN ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 191 HIS d 39 GLN e 78 ASN ** f 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 172 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.084906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065227 restraints weight = 143521.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.063684 restraints weight = 91854.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.064204 restraints weight = 78988.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064542 restraints weight = 63411.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.064709 restraints weight = 56775.349| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36072 Z= 0.197 Angle : 0.631 14.564 49296 Z= 0.314 Chirality : 0.044 0.284 5760 Planarity : 0.004 0.066 6258 Dihedral : 5.605 56.652 5757 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.13 % Allowed : 17.64 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.12), residues: 4470 helix: 1.79 (0.21), residues: 624 sheet: -2.22 (0.15), residues: 1036 loop : -2.54 (0.11), residues: 2810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 99 TYR 0.035 0.002 TYR d 32 PHE 0.015 0.002 PHE A1121 TRP 0.022 0.002 TRP b 188 HIS 0.007 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00454 (35973) covalent geometry : angle 0.61812 (49053) SS BOND : bond 0.00356 ( 54) SS BOND : angle 1.78008 ( 108) hydrogen bonds : bond 0.04039 ( 902) hydrogen bonds : angle 5.46632 ( 2535) link_NAG-ASN : bond 0.00317 ( 45) link_NAG-ASN : angle 1.97018 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 275 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8209 (pp) REVERT: A 651 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8769 (pt) REVERT: A 756 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8024 (t80) REVERT: A 762 GLN cc_start: 0.9202 (mt0) cc_final: 0.8977 (mt0) REVERT: A 779 GLN cc_start: 0.9193 (tm-30) cc_final: 0.8935 (tm-30) REVERT: A 1029 MET cc_start: 0.8466 (tpp) cc_final: 0.7924 (ttm) REVERT: C 153 MET cc_start: 0.6420 (ptp) cc_final: 0.5642 (pmm) REVERT: C 369 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: C 441 LEU cc_start: 0.7430 (mm) cc_final: 0.7067 (mm) REVERT: C 571 ASP cc_start: 0.7319 (t0) cc_final: 0.6986 (t0) REVERT: C 658 ASN cc_start: 0.7571 (p0) cc_final: 0.7210 (p0) REVERT: C 697 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7606 (ttt) REVERT: C 773 GLU cc_start: 0.7920 (tp30) cc_final: 0.7334 (tp30) REVERT: C 902 MET cc_start: 0.8893 (tpt) cc_final: 0.8373 (tpt) REVERT: C 1050 MET cc_start: 0.7522 (ptm) cc_final: 0.7128 (ptm) REVERT: E 52 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7776 (mm110) REVERT: E 55 PHE cc_start: 0.6871 (m-80) cc_final: 0.6164 (m-80) REVERT: E 212 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7882 (pp) REVERT: E 869 MET cc_start: 0.8900 (mmm) cc_final: 0.8281 (mmm) REVERT: E 900 MET cc_start: 0.8351 (mtp) cc_final: 0.8103 (ttm) REVERT: E 1050 MET cc_start: 0.8517 (ptm) cc_final: 0.8065 (ptm) REVERT: a 74 ASP cc_start: 0.8119 (t0) cc_final: 0.7488 (t0) REVERT: a 99 ARG cc_start: 0.8040 (tpt-90) cc_final: 0.7618 (tpt-90) REVERT: a 105 THR cc_start: 0.6718 (OUTLIER) cc_final: 0.6434 (p) REVERT: b 87 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7420 (t0) REVERT: b 152 LYS cc_start: 0.7140 (mptt) cc_final: 0.6737 (pttt) REVERT: b 188 TRP cc_start: 0.5328 (t-100) cc_final: 0.4600 (t-100) REVERT: e 71 ILE cc_start: 0.8074 (mm) cc_final: 0.7721 (tt) REVERT: e 87 MET cc_start: 0.8124 (tpp) cc_final: 0.7755 (tpp) REVERT: e 118 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8318 (p) REVERT: f 38 TYR cc_start: 0.7106 (m-10) cc_final: 0.6829 (m-10) REVERT: f 44 GLN cc_start: 0.8548 (mp-120) cc_final: 0.8116 (mp10) outliers start: 121 outliers final: 75 residues processed: 376 average time/residue: 0.1885 time to fit residues: 123.3182 Evaluate side-chains 343 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 259 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 733 LYS Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 105 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 204 ASN Chi-restraints excluded: chain b residue 32 TYR Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 188 VAL Chi-restraints excluded: chain e residue 190 THR Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 199 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 199 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 339 optimal weight: 9.9990 chunk 289 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 407 optimal weight: 7.9990 chunk 7 optimal weight: 0.0020 chunk 422 optimal weight: 9.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN a 86 ASN ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.086098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066337 restraints weight = 142590.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064964 restraints weight = 89673.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065507 restraints weight = 75688.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.065986 restraints weight = 60594.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.066078 restraints weight = 53385.827| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36072 Z= 0.116 Angle : 0.580 18.456 49296 Z= 0.287 Chirality : 0.044 0.314 5760 Planarity : 0.004 0.063 6258 Dihedral : 5.252 55.683 5757 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.75 % Allowed : 18.91 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.12), residues: 4470 helix: 2.00 (0.21), residues: 631 sheet: -2.04 (0.15), residues: 1063 loop : -2.44 (0.11), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 56 TYR 0.032 0.001 TYR d 32 PHE 0.017 0.001 PHE C 497 TRP 0.026 0.001 TRP C 258 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00267 (35973) covalent geometry : angle 0.56869 (49053) SS BOND : bond 0.00397 ( 54) SS BOND : angle 1.52186 ( 108) hydrogen bonds : bond 0.03616 ( 902) hydrogen bonds : angle 5.25904 ( 2535) link_NAG-ASN : bond 0.00328 ( 45) link_NAG-ASN : angle 1.85473 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 286 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 725 GLU cc_start: 0.8581 (tt0) cc_final: 0.8070 (pt0) REVERT: A 756 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7937 (t80) REVERT: A 762 GLN cc_start: 0.9165 (mt0) cc_final: 0.8961 (mt0) REVERT: A 779 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8881 (tm-30) REVERT: A 1029 MET cc_start: 0.8342 (tpp) cc_final: 0.7997 (ttm) REVERT: C 153 MET cc_start: 0.6482 (ptp) cc_final: 0.5739 (pmm) REVERT: C 369 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: C 441 LEU cc_start: 0.7299 (mm) cc_final: 0.6931 (mm) REVERT: C 571 ASP cc_start: 0.7284 (t0) cc_final: 0.6956 (t0) REVERT: C 658 ASN cc_start: 0.7592 (p0) cc_final: 0.7173 (p0) REVERT: C 697 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7524 (ttt) REVERT: C 710 ASN cc_start: 0.8320 (p0) cc_final: 0.7929 (p0) REVERT: C 773 GLU cc_start: 0.7810 (tp30) cc_final: 0.7193 (tp30) REVERT: C 902 MET cc_start: 0.8812 (tpt) cc_final: 0.8315 (tpt) REVERT: C 1050 MET cc_start: 0.7577 (ptm) cc_final: 0.7227 (ptm) REVERT: E 52 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7749 (mm110) REVERT: E 55 PHE cc_start: 0.6795 (m-80) cc_final: 0.6085 (m-80) REVERT: E 274 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8898 (t) REVERT: E 900 MET cc_start: 0.8317 (mtp) cc_final: 0.7798 (ttm) REVERT: E 1050 MET cc_start: 0.8637 (ptm) cc_final: 0.8327 (ptm) REVERT: a 56 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7808 (t0) REVERT: a 74 ASP cc_start: 0.8135 (t0) cc_final: 0.7500 (t0) REVERT: a 83 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8161 (p) REVERT: a 104 ASP cc_start: 0.7973 (p0) cc_final: 0.7699 (p0) REVERT: a 105 THR cc_start: 0.6643 (OUTLIER) cc_final: 0.6303 (p) REVERT: b 87 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7244 (t0) REVERT: b 152 LYS cc_start: 0.7109 (mptt) cc_final: 0.6704 (pttt) REVERT: b 188 TRP cc_start: 0.5200 (t-100) cc_final: 0.4726 (t-100) REVERT: d 56 ARG cc_start: 0.7796 (mpp-170) cc_final: 0.7475 (mtt90) REVERT: d 139 ILE cc_start: 0.5713 (mm) cc_final: 0.5319 (mm) REVERT: e 71 ILE cc_start: 0.8207 (mm) cc_final: 0.7826 (tt) REVERT: e 87 MET cc_start: 0.8132 (tpp) cc_final: 0.7821 (tpp) REVERT: e 118 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8326 (p) REVERT: e 183 TYR cc_start: 0.5954 (m-10) cc_final: 0.5294 (m-10) REVERT: f 38 TYR cc_start: 0.7103 (m-10) cc_final: 0.6856 (m-10) REVERT: f 44 GLN cc_start: 0.8564 (mp-120) cc_final: 0.8117 (mp10) outliers start: 106 outliers final: 70 residues processed: 373 average time/residue: 0.1994 time to fit residues: 128.0820 Evaluate side-chains 347 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 268 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 733 LYS Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 83 THR Chi-restraints excluded: chain a residue 105 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 204 ASN Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 164 THR Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 57 ASP Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 188 VAL Chi-restraints excluded: chain e residue 190 THR Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 89 TYR Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain f residue 199 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 280 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 784 GLN A 856 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 856 ASN E 211 ASN ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.084705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065176 restraints weight = 143154.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063459 restraints weight = 92370.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064057 restraints weight = 76762.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.064429 restraints weight = 61207.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064540 restraints weight = 54826.771| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36072 Z= 0.175 Angle : 0.614 14.545 49296 Z= 0.307 Chirality : 0.044 0.284 5760 Planarity : 0.004 0.059 6258 Dihedral : 5.408 56.756 5757 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.95 % Allowed : 19.74 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.12), residues: 4470 helix: 1.92 (0.21), residues: 631 sheet: -1.99 (0.15), residues: 1057 loop : -2.40 (0.11), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 63 TYR 0.033 0.001 TYR d 32 PHE 0.019 0.001 PHE A 318 TRP 0.030 0.001 TRP C 258 HIS 0.006 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00406 (35973) covalent geometry : angle 0.60119 (49053) SS BOND : bond 0.00409 ( 54) SS BOND : angle 1.77518 ( 108) hydrogen bonds : bond 0.03862 ( 902) hydrogen bonds : angle 5.27025 ( 2535) link_NAG-ASN : bond 0.00302 ( 45) link_NAG-ASN : angle 1.94644 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 273 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8172 (pp) REVERT: A 592 PHE cc_start: 0.7115 (p90) cc_final: 0.6905 (p90) REVERT: A 756 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7914 (t80) REVERT: A 1029 MET cc_start: 0.8412 (tpp) cc_final: 0.7884 (ttm) REVERT: C 153 MET cc_start: 0.6618 (ptp) cc_final: 0.5863 (pmm) REVERT: C 369 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7211 (m-10) REVERT: C 410 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.7323 (mm) REVERT: C 441 LEU cc_start: 0.7368 (mm) cc_final: 0.6993 (mm) REVERT: C 497 PHE cc_start: 0.3370 (m-80) cc_final: 0.2993 (m-80) REVERT: C 571 ASP cc_start: 0.7368 (t0) cc_final: 0.7037 (t0) REVERT: C 658 ASN cc_start: 0.7670 (p0) cc_final: 0.7287 (p0) REVERT: C 697 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7584 (ttt) REVERT: C 773 GLU cc_start: 0.7922 (tp30) cc_final: 0.7127 (tp30) REVERT: C 902 MET cc_start: 0.8860 (tpt) cc_final: 0.8352 (tpt) REVERT: C 1050 MET cc_start: 0.7612 (ptm) cc_final: 0.7244 (ptm) REVERT: E 55 PHE cc_start: 0.6906 (m-80) cc_final: 0.6197 (m-80) REVERT: E 274 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9040 (t) REVERT: E 900 MET cc_start: 0.8412 (mtp) cc_final: 0.8125 (ttm) REVERT: E 1050 MET cc_start: 0.8594 (ptm) cc_final: 0.8236 (ptm) REVERT: a 74 ASP cc_start: 0.8220 (t0) cc_final: 0.7602 (t0) REVERT: a 99 ARG cc_start: 0.8057 (tpt-90) cc_final: 0.7702 (tpt-90) REVERT: a 105 THR cc_start: 0.6721 (OUTLIER) cc_final: 0.6409 (p) REVERT: b 87 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7502 (t0) REVERT: b 152 LYS cc_start: 0.7264 (mptt) cc_final: 0.6855 (pttt) REVERT: b 188 TRP cc_start: 0.5339 (t-100) cc_final: 0.4808 (t-100) REVERT: c 74 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.5909 (t70) REVERT: c 79 GLN cc_start: 0.8220 (pm20) cc_final: 0.7657 (mp10) REVERT: d 56 ARG cc_start: 0.7731 (mpp-170) cc_final: 0.7222 (mtt90) REVERT: d 139 ILE cc_start: 0.5922 (mm) cc_final: 0.5570 (mm) REVERT: e 84 MET cc_start: 0.7914 (tpt) cc_final: 0.7047 (tpt) REVERT: e 87 MET cc_start: 0.8180 (tpp) cc_final: 0.7495 (tpp) REVERT: e 183 TYR cc_start: 0.6292 (m-80) cc_final: 0.5603 (m-10) outliers start: 114 outliers final: 82 residues processed: 366 average time/residue: 0.1936 time to fit residues: 122.4101 Evaluate side-chains 353 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 262 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 733 LYS Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 105 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 204 ASN Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 57 ASP Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 188 VAL Chi-restraints excluded: chain e residue 190 THR Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 89 TYR Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 199 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 218 optimal weight: 0.9980 chunk 252 optimal weight: 8.9990 chunk 345 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 443 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 401 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN a 86 ASN a 171 HIS ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.085604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065931 restraints weight = 142651.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064451 restraints weight = 89662.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064991 restraints weight = 75309.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065447 restraints weight = 60093.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.065547 restraints weight = 53068.097| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36072 Z= 0.124 Angle : 0.587 19.957 49296 Z= 0.292 Chirality : 0.043 0.298 5760 Planarity : 0.004 0.061 6258 Dihedral : 5.159 55.835 5757 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.80 % Allowed : 20.05 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.12), residues: 4470 helix: 1.98 (0.21), residues: 636 sheet: -1.87 (0.15), residues: 1059 loop : -2.31 (0.11), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 63 TYR 0.035 0.001 TYR d 32 PHE 0.020 0.001 PHE A 855 TRP 0.040 0.001 TRP C 258 HIS 0.011 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00288 (35973) covalent geometry : angle 0.57539 (49053) SS BOND : bond 0.00348 ( 54) SS BOND : angle 1.70270 ( 108) hydrogen bonds : bond 0.03569 ( 902) hydrogen bonds : angle 5.11664 ( 2535) link_NAG-ASN : bond 0.00309 ( 45) link_NAG-ASN : angle 1.84306 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 276 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8171 (pt) REVERT: A 756 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7862 (t80) REVERT: A 1029 MET cc_start: 0.8317 (tpp) cc_final: 0.7837 (ttm) REVERT: C 153 MET cc_start: 0.6440 (ptp) cc_final: 0.5719 (pmm) REVERT: C 410 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.7327 (mm) REVERT: C 441 LEU cc_start: 0.7284 (mm) cc_final: 0.6918 (mm) REVERT: C 497 PHE cc_start: 0.3318 (m-80) cc_final: 0.3054 (m-10) REVERT: C 571 ASP cc_start: 0.7252 (t0) cc_final: 0.6889 (t0) REVERT: C 697 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7606 (ttt) REVERT: C 710 ASN cc_start: 0.8383 (p0) cc_final: 0.7969 (p0) REVERT: C 773 GLU cc_start: 0.7830 (tp30) cc_final: 0.7095 (tp30) REVERT: C 902 MET cc_start: 0.8848 (tpt) cc_final: 0.8360 (tpt) REVERT: C 1017 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7194 (tm-30) REVERT: C 1050 MET cc_start: 0.7644 (ptm) cc_final: 0.7327 (ptm) REVERT: E 21 ARG cc_start: 0.7455 (mtt-85) cc_final: 0.7136 (mtt180) REVERT: E 52 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7728 (mm110) REVERT: E 55 PHE cc_start: 0.6835 (m-80) cc_final: 0.6123 (m-80) REVERT: E 742 ILE cc_start: 0.9070 (mm) cc_final: 0.8766 (mt) REVERT: E 777 ASN cc_start: 0.7424 (m110) cc_final: 0.7081 (m-40) REVERT: E 900 MET cc_start: 0.8398 (mtp) cc_final: 0.7815 (ttm) REVERT: E 1050 MET cc_start: 0.8590 (ptm) cc_final: 0.8206 (ptm) REVERT: a 56 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7867 (t0) REVERT: a 74 ASP cc_start: 0.8167 (t0) cc_final: 0.7563 (t0) REVERT: a 99 ARG cc_start: 0.8107 (tpt-90) cc_final: 0.7814 (tpt-90) REVERT: a 104 ASP cc_start: 0.7921 (p0) cc_final: 0.7703 (p0) REVERT: a 105 THR cc_start: 0.6621 (OUTLIER) cc_final: 0.6391 (p) REVERT: b 87 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7389 (t0) REVERT: b 152 LYS cc_start: 0.7246 (mptt) cc_final: 0.6772 (pttt) REVERT: b 186 GLU cc_start: 0.6921 (pp20) cc_final: 0.5976 (pm20) REVERT: b 188 TRP cc_start: 0.5104 (t-100) cc_final: 0.4619 (t-100) REVERT: d 56 ARG cc_start: 0.7680 (mpp-170) cc_final: 0.7322 (mtt90) REVERT: d 139 ILE cc_start: 0.5860 (mm) cc_final: 0.5569 (mm) REVERT: e 84 MET cc_start: 0.7752 (tpt) cc_final: 0.7014 (tpt) REVERT: e 87 MET cc_start: 0.8075 (tpp) cc_final: 0.7497 (tpp) REVERT: e 183 TYR cc_start: 0.6142 (m-80) cc_final: 0.5444 (m-10) REVERT: f 44 GLN cc_start: 0.8338 (mp10) cc_final: 0.8001 (mp10) outliers start: 108 outliers final: 87 residues processed: 364 average time/residue: 0.1930 time to fit residues: 120.5789 Evaluate side-chains 359 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 265 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 733 LYS Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 86 ASN Chi-restraints excluded: chain a residue 105 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 204 ASN Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 164 THR Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 57 ASP Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 188 VAL Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 117 THR Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 188 VAL Chi-restraints excluded: chain e residue 190 THR Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 89 TYR Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain f residue 199 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 404 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 389 optimal weight: 0.9990 chunk 439 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 398 optimal weight: 6.9990 chunk 423 optimal weight: 4.9990 chunk 435 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 856 ASN A 978 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN C 245 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN E 394 ASN E 777 ASN ** E 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 HIS ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.082682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.062436 restraints weight = 143547.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061611 restraints weight = 92026.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.062162 restraints weight = 82733.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.062355 restraints weight = 65208.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.062676 restraints weight = 60520.391| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 36072 Z= 0.281 Angle : 0.728 21.008 49296 Z= 0.362 Chirality : 0.046 0.301 5760 Planarity : 0.005 0.073 6258 Dihedral : 5.885 58.711 5757 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 2.98 % Allowed : 20.23 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.12), residues: 4470 helix: 1.47 (0.21), residues: 642 sheet: -1.91 (0.16), residues: 1024 loop : -2.39 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 273 TYR 0.040 0.002 TYR d 32 PHE 0.022 0.002 PHE A 855 TRP 0.040 0.002 TRP C 258 HIS 0.015 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00644 (35973) covalent geometry : angle 0.71318 (49053) SS BOND : bond 0.00475 ( 54) SS BOND : angle 2.16548 ( 108) hydrogen bonds : bond 0.04514 ( 902) hydrogen bonds : angle 5.47256 ( 2535) link_NAG-ASN : bond 0.00409 ( 45) link_NAG-ASN : angle 2.20589 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 256 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8127 (pt) REVERT: A 429 PHE cc_start: 0.8365 (t80) cc_final: 0.8138 (t80) REVERT: A 756 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7942 (t80) REVERT: A 1029 MET cc_start: 0.8488 (tpp) cc_final: 0.7961 (ttm) REVERT: C 153 MET cc_start: 0.6632 (ptp) cc_final: 0.5885 (pmm) REVERT: C 410 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.7368 (mm) REVERT: C 441 LEU cc_start: 0.7399 (mm) cc_final: 0.7028 (mm) REVERT: C 497 PHE cc_start: 0.3343 (m-80) cc_final: 0.3072 (m-10) REVERT: C 571 ASP cc_start: 0.7332 (t0) cc_final: 0.6974 (t0) REVERT: C 697 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7661 (ttt) REVERT: C 773 GLU cc_start: 0.7952 (tp30) cc_final: 0.7517 (tp30) REVERT: C 902 MET cc_start: 0.8915 (tpt) cc_final: 0.8261 (tpt) REVERT: C 1050 MET cc_start: 0.7723 (ptm) cc_final: 0.7315 (ptm) REVERT: C 1101 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7205 (m-70) REVERT: E 55 PHE cc_start: 0.6885 (m-80) cc_final: 0.6339 (m-80) REVERT: E 495 TYR cc_start: 0.5623 (OUTLIER) cc_final: 0.5178 (t80) REVERT: E 742 ILE cc_start: 0.9120 (mm) cc_final: 0.8847 (mt) REVERT: E 902 MET cc_start: 0.9047 (tpp) cc_final: 0.8770 (tpp) REVERT: E 1050 MET cc_start: 0.8659 (ptm) cc_final: 0.8220 (ptm) REVERT: a 74 ASP cc_start: 0.8311 (t0) cc_final: 0.7776 (t0) REVERT: b 87 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7809 (t0) REVERT: b 152 LYS cc_start: 0.7381 (mptt) cc_final: 0.6882 (pttt) REVERT: b 186 GLU cc_start: 0.6914 (pp20) cc_final: 0.5888 (pm20) REVERT: b 188 TRP cc_start: 0.5222 (t-100) cc_final: 0.4962 (t-100) REVERT: d 139 ILE cc_start: 0.6090 (mm) cc_final: 0.5814 (mm) REVERT: e 84 MET cc_start: 0.7831 (tpt) cc_final: 0.6996 (tpt) REVERT: e 87 MET cc_start: 0.8077 (tpp) cc_final: 0.7520 (tpp) REVERT: f 123 PRO cc_start: 0.4924 (Cg_endo) cc_final: 0.4597 (Cg_exo) outliers start: 115 outliers final: 93 residues processed: 350 average time/residue: 0.2015 time to fit residues: 121.4567 Evaluate side-chains 348 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 248 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 662 CYS Chi-restraints excluded: chain E residue 733 LYS Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 83 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 105 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 204 ASN Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain c residue 188 VAL Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 117 THR Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 188 VAL Chi-restraints excluded: chain e residue 190 THR Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain f residue 199 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 445 optimal weight: 6.9990 chunk 419 optimal weight: 0.0000 chunk 279 optimal weight: 0.4980 chunk 326 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 322 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN a 171 HIS ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.084439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.064630 restraints weight = 142666.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.063208 restraints weight = 88885.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063766 restraints weight = 73281.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.064071 restraints weight = 59124.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.064298 restraints weight = 53074.050| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 36072 Z= 0.138 Angle : 0.627 24.654 49296 Z= 0.311 Chirality : 0.044 0.297 5760 Planarity : 0.004 0.069 6258 Dihedral : 5.464 56.028 5757 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.54 % Allowed : 20.80 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.12), residues: 4470 helix: 1.81 (0.21), residues: 631 sheet: -1.78 (0.16), residues: 976 loop : -2.28 (0.11), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG f 63 TYR 0.040 0.001 TYR d 32 PHE 0.033 0.001 PHE E 157 TRP 0.047 0.001 TRP C 258 HIS 0.016 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00321 (35973) covalent geometry : angle 0.61470 (49053) SS BOND : bond 0.00335 ( 54) SS BOND : angle 1.74671 ( 108) hydrogen bonds : bond 0.03786 ( 902) hydrogen bonds : angle 5.19456 ( 2535) link_NAG-ASN : bond 0.00316 ( 45) link_NAG-ASN : angle 1.94909 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 267 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8187 (pt) REVERT: A 429 PHE cc_start: 0.8381 (t80) cc_final: 0.8175 (t80) REVERT: A 756 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7980 (t80) REVERT: A 900 MET cc_start: 0.8665 (mtp) cc_final: 0.8229 (mtt) REVERT: A 1029 MET cc_start: 0.8407 (tpp) cc_final: 0.7880 (ttm) REVERT: A 1050 MET cc_start: 0.8233 (ptm) cc_final: 0.7936 (ptt) REVERT: C 153 MET cc_start: 0.6488 (ptp) cc_final: 0.5826 (pmm) REVERT: C 410 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.7403 (mm) REVERT: C 441 LEU cc_start: 0.7254 (mm) cc_final: 0.6869 (mm) REVERT: C 571 ASP cc_start: 0.7328 (t0) cc_final: 0.6952 (t0) REVERT: C 697 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7585 (ttt) REVERT: C 773 GLU cc_start: 0.7912 (tp30) cc_final: 0.7248 (tp30) REVERT: C 780 GLU cc_start: 0.7781 (tp30) cc_final: 0.7552 (tp30) REVERT: C 902 MET cc_start: 0.8853 (tpt) cc_final: 0.8366 (tpt) REVERT: C 1050 MET cc_start: 0.7669 (ptm) cc_final: 0.7305 (ptm) REVERT: E 55 PHE cc_start: 0.6822 (m-80) cc_final: 0.6115 (m-80) REVERT: E 742 ILE cc_start: 0.9072 (mm) cc_final: 0.8792 (mt) REVERT: E 900 MET cc_start: 0.8419 (mtp) cc_final: 0.7839 (ttm) REVERT: E 1050 MET cc_start: 0.8495 (ptm) cc_final: 0.8138 (ptm) REVERT: a 74 ASP cc_start: 0.8358 (t0) cc_final: 0.7841 (t0) REVERT: a 99 ARG cc_start: 0.8058 (tpt-90) cc_final: 0.7561 (tpt90) REVERT: a 204 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6802 (p0) REVERT: b 87 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7450 (t0) REVERT: b 152 LYS cc_start: 0.7303 (mptt) cc_final: 0.6833 (pttt) REVERT: b 186 GLU cc_start: 0.6854 (pp20) cc_final: 0.5952 (pm20) REVERT: b 188 TRP cc_start: 0.5089 (t-100) cc_final: 0.4662 (t-100) REVERT: d 56 ARG cc_start: 0.8256 (mtt90) cc_final: 0.7920 (mpt180) REVERT: d 139 ILE cc_start: 0.5940 (mm) cc_final: 0.5673 (mm) REVERT: e 53 ILE cc_start: 0.8651 (tp) cc_final: 0.8423 (tp) REVERT: e 71 ILE cc_start: 0.8532 (mp) cc_final: 0.8330 (tt) REVERT: e 84 MET cc_start: 0.7740 (tpt) cc_final: 0.6936 (tpt) REVERT: e 87 MET cc_start: 0.8071 (tpp) cc_final: 0.7491 (tpp) REVERT: f 123 PRO cc_start: 0.4779 (Cg_endo) cc_final: 0.4441 (Cg_exo) outliers start: 98 outliers final: 82 residues processed: 347 average time/residue: 0.2041 time to fit residues: 121.8265 Evaluate side-chains 342 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 254 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 662 CYS Chi-restraints excluded: chain E residue 733 LYS Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 86 ASN Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 204 ASN Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain c residue 188 VAL Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 117 THR Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 188 VAL Chi-restraints excluded: chain e residue 190 THR Chi-restraints excluded: chain f residue 89 TYR Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain f residue 199 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 206 optimal weight: 0.5980 chunk 322 optimal weight: 1.9990 chunk 393 optimal weight: 6.9990 chunk 114 optimal weight: 0.0770 chunk 99 optimal weight: 0.7980 chunk 390 optimal weight: 0.0970 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN ** E 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 171 HIS ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 170 GLN f 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.085305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.065489 restraints weight = 141753.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.064176 restraints weight = 90632.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.064775 restraints weight = 72889.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065063 restraints weight = 59463.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.065360 restraints weight = 53024.909| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 36072 Z= 0.114 Angle : 0.608 25.647 49296 Z= 0.299 Chirality : 0.043 0.306 5760 Planarity : 0.004 0.064 6258 Dihedral : 5.212 56.477 5757 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.41 % Allowed : 21.16 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.13), residues: 4470 helix: 1.96 (0.21), residues: 637 sheet: -1.70 (0.16), residues: 1001 loop : -2.23 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 63 TYR 0.042 0.001 TYR d 32 PHE 0.028 0.001 PHE E 157 TRP 0.044 0.001 TRP C 258 HIS 0.014 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00266 (35973) covalent geometry : angle 0.59691 (49053) SS BOND : bond 0.00389 ( 54) SS BOND : angle 1.61347 ( 108) hydrogen bonds : bond 0.03568 ( 902) hydrogen bonds : angle 5.04026 ( 2535) link_NAG-ASN : bond 0.00318 ( 45) link_NAG-ASN : angle 1.85804 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5982.30 seconds wall clock time: 104 minutes 49.09 seconds (6289.09 seconds total)