Starting phenix.real_space_refine on Fri Mar 6 20:03:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xob_33343/03_2026/7xob_33343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xob_33343/03_2026/7xob_33343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xob_33343/03_2026/7xob_33343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xob_33343/03_2026/7xob_33343.map" model { file = "/net/cci-nas-00/data/ceres_data/7xob_33343/03_2026/7xob_33343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xob_33343/03_2026/7xob_33343.cif" } resolution = 3.3 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 163 5.16 5 C 21781 2.51 5 N 5634 2.21 5 O 6528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34108 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 7938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7938 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 55, 'TRANS': 968} Chain breaks: 8 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "C" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.07, per 1000 atoms: 0.21 Number of scatterers: 34108 At special positions: 0 Unit cell: (159.032, 140.08, 247.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 163 16.00 O 6528 8.00 N 5634 7.00 C 21781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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 B 131 " - pdb=" SG CYS B 166 " distance=1.32 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.08 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.65 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.01 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 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 A1074 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 122 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B1098 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C 331 " " NAG D 902 " - " ASN D 546 " " NAG D 903 " - " ASN D 53 " " NAG E 902 " - " ASN E 546 " " NAG E 903 " - " ASN E 53 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8006 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 51 sheets defined 35.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.689A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.883A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.503A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 778 removed outlier: 3.864A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.690A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.013A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.629A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.553A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.508A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.975A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 778 removed outlier: 3.953A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.711A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.020A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.066A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.834A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.588A pdb=" N ASN D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.599A pdb=" N LEU D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.771A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.253A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.614A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 219 through 232 removed outlier: 4.068A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.349A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 removed outlier: 4.207A pdb=" N ILE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.641A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.656A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.220A pdb=" N ARG D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.596A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.700A pdb=" N LYS D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.813A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.275A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.698A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.591A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.575A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.835A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.626A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.904A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.883A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.503A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 778 removed outlier: 3.865A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.690A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.014A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.062A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.628A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.554A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.589A pdb=" N ASN E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP E 38 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.598A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.771A pdb=" N ALA E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 4.253A pdb=" N ALA E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY E 173 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.615A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 219 through 232 removed outlier: 4.068A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU E 224 " --> pdb=" O ASN E 220 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 4.349A pdb=" N ASP E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 256 removed outlier: 4.208A pdb=" N ILE E 256 " --> pdb=" O PRO E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 256' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.641A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 329 Processing helix chain 'E' and resid 365 through 383 removed outlier: 3.655A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 removed outlier: 4.221A pdb=" N ARG E 387 " --> pdb=" O ALA E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 3.596A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.700A pdb=" N LYS E 419 " --> pdb=" O PRO E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.812A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.276A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 532 removed outlier: 3.699A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.591A pdb=" N CYS E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.576A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.836A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.626A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.645A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.157A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.798A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 4.339A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.757A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.617A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.625A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.085A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.074A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.639A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.767A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.981A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.719A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.700A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.101A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 126 through 132 removed outlier: 4.166A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 189 through 194 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.666A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.104A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.663A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.946A pdb=" N TYR B 453 " --> pdb=" O ARG B 493 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.840A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.764A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.765A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 3.869A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.675A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.000A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.644A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.157A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.798A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 171 through 172 removed outlier: 4.339A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.756A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.552A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.617A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.085A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 714 removed outlier: 3.639A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.767A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.675A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.000A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 347 through 350 1335 hydrogen bonds defined for protein. 3699 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: 10.36 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5912 1.32 - 1.46: 11401 1.46 - 1.59: 17399 1.59 - 1.73: 0 1.73 - 1.86: 229 Bond restraints: 34941 Sorted by residual: bond pdb=" CA SER A 555 " pdb=" CB SER A 555 " ideal model delta sigma weight residual 1.532 1.450 0.081 1.56e-02 4.11e+03 2.73e+01 bond pdb=" CA SER C 555 " pdb=" CB SER C 555 " ideal model delta sigma weight residual 1.530 1.453 0.077 1.69e-02 3.50e+03 2.06e+01 bond pdb=" CA THR C 866 " pdb=" C THR C 866 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.39e-02 5.18e+03 1.74e+01 bond pdb=" CA THR A 866 " pdb=" C THR A 866 " ideal model delta sigma weight residual 1.528 1.471 0.058 1.39e-02 5.18e+03 1.72e+01 bond pdb=" CA SER A 530 " pdb=" CB SER A 530 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.34e-02 5.57e+03 1.71e+01 ... (remaining 34936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 45697 2.33 - 4.66: 1542 4.66 - 6.98: 237 6.98 - 9.31: 45 9.31 - 11.64: 11 Bond angle restraints: 47532 Sorted by residual: angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 112.17 101.34 10.83 9.50e-01 1.11e+00 1.30e+02 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 121.97 -11.27 1.22e+00 6.72e-01 8.54e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 121.96 -11.26 1.22e+00 6.72e-01 8.51e+01 angle pdb=" O ALA B 372 " pdb=" C ALA B 372 " pdb=" N PRO B 373 " ideal model delta sigma weight residual 120.48 112.39 8.09 8.90e-01 1.26e+00 8.26e+01 angle pdb=" N ILE A 569 " pdb=" CA ILE A 569 " pdb=" C ILE A 569 " ideal model delta sigma weight residual 111.81 104.21 7.60 8.60e-01 1.35e+00 7.82e+01 ... (remaining 47527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.67: 19808 20.67 - 41.35: 1139 41.35 - 62.02: 210 62.02 - 82.69: 37 82.69 - 103.37: 32 Dihedral angle restraints: 21226 sinusoidal: 8790 harmonic: 12436 Sorted by residual: dihedral pdb=" CB CYS E 344 " pdb=" SG CYS E 344 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -170.71 84.71 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -170.71 84.71 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -163.39 77.39 1 1.00e+01 1.00e-02 7.50e+01 ... (remaining 21223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 5298 0.261 - 0.523: 62 0.523 - 0.784: 10 0.784 - 1.045: 2 1.045 - 1.307: 2 Chirality restraints: 5374 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.27e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.22e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 5371 not shown) Planarity restraints: 6135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " -0.332 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B1309 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " 0.508 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " 0.321 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG B1310 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " 0.117 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.320 2.00e-02 2.50e+03 2.77e-01 9.61e+02 pdb=" C7 NAG A1304 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.484 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.203 2.00e-02 2.50e+03 ... (remaining 6132 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 3 2.04 - 2.76: 4707 2.76 - 3.47: 46669 3.47 - 4.19: 80006 4.19 - 4.90: 140348 Nonbonded interactions: 271733 Sorted by model distance: nonbonded pdb=" O VAL B 367 " pdb=" CE2 PHE B 371 " model vdw 1.329 3.340 nonbonded pdb=" CA CYS B 131 " pdb=" SG CYS B 166 " model vdw 1.977 3.064 nonbonded pdb=" O ASN C 657 " pdb=" OD1 ASN C 657 " model vdw 1.981 3.040 nonbonded pdb=" O PHE A 562 " pdb=" CE LYS C 41 " model vdw 2.047 3.440 nonbonded pdb=" O THR B 124 " pdb=" OD1 ASN B 125 " model vdw 2.075 3.040 ... (remaining 271728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 426 or (resid 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 464 or (resid 465 and (name N or name CA or name C or name O or name CB \ )) or resid 466 through 473 or (resid 474 through 475 and (name N or name CA or \ name C or name O or name CB )) or resid 476 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 520 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 1311)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 426 or (resid 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 464 or (resid 465 and (name N or name CA or name C or name O or name CB \ )) or resid 466 through 473 or (resid 474 through 475 and (name N or name CA or \ name C or name O or name CB )) or resid 476 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 520 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 32.890 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4163 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 : 0.007 0.708 35018 Z= 0.414 Angle : 1.026 39.784 47723 Z= 0.613 Chirality : 0.076 1.307 5374 Planarity : 0.013 0.286 6098 Dihedral : 13.732 103.368 13100 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.95 % Rotamer: Outliers : 0.57 % Allowed : 10.12 % Favored : 89.31 % Cbeta Deviations : 0.30 % 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: -3.07 (0.11), residues: 4202 helix: -0.73 (0.13), residues: 1370 sheet: -1.70 (0.18), residues: 613 loop : -3.11 (0.11), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 646 TYR 0.062 0.001 TYR B 37 PHE 0.069 0.002 PHE B 92 TRP 0.039 0.001 TRP B 104 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00523 (34941) covalent geometry : angle 0.91622 (47532) SS BOND : bond 0.14852 ( 40) SS BOND : angle 6.36389 ( 80) hydrogen bonds : bond 0.16866 ( 1335) hydrogen bonds : angle 6.28804 ( 3699) link_NAG-ASN : bond 0.02031 ( 37) link_NAG-ASN : angle 8.02105 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 894 time to evaluate : 0.886 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: 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 328 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.7462 (mmm160) REVERT: A 543 PHE cc_start: 0.8287 (m-10) cc_final: 0.7963 (m-80) REVERT: A 547 THR cc_start: 0.8006 (p) cc_final: 0.7789 (p) REVERT: A 551 VAL cc_start: 0.8022 (t) cc_final: 0.7647 (m) REVERT: A 569 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8168 (tp) REVERT: A 578 ASP cc_start: 0.6945 (t70) cc_final: 0.6733 (t70) REVERT: A 610 VAL cc_start: 0.7896 (t) cc_final: 0.7693 (t) REVERT: A 692 ILE cc_start: 0.7976 (mm) cc_final: 0.7655 (mt) REVERT: A 737 ASP cc_start: 0.6872 (t0) cc_final: 0.6153 (t70) REVERT: A 774 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7238 (mp10) REVERT: A 819 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6925 (mt-10) REVERT: A 820 ASP cc_start: 0.6815 (t0) cc_final: 0.6551 (t0) REVERT: A 821 LEU cc_start: 0.8767 (tt) cc_final: 0.8556 (tp) REVERT: A 929 SER cc_start: 0.8426 (t) cc_final: 0.8153 (m) REVERT: A 934 ILE cc_start: 0.7936 (tt) cc_final: 0.7705 (tt) REVERT: A 949 GLN cc_start: 0.7729 (tp40) cc_final: 0.7511 (mm-40) REVERT: A 1019 ARG cc_start: 0.6932 (ttm110) cc_final: 0.6449 (ttp80) REVERT: A 1091 ARG cc_start: 0.7183 (mtt90) cc_final: 0.6963 (mtt90) REVERT: A 1122 VAL cc_start: 0.8323 (p) cc_final: 0.8043 (m) REVERT: A 1136 THR cc_start: 0.7856 (t) cc_final: 0.7570 (p) REVERT: B 36 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7625 (p) REVERT: B 308 VAL cc_start: 0.7264 (m) cc_final: 0.5992 (t) REVERT: B 309 GLU cc_start: 0.6944 (mp0) cc_final: 0.6694 (mp0) REVERT: B 317 ASN cc_start: 0.7161 (m110) cc_final: 0.6593 (m110) REVERT: B 340 GLU cc_start: 0.7219 (tp30) cc_final: 0.6662 (tp30) REVERT: B 615 VAL cc_start: 0.8265 (p) cc_final: 0.8033 (p) REVERT: B 645 THR cc_start: 0.8366 (p) cc_final: 0.7166 (m) REVERT: B 670 ILE cc_start: 0.7990 (mp) cc_final: 0.7762 (mt) REVERT: B 698 SER cc_start: 0.8261 (t) cc_final: 0.7860 (p) REVERT: B 774 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7238 (mp10) REVERT: B 981 LEU cc_start: 0.7542 (mm) cc_final: 0.7167 (mm) REVERT: B 994 ASP cc_start: 0.7474 (t0) cc_final: 0.7097 (t0) REVERT: D 39 LEU cc_start: 0.4606 (mt) cc_final: 0.4342 (mt) REVERT: D 334 THR cc_start: 0.3953 (t) cc_final: 0.3626 (p) REVERT: C 44 ARG cc_start: 0.7744 (mtt180) cc_final: 0.6823 (mtt180) REVERT: C 309 GLU cc_start: 0.5828 (mm-30) cc_final: 0.5545 (mm-30) REVERT: C 329 PHE cc_start: 0.7600 (m-80) cc_final: 0.7367 (m-80) REVERT: C 542 ASN cc_start: 0.7841 (t0) cc_final: 0.7402 (t0) REVERT: C 567 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7961 (ptp-170) REVERT: C 584 ILE cc_start: 0.7905 (tp) cc_final: 0.7571 (mm) REVERT: C 606 ASN cc_start: 0.6981 (m-40) cc_final: 0.6778 (m-40) REVERT: C 644 GLN cc_start: 0.7003 (tp40) cc_final: 0.6736 (tp40) REVERT: C 655 TYR cc_start: 0.7618 (t80) cc_final: 0.7306 (t80) REVERT: C 772 VAL cc_start: 0.8023 (p) cc_final: 0.7724 (m) REVERT: C 816 SER cc_start: 0.8499 (p) cc_final: 0.8297 (p) REVERT: C 819 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7384 (mt-10) REVERT: C 1018 ILE cc_start: 0.7031 (mm) cc_final: 0.6805 (mm) REVERT: C 1128 VAL cc_start: 0.8708 (m) cc_final: 0.8500 (p) outliers start: 21 outliers final: 2 residues processed: 908 average time/residue: 0.2024 time to fit residues: 296.3045 Evaluate side-chains 738 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 733 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 567 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 0.0770 chunk 244 optimal weight: 10.0000 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 188 ASN A 394 ASN A 505 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 755 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1106 GLN A1135 ASN B 49 HIS B 81 ASN B 282 ASN B 606 ASN B 613 GLN B 804 GLN B 935 GLN B 957 GLN B 965 GLN B1106 GLN B1135 ASN D 60 GLN D 98 GLN D 117 ASN D 345 HIS D 417 HIS D 472 GLN C 125 ASN C 188 ASN C 314 GLN C 505 HIS C 563 GLN C 755 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1135 ASN E 42 GLN E 51 ASN E 60 GLN E 96 GLN E 98 GLN E 113 ASN E 188 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN E 368 ASN E 472 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.214188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160817 restraints weight = 55926.647| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.93 r_work: 0.3741 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35018 Z= 0.233 Angle : 0.745 14.391 47723 Z= 0.372 Chirality : 0.050 0.734 5374 Planarity : 0.005 0.055 6098 Dihedral : 6.634 107.131 5363 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.85 % Allowed : 15.46 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4202 helix: 0.08 (0.14), residues: 1370 sheet: -1.11 (0.19), residues: 601 loop : -2.52 (0.11), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 204 TYR 0.026 0.002 TYR A 279 PHE 0.048 0.003 PHE E 315 TRP 0.029 0.003 TRP D 165 HIS 0.012 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00537 (34941) covalent geometry : angle 0.72172 (47532) SS BOND : bond 0.01497 ( 40) SS BOND : angle 1.98711 ( 80) hydrogen bonds : bond 0.04308 ( 1335) hydrogen bonds : angle 5.06024 ( 3699) link_NAG-ASN : bond 0.00756 ( 37) link_NAG-ASN : angle 3.53635 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 839 time to evaluate : 1.003 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: 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 193 VAL cc_start: 0.8079 (t) cc_final: 0.7705 (p) REVERT: A 275 PHE cc_start: 0.8199 (m-80) cc_final: 0.7898 (m-80) REVERT: A 377 PHE cc_start: 0.8586 (t80) cc_final: 0.8173 (t80) REVERT: A 378 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7825 (ttpp) REVERT: A 541 PHE cc_start: 0.8188 (p90) cc_final: 0.7967 (p90) REVERT: A 543 PHE cc_start: 0.8512 (m-10) cc_final: 0.8287 (m-80) REVERT: A 551 VAL cc_start: 0.8713 (t) cc_final: 0.8403 (m) REVERT: A 576 VAL cc_start: 0.8762 (p) cc_final: 0.8427 (t) REVERT: A 580 GLN cc_start: 0.8154 (mm110) cc_final: 0.7577 (mt0) REVERT: A 710 ASN cc_start: 0.7924 (p0) cc_final: 0.7707 (p0) REVERT: A 790 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7955 (mtmm) REVERT: A 819 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 900 MET cc_start: 0.8277 (mtm) cc_final: 0.7946 (mtp) REVERT: A 934 ILE cc_start: 0.8466 (tt) cc_final: 0.8139 (tp) REVERT: A 1003 SER cc_start: 0.9002 (p) cc_final: 0.8698 (t) REVERT: A 1077 THR cc_start: 0.8508 (m) cc_final: 0.8296 (t) REVERT: A 1105 THR cc_start: 0.8242 (t) cc_final: 0.8012 (p) REVERT: A 1130 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8323 (mt) REVERT: B 29 THR cc_start: 0.6817 (t) cc_final: 0.5075 (p) REVERT: B 40 ASP cc_start: 0.8057 (m-30) cc_final: 0.7776 (m-30) REVERT: B 70 VAL cc_start: 0.4152 (OUTLIER) cc_final: 0.3685 (p) REVERT: B 307 THR cc_start: 0.8040 (p) cc_final: 0.7821 (m) REVERT: B 309 GLU cc_start: 0.7740 (mp0) cc_final: 0.7517 (mp0) REVERT: B 340 GLU cc_start: 0.7607 (tp30) cc_final: 0.7093 (tp30) REVERT: B 347 PHE cc_start: 0.7391 (m-80) cc_final: 0.6761 (m-10) REVERT: B 360 ASN cc_start: 0.8197 (m-40) cc_final: 0.7881 (m-40) REVERT: B 361 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.6961 (p) REVERT: B 398 ASP cc_start: 0.7865 (m-30) cc_final: 0.7651 (m-30) REVERT: B 436 TRP cc_start: 0.7591 (p90) cc_final: 0.7322 (p90) REVERT: B 698 SER cc_start: 0.8757 (t) cc_final: 0.8382 (p) REVERT: B 710 ASN cc_start: 0.8060 (p0) cc_final: 0.7756 (p0) REVERT: B 774 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7763 (mp10) REVERT: B 934 ILE cc_start: 0.7964 (tt) cc_final: 0.7628 (tt) REVERT: B 963 VAL cc_start: 0.8667 (t) cc_final: 0.8454 (m) REVERT: B 994 ASP cc_start: 0.8028 (t70) cc_final: 0.7706 (t0) REVERT: B 1073 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7985 (mtpp) REVERT: B 1104 VAL cc_start: 0.8784 (t) cc_final: 0.8550 (p) REVERT: B 1119 ASN cc_start: 0.8051 (p0) cc_final: 0.7822 (p0) REVERT: B 1125 ASN cc_start: 0.7957 (p0) cc_final: 0.7733 (p0) REVERT: B 1127 ASP cc_start: 0.7746 (t0) cc_final: 0.7154 (t0) REVERT: D 38 ASP cc_start: 0.7532 (t0) cc_final: 0.7268 (t0) REVERT: D 61 LYS cc_start: 0.8531 (mttt) cc_final: 0.8130 (mttt) REVERT: D 225 ASP cc_start: 0.7432 (m-30) cc_final: 0.7125 (m-30) REVERT: D 249 MET cc_start: 0.4891 (mmm) cc_final: 0.3586 (mtt) REVERT: D 327 PHE cc_start: 0.7435 (t80) cc_final: 0.6376 (t80) REVERT: D 334 THR cc_start: 0.5405 (t) cc_final: 0.4888 (p) REVERT: D 385 TYR cc_start: 0.7161 (p90) cc_final: 0.5891 (p90) REVERT: D 400 PHE cc_start: 0.4162 (m-80) cc_final: 0.3701 (m-80) REVERT: D 444 LEU cc_start: 0.4713 (mt) cc_final: 0.4316 (mm) REVERT: D 477 TRP cc_start: 0.6623 (t-100) cc_final: 0.6304 (t-100) REVERT: D 557 MET cc_start: 0.7383 (tmm) cc_final: 0.6768 (tmm) REVERT: C 42 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7996 (p) REVERT: C 47 VAL cc_start: 0.8398 (p) cc_final: 0.8164 (t) REVERT: C 307 THR cc_start: 0.7587 (p) cc_final: 0.7297 (p) REVERT: C 317 ASN cc_start: 0.7801 (m-40) cc_final: 0.7519 (m-40) REVERT: C 346 ARG cc_start: 0.7597 (ttm110) cc_final: 0.7328 (ttm110) REVERT: C 542 ASN cc_start: 0.8302 (t0) cc_final: 0.7827 (t0) REVERT: C 543 PHE cc_start: 0.8383 (m-10) cc_final: 0.7988 (m-10) REVERT: C 558 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7563 (mmmm) REVERT: C 576 VAL cc_start: 0.8762 (p) cc_final: 0.8521 (t) REVERT: C 580 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7564 (mt0) REVERT: C 644 GLN cc_start: 0.7415 (tp40) cc_final: 0.7167 (tp40) REVERT: C 654 GLU cc_start: 0.7902 (tt0) cc_final: 0.7633 (tt0) REVERT: C 703 ASN cc_start: 0.7652 (t0) cc_final: 0.7449 (t0) REVERT: C 708 SER cc_start: 0.8298 (m) cc_final: 0.7780 (p) REVERT: C 718 PHE cc_start: 0.7992 (p90) cc_final: 0.7576 (p90) REVERT: C 772 VAL cc_start: 0.8427 (p) cc_final: 0.8149 (m) REVERT: C 820 ASP cc_start: 0.7938 (t0) cc_final: 0.7685 (m-30) REVERT: C 947 LYS cc_start: 0.8350 (mttt) cc_final: 0.8130 (mttp) REVERT: C 979 ASP cc_start: 0.7709 (t70) cc_final: 0.7414 (m-30) REVERT: C 1010 GLN cc_start: 0.7657 (mt0) cc_final: 0.7433 (mm-40) REVERT: C 1128 VAL cc_start: 0.8773 (m) cc_final: 0.8475 (p) REVERT: E 40 SER cc_start: 0.7742 (t) cc_final: 0.7222 (p) REVERT: E 61 LYS cc_start: 0.8104 (mttt) cc_final: 0.7726 (mttt) REVERT: E 64 GLU cc_start: 0.6058 (mm-30) cc_final: 0.5755 (mm-30) REVERT: E 75 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6542 (pp20) REVERT: E 381 TYR cc_start: 0.5712 (t80) cc_final: 0.5376 (t80) REVERT: E 502 SER cc_start: -0.4917 (OUTLIER) cc_final: -0.5214 (t) REVERT: E 562 ASN cc_start: 0.6637 (t0) cc_final: 0.6314 (t0) REVERT: E 568 LYS cc_start: 0.7574 (tptp) cc_final: 0.7322 (mmtp) REVERT: E 609 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5957 (pm20) outliers start: 105 outliers final: 48 residues processed: 904 average time/residue: 0.1978 time to fit residues: 292.4814 Evaluate side-chains 811 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 755 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 552 GLN Chi-restraints excluded: chain E residue 609 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 207 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 376 optimal weight: 0.5980 chunk 346 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 341 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 388 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN B 30 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 218 GLN B 613 GLN B 784 GLN D 221 GLN D 239 HIS D 322 HIS D 373 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 901 GLN E 30 ASN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS E 397 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.209614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156184 restraints weight = 54285.196| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.91 r_work: 0.3655 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 35018 Z= 0.214 Angle : 0.676 14.384 47723 Z= 0.341 Chirality : 0.047 0.567 5374 Planarity : 0.005 0.087 6098 Dihedral : 5.542 96.273 5355 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.53 % Allowed : 17.58 % Favored : 78.89 % 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: -1.62 (0.12), residues: 4202 helix: 0.42 (0.14), residues: 1411 sheet: -0.84 (0.19), residues: 611 loop : -2.25 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 95 TYR 0.023 0.002 TYR B 204 PHE 0.027 0.002 PHE B 201 TRP 0.031 0.002 TRP D 461 HIS 0.009 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00495 (34941) covalent geometry : angle 0.65112 (47532) SS BOND : bond 0.00501 ( 40) SS BOND : angle 2.22996 ( 80) hydrogen bonds : bond 0.04145 ( 1335) hydrogen bonds : angle 4.98436 ( 3699) link_NAG-ASN : bond 0.00817 ( 37) link_NAG-ASN : angle 3.34529 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 813 time to evaluate : 1.175 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7069 (t80) cc_final: 0.6754 (t80) REVERT: A 203 ILE cc_start: 0.8398 (pt) cc_final: 0.8110 (mt) REVERT: A 234 ASN cc_start: 0.5299 (t0) cc_final: 0.4872 (t0) REVERT: A 302 THR cc_start: 0.8659 (m) cc_final: 0.8446 (t) REVERT: A 377 PHE cc_start: 0.8786 (t80) cc_final: 0.8393 (t80) REVERT: A 378 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8291 (ttpp) REVERT: A 524 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7244 (m) REVERT: A 541 PHE cc_start: 0.8329 (p90) cc_final: 0.7934 (p90) REVERT: A 580 GLN cc_start: 0.8168 (mm110) cc_final: 0.7895 (mt0) REVERT: A 710 ASN cc_start: 0.8283 (p0) cc_final: 0.8081 (p0) REVERT: A 725 GLU cc_start: 0.8268 (tt0) cc_final: 0.8057 (tt0) REVERT: A 748 GLU cc_start: 0.7782 (pm20) cc_final: 0.7400 (mp0) REVERT: A 775 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: A 790 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8027 (mtmm) REVERT: A 814 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7791 (mppt) REVERT: A 900 MET cc_start: 0.8452 (mtm) cc_final: 0.8161 (mtp) REVERT: A 934 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8165 (tp) REVERT: A 957 GLN cc_start: 0.8356 (tt0) cc_final: 0.8104 (tt0) REVERT: A 1003 SER cc_start: 0.9057 (p) cc_final: 0.8813 (t) REVERT: A 1084 ASP cc_start: 0.8145 (t0) cc_final: 0.7691 (t0) REVERT: A 1105 THR cc_start: 0.8483 (t) cc_final: 0.8274 (p) REVERT: A 1136 THR cc_start: 0.8552 (t) cc_final: 0.8326 (p) REVERT: B 29 THR cc_start: 0.7195 (t) cc_final: 0.5143 (p) REVERT: B 51 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8537 (p) REVERT: B 129 LYS cc_start: 0.7322 (mmtt) cc_final: 0.6797 (mtmm) REVERT: B 170 TYR cc_start: 0.6037 (m-80) cc_final: 0.5609 (m-80) REVERT: B 196 ASN cc_start: 0.7466 (t0) cc_final: 0.7225 (t0) REVERT: B 298 GLU cc_start: 0.8038 (tp30) cc_final: 0.7653 (tt0) REVERT: B 317 ASN cc_start: 0.8264 (m110) cc_final: 0.7936 (m-40) REVERT: B 340 GLU cc_start: 0.7979 (tp30) cc_final: 0.7551 (tp30) REVERT: B 347 PHE cc_start: 0.7854 (m-80) cc_final: 0.7394 (m-10) REVERT: B 360 ASN cc_start: 0.8486 (m-40) cc_final: 0.8198 (m-40) REVERT: B 361 CYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7130 (p) REVERT: B 385 THR cc_start: 0.8712 (m) cc_final: 0.8423 (t) REVERT: B 514 SER cc_start: 0.8639 (t) cc_final: 0.8268 (p) REVERT: B 619 GLU cc_start: 0.7401 (mp0) cc_final: 0.7046 (mp0) REVERT: B 698 SER cc_start: 0.8918 (t) cc_final: 0.8567 (p) REVERT: B 710 ASN cc_start: 0.8296 (p0) cc_final: 0.8021 (p0) REVERT: B 719 THR cc_start: 0.8617 (t) cc_final: 0.8314 (p) REVERT: B 751 ASN cc_start: 0.8414 (m-40) cc_final: 0.8123 (m-40) REVERT: B 781 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8172 (t) REVERT: B 825 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8043 (mttm) REVERT: B 934 ILE cc_start: 0.8061 (tt) cc_final: 0.7765 (tt) REVERT: B 994 ASP cc_start: 0.8319 (t70) cc_final: 0.8041 (t0) REVERT: B 1017 GLU cc_start: 0.8051 (tp30) cc_final: 0.7772 (tp30) REVERT: B 1073 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8031 (mtpp) REVERT: B 1104 VAL cc_start: 0.8823 (t) cc_final: 0.8455 (p) REVERT: B 1119 ASN cc_start: 0.8170 (p0) cc_final: 0.7945 (p0) REVERT: B 1125 ASN cc_start: 0.8125 (p0) cc_final: 0.7880 (p0) REVERT: B 1127 ASP cc_start: 0.8161 (t0) cc_final: 0.7702 (t0) REVERT: B 1128 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8479 (p) REVERT: D 38 ASP cc_start: 0.7557 (t0) cc_final: 0.7228 (t0) REVERT: D 61 LYS cc_start: 0.8617 (mttt) cc_final: 0.8219 (mttt) REVERT: D 163 TRP cc_start: 0.4196 (p-90) cc_final: 0.3326 (p-90) REVERT: D 190 MET cc_start: 0.7662 (ptm) cc_final: 0.5956 (tpt) REVERT: D 225 ASP cc_start: 0.7503 (m-30) cc_final: 0.7229 (m-30) REVERT: D 246 ARG cc_start: 0.0600 (mtm110) cc_final: 0.0377 (mmm160) REVERT: D 365 THR cc_start: 0.7479 (p) cc_final: 0.7173 (t) REVERT: D 376 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5602 (ppp) REVERT: D 400 PHE cc_start: 0.4539 (m-80) cc_final: 0.3857 (m-80) REVERT: D 476 LYS cc_start: 0.6030 (pttm) cc_final: 0.5756 (pttm) REVERT: D 515 TYR cc_start: 0.5576 (m-80) cc_final: 0.5113 (m-80) REVERT: D 557 MET cc_start: 0.7579 (tmm) cc_final: 0.7018 (tmm) REVERT: C 204 TYR cc_start: 0.8466 (m-80) cc_final: 0.8265 (m-80) REVERT: C 317 ASN cc_start: 0.8122 (m-40) cc_final: 0.7906 (m-40) REVERT: C 319 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7544 (mtp85) REVERT: C 346 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7565 (ttm110) REVERT: C 529 LYS cc_start: 0.6089 (mtmt) cc_final: 0.5796 (mtmt) REVERT: C 542 ASN cc_start: 0.8284 (t0) cc_final: 0.7781 (t0) REVERT: C 558 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7850 (mmmm) REVERT: C 576 VAL cc_start: 0.8847 (p) cc_final: 0.8624 (t) REVERT: C 610 VAL cc_start: 0.8473 (t) cc_final: 0.8190 (m) REVERT: C 654 GLU cc_start: 0.8504 (tt0) cc_final: 0.8235 (tt0) REVERT: C 663 ASP cc_start: 0.7763 (t0) cc_final: 0.7503 (t0) REVERT: C 708 SER cc_start: 0.8432 (m) cc_final: 0.7978 (p) REVERT: C 710 ASN cc_start: 0.8036 (p0) cc_final: 0.7796 (p0) REVERT: C 781 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (t) REVERT: C 820 ASP cc_start: 0.8114 (t0) cc_final: 0.7896 (m-30) REVERT: C 947 LYS cc_start: 0.8543 (mttt) cc_final: 0.8320 (mttp) REVERT: C 949 GLN cc_start: 0.8306 (mt0) cc_final: 0.8086 (mm-40) REVERT: C 1084 ASP cc_start: 0.8152 (m-30) cc_final: 0.7937 (t0) REVERT: C 1128 VAL cc_start: 0.8745 (m) cc_final: 0.8482 (p) REVERT: C 1136 THR cc_start: 0.8523 (t) cc_final: 0.8138 (p) REVERT: E 61 LYS cc_start: 0.8075 (mttt) cc_final: 0.7698 (mttt) REVERT: E 64 GLU cc_start: 0.6140 (mm-30) cc_final: 0.5785 (mm-30) REVERT: E 75 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6715 (pp20) REVERT: E 87 GLU cc_start: 0.5096 (mp0) cc_final: 0.4408 (mp0) REVERT: E 366 MET cc_start: 0.3128 (mmm) cc_final: 0.2381 (mmp) REVERT: E 562 ASN cc_start: 0.7130 (t0) cc_final: 0.6780 (t0) outliers start: 130 outliers final: 73 residues processed: 881 average time/residue: 0.2004 time to fit residues: 285.7404 Evaluate side-chains 839 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 756 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 369 PHE Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 473 TRP Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 304 optimal weight: 0.4980 chunk 282 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 218 optimal weight: 9.9990 chunk 280 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 208 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 784 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 925 ASN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.207357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153429 restraints weight = 54174.368| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.80 r_work: 0.3642 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 35018 Z= 0.154 Angle : 0.616 13.506 47723 Z= 0.309 Chirality : 0.045 0.518 5374 Planarity : 0.004 0.053 6098 Dihedral : 5.321 87.207 5355 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.58 % Allowed : 19.29 % Favored : 77.13 % 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: -1.27 (0.13), residues: 4202 helix: 0.70 (0.14), residues: 1415 sheet: -0.57 (0.19), residues: 629 loop : -2.06 (0.12), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 95 TYR 0.020 0.001 TYR E 41 PHE 0.026 0.002 PHE C 970 TRP 0.032 0.001 TRP D 461 HIS 0.006 0.001 HIS E 493 Details of bonding type rmsd covalent geometry : bond 0.00361 (34941) covalent geometry : angle 0.59166 (47532) SS BOND : bond 0.00503 ( 40) SS BOND : angle 2.29341 ( 80) hydrogen bonds : bond 0.03607 ( 1335) hydrogen bonds : angle 4.86250 ( 3699) link_NAG-ASN : bond 0.00449 ( 37) link_NAG-ASN : angle 3.11090 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 760 time to evaluate : 1.081 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: A 234 ASN cc_start: 0.5286 (t0) cc_final: 0.4879 (t0) REVERT: A 239 GLN cc_start: 0.7925 (mp10) cc_final: 0.7591 (mp10) REVERT: A 240 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7887 (t) REVERT: A 302 THR cc_start: 0.8656 (m) cc_final: 0.8437 (t) REVERT: A 377 PHE cc_start: 0.8775 (t80) cc_final: 0.8409 (t80) REVERT: A 378 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8199 (ttpp) REVERT: A 388 ASN cc_start: 0.8079 (t0) cc_final: 0.7871 (t0) REVERT: A 524 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.7229 (m) REVERT: A 541 PHE cc_start: 0.8287 (p90) cc_final: 0.8037 (p90) REVERT: A 576 VAL cc_start: 0.8945 (p) cc_final: 0.8736 (t) REVERT: A 580 GLN cc_start: 0.8145 (mm110) cc_final: 0.7835 (mt0) REVERT: A 710 ASN cc_start: 0.8285 (p0) cc_final: 0.8047 (p0) REVERT: A 725 GLU cc_start: 0.8273 (tt0) cc_final: 0.8016 (tt0) REVERT: A 737 ASP cc_start: 0.7625 (t70) cc_final: 0.7221 (t0) REVERT: A 790 LYS cc_start: 0.8524 (mtpt) cc_final: 0.8194 (mtmm) REVERT: A 820 ASP cc_start: 0.7840 (t0) cc_final: 0.7428 (m-30) REVERT: A 900 MET cc_start: 0.8478 (mtm) cc_final: 0.8163 (mtp) REVERT: A 934 ILE cc_start: 0.8636 (tt) cc_final: 0.8241 (tp) REVERT: A 957 GLN cc_start: 0.8308 (tt0) cc_final: 0.8035 (tt0) REVERT: A 1003 SER cc_start: 0.9000 (p) cc_final: 0.8742 (t) REVERT: A 1105 THR cc_start: 0.8478 (t) cc_final: 0.8217 (p) REVERT: A 1136 THR cc_start: 0.8576 (t) cc_final: 0.8358 (p) REVERT: B 29 THR cc_start: 0.7263 (t) cc_final: 0.5190 (p) REVERT: B 51 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8511 (p) REVERT: B 129 LYS cc_start: 0.7335 (mmtt) cc_final: 0.6789 (mtmm) REVERT: B 142 ASP cc_start: 0.6370 (p0) cc_final: 0.6012 (p0) REVERT: B 170 TYR cc_start: 0.6137 (m-80) cc_final: 0.5838 (m-80) REVERT: B 317 ASN cc_start: 0.8266 (m110) cc_final: 0.7947 (m-40) REVERT: B 340 GLU cc_start: 0.8005 (tp30) cc_final: 0.7586 (tp30) REVERT: B 347 PHE cc_start: 0.7918 (m-80) cc_final: 0.7460 (m-10) REVERT: B 360 ASN cc_start: 0.8480 (m-40) cc_final: 0.8214 (m-40) REVERT: B 361 CYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7145 (p) REVERT: B 385 THR cc_start: 0.8684 (m) cc_final: 0.8446 (t) REVERT: B 396 TYR cc_start: 0.8150 (m-80) cc_final: 0.7946 (m-10) REVERT: B 453 TYR cc_start: 0.8122 (p90) cc_final: 0.7789 (p90) REVERT: B 514 SER cc_start: 0.8627 (t) cc_final: 0.8220 (p) REVERT: B 543 PHE cc_start: 0.7977 (m-80) cc_final: 0.7645 (m-80) REVERT: B 619 GLU cc_start: 0.7132 (mp0) cc_final: 0.6803 (mp0) REVERT: B 651 ILE cc_start: 0.8606 (pt) cc_final: 0.8247 (mt) REVERT: B 698 SER cc_start: 0.8897 (t) cc_final: 0.8569 (p) REVERT: B 710 ASN cc_start: 0.8344 (p0) cc_final: 0.8090 (p0) REVERT: B 719 THR cc_start: 0.8643 (t) cc_final: 0.8374 (p) REVERT: B 747 THR cc_start: 0.8320 (p) cc_final: 0.7858 (p) REVERT: B 751 ASN cc_start: 0.8449 (m-40) cc_final: 0.8154 (m-40) REVERT: B 781 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8099 (t) REVERT: B 934 ILE cc_start: 0.8119 (tt) cc_final: 0.7837 (tt) REVERT: B 994 ASP cc_start: 0.8192 (t70) cc_final: 0.7922 (t0) REVERT: B 1017 GLU cc_start: 0.7981 (tp30) cc_final: 0.7713 (tp30) REVERT: B 1028 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8125 (mttm) REVERT: B 1104 VAL cc_start: 0.8837 (t) cc_final: 0.8481 (p) REVERT: B 1119 ASN cc_start: 0.8175 (p0) cc_final: 0.7891 (p0) REVERT: B 1127 ASP cc_start: 0.8186 (t0) cc_final: 0.7819 (t0) REVERT: B 1128 VAL cc_start: 0.8752 (m) cc_final: 0.8488 (p) REVERT: D 38 ASP cc_start: 0.7556 (t0) cc_final: 0.7215 (t0) REVERT: D 61 LYS cc_start: 0.8592 (mttt) cc_final: 0.8208 (mttt) REVERT: D 114 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8446 (pttt) REVERT: D 152 MET cc_start: 0.4229 (OUTLIER) cc_final: 0.4028 (ptt) REVERT: D 190 MET cc_start: 0.7488 (ptm) cc_final: 0.5729 (tpt) REVERT: D 225 ASP cc_start: 0.7518 (m-30) cc_final: 0.7161 (m-30) REVERT: D 246 ARG cc_start: 0.0784 (mtm110) cc_final: 0.0538 (mmm160) REVERT: D 298 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6357 (ttm) REVERT: D 313 LYS cc_start: 0.7328 (tptp) cc_final: 0.6939 (mtmm) REVERT: D 327 PHE cc_start: 0.7253 (t80) cc_final: 0.6992 (m-80) REVERT: D 365 THR cc_start: 0.7433 (p) cc_final: 0.7159 (t) REVERT: D 400 PHE cc_start: 0.4472 (m-80) cc_final: 0.3822 (m-80) REVERT: D 557 MET cc_start: 0.7625 (tmm) cc_final: 0.7061 (tmm) REVERT: C 58 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7748 (m-10) REVERT: C 317 ASN cc_start: 0.8208 (m-40) cc_final: 0.7972 (m-40) REVERT: C 319 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7489 (mtp85) REVERT: C 339 ASP cc_start: 0.7954 (p0) cc_final: 0.7654 (p0) REVERT: C 346 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7653 (ttm110) REVERT: C 542 ASN cc_start: 0.8315 (t0) cc_final: 0.7860 (t0) REVERT: C 558 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7955 (mmmm) REVERT: C 607 GLN cc_start: 0.8393 (mt0) cc_final: 0.8152 (mt0) REVERT: C 610 VAL cc_start: 0.8457 (t) cc_final: 0.8191 (m) REVERT: C 654 GLU cc_start: 0.8457 (tt0) cc_final: 0.8212 (tt0) REVERT: C 708 SER cc_start: 0.8397 (m) cc_final: 0.7949 (p) REVERT: C 710 ASN cc_start: 0.8050 (p0) cc_final: 0.7815 (p0) REVERT: C 820 ASP cc_start: 0.8060 (t0) cc_final: 0.7804 (m-30) REVERT: C 947 LYS cc_start: 0.8507 (mttt) cc_final: 0.8262 (mtmm) REVERT: C 949 GLN cc_start: 0.8280 (mt0) cc_final: 0.8060 (mm-40) REVERT: C 980 ILE cc_start: 0.8069 (mm) cc_final: 0.7636 (mt) REVERT: C 1128 VAL cc_start: 0.8734 (m) cc_final: 0.8445 (p) REVERT: C 1130 ILE cc_start: 0.8486 (pt) cc_final: 0.8123 (mt) REVERT: C 1136 THR cc_start: 0.8516 (t) cc_final: 0.8174 (p) REVERT: E 58 ASN cc_start: 0.6246 (m-40) cc_final: 0.4562 (m-40) REVERT: E 61 LYS cc_start: 0.8143 (mttt) cc_final: 0.7764 (mttt) REVERT: E 64 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5793 (mm-30) REVERT: E 75 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6840 (pp20) REVERT: E 94 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7700 (pttt) REVERT: E 309 GLN cc_start: 0.7127 (tm-30) cc_final: 0.6488 (pp30) REVERT: E 349 TRP cc_start: 0.5400 (m100) cc_final: 0.5111 (m100) REVERT: E 521 TYR cc_start: 0.6268 (m-10) cc_final: 0.6035 (m-10) REVERT: E 562 ASN cc_start: 0.7194 (t0) cc_final: 0.6874 (t0) REVERT: E 568 LYS cc_start: 0.7337 (mmmt) cc_final: 0.7044 (mmmm) outliers start: 132 outliers final: 84 residues processed: 830 average time/residue: 0.1991 time to fit residues: 268.4186 Evaluate side-chains 838 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 742 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 272 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 346 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 188 ASN D 277 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS D 586 ASN C1054 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.205231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.151245 restraints weight = 54655.797| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.76 r_work: 0.3618 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35018 Z= 0.149 Angle : 0.609 13.189 47723 Z= 0.305 Chirality : 0.045 0.515 5374 Planarity : 0.004 0.051 6098 Dihedral : 5.141 83.368 5354 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.93 % Allowed : 19.02 % Favored : 77.05 % 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: -1.04 (0.13), residues: 4202 helix: 0.81 (0.14), residues: 1412 sheet: -0.36 (0.19), residues: 628 loop : -1.88 (0.12), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 95 TYR 0.020 0.001 TYR E 127 PHE 0.027 0.002 PHE B 970 TRP 0.046 0.001 TRP D 461 HIS 0.006 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00344 (34941) covalent geometry : angle 0.58584 (47532) SS BOND : bond 0.00486 ( 40) SS BOND : angle 2.19461 ( 80) hydrogen bonds : bond 0.03593 ( 1335) hydrogen bonds : angle 4.77673 ( 3699) link_NAG-ASN : bond 0.00463 ( 37) link_NAG-ASN : angle 3.01073 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 786 time to evaluate : 1.203 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: symmetry clash REVERT: A 204 TYR cc_start: 0.7456 (m-80) cc_final: 0.6912 (m-80) REVERT: A 239 GLN cc_start: 0.7926 (mp10) cc_final: 0.7590 (mp10) REVERT: A 240 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7822 (t) REVERT: A 377 PHE cc_start: 0.8783 (t80) cc_final: 0.8457 (t80) REVERT: A 378 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8198 (ttpp) REVERT: A 388 ASN cc_start: 0.8135 (t0) cc_final: 0.7899 (t0) REVERT: A 524 VAL cc_start: 0.7428 (OUTLIER) cc_final: 0.7124 (m) REVERT: A 541 PHE cc_start: 0.8247 (p90) cc_final: 0.7972 (p90) REVERT: A 554 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 576 VAL cc_start: 0.8928 (p) cc_final: 0.8716 (t) REVERT: A 580 GLN cc_start: 0.8220 (mm110) cc_final: 0.7851 (mt0) REVERT: A 583 GLU cc_start: 0.7720 (tp30) cc_final: 0.7450 (tp30) REVERT: A 710 ASN cc_start: 0.8325 (p0) cc_final: 0.8102 (p0) REVERT: A 737 ASP cc_start: 0.7589 (t70) cc_final: 0.7317 (t0) REVERT: A 790 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8163 (mtmm) REVERT: A 820 ASP cc_start: 0.7805 (t0) cc_final: 0.7384 (m-30) REVERT: A 900 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8122 (mtp) REVERT: A 934 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8357 (tp) REVERT: A 957 GLN cc_start: 0.8282 (tt0) cc_final: 0.8013 (tt0) REVERT: A 1003 SER cc_start: 0.9006 (p) cc_final: 0.8757 (t) REVERT: A 1028 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8147 (mttm) REVERT: A 1050 MET cc_start: 0.8514 (ptm) cc_final: 0.8308 (ptp) REVERT: A 1105 THR cc_start: 0.8516 (t) cc_final: 0.8243 (p) REVERT: A 1120 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 29 THR cc_start: 0.7289 (t) cc_final: 0.5042 (p) REVERT: B 118 LEU cc_start: 0.8344 (tp) cc_final: 0.8127 (tt) REVERT: B 129 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6853 (mtmm) REVERT: B 142 ASP cc_start: 0.6515 (p0) cc_final: 0.6130 (p0) REVERT: B 298 GLU cc_start: 0.7998 (tp30) cc_final: 0.7731 (tp30) REVERT: B 317 ASN cc_start: 0.8375 (m110) cc_final: 0.8082 (m-40) REVERT: B 340 GLU cc_start: 0.8037 (tp30) cc_final: 0.7661 (tp30) REVERT: B 347 PHE cc_start: 0.7911 (m-80) cc_final: 0.7574 (m-10) REVERT: B 360 ASN cc_start: 0.8455 (m-40) cc_final: 0.8205 (m-40) REVERT: B 361 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7288 (p) REVERT: B 385 THR cc_start: 0.8709 (m) cc_final: 0.8473 (t) REVERT: B 430 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8827 (p) REVERT: B 453 TYR cc_start: 0.8159 (p90) cc_final: 0.7684 (p90) REVERT: B 514 SER cc_start: 0.8602 (t) cc_final: 0.8229 (p) REVERT: B 543 PHE cc_start: 0.8057 (m-80) cc_final: 0.7734 (m-80) REVERT: B 619 GLU cc_start: 0.7105 (mp0) cc_final: 0.6841 (mp0) REVERT: B 651 ILE cc_start: 0.8609 (pt) cc_final: 0.8254 (mt) REVERT: B 698 SER cc_start: 0.8880 (t) cc_final: 0.8549 (p) REVERT: B 710 ASN cc_start: 0.8406 (p0) cc_final: 0.8143 (p0) REVERT: B 719 THR cc_start: 0.8635 (t) cc_final: 0.8402 (p) REVERT: B 730 SER cc_start: 0.8824 (t) cc_final: 0.8489 (m) REVERT: B 747 THR cc_start: 0.8326 (p) cc_final: 0.7900 (p) REVERT: B 751 ASN cc_start: 0.8426 (m-40) cc_final: 0.8134 (m-40) REVERT: B 781 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8144 (t) REVERT: B 934 ILE cc_start: 0.8123 (tt) cc_final: 0.7825 (tt) REVERT: B 950 ASP cc_start: 0.8026 (m-30) cc_final: 0.7628 (m-30) REVERT: B 994 ASP cc_start: 0.8212 (t70) cc_final: 0.7943 (t0) REVERT: B 1017 GLU cc_start: 0.7954 (tp30) cc_final: 0.7663 (tp30) REVERT: B 1028 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8192 (mttm) REVERT: B 1104 VAL cc_start: 0.8838 (t) cc_final: 0.8457 (p) REVERT: B 1127 ASP cc_start: 0.8109 (t0) cc_final: 0.7829 (t0) REVERT: D 22 GLU cc_start: 0.6993 (tp30) cc_final: 0.6747 (mm-30) REVERT: D 27 THR cc_start: 0.7925 (p) cc_final: 0.7601 (m) REVERT: D 42 GLN cc_start: 0.7182 (mt0) cc_final: 0.6702 (mt0) REVERT: D 61 LYS cc_start: 0.8645 (mttt) cc_final: 0.8412 (ptpt) REVERT: D 114 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8494 (pttt) REVERT: D 225 ASP cc_start: 0.7472 (m-30) cc_final: 0.7181 (m-30) REVERT: D 246 ARG cc_start: 0.0687 (mtm110) cc_final: 0.0483 (mmp-170) REVERT: D 249 MET cc_start: 0.5897 (tpt) cc_final: 0.4444 (mmp) REVERT: D 308 PHE cc_start: 0.8175 (m-80) cc_final: 0.7899 (m-80) REVERT: D 365 THR cc_start: 0.7235 (p) cc_final: 0.6932 (t) REVERT: D 366 MET cc_start: 0.5112 (mmm) cc_final: 0.4194 (mmm) REVERT: D 381 TYR cc_start: 0.8479 (t80) cc_final: 0.7858 (t80) REVERT: D 400 PHE cc_start: 0.4554 (m-80) cc_final: 0.3983 (m-80) REVERT: D 557 MET cc_start: 0.7661 (tmm) cc_final: 0.7179 (tmm) REVERT: D 568 LYS cc_start: 0.7870 (tttm) cc_final: 0.7566 (tptp) REVERT: D 586 ASN cc_start: 0.6409 (m-40) cc_final: 0.5941 (t0) REVERT: C 317 ASN cc_start: 0.8244 (m-40) cc_final: 0.7984 (m-40) REVERT: C 339 ASP cc_start: 0.7983 (p0) cc_final: 0.7702 (p0) REVERT: C 516 GLU cc_start: 0.6426 (tt0) cc_final: 0.6150 (tt0) REVERT: C 542 ASN cc_start: 0.8252 (t0) cc_final: 0.7781 (t0) REVERT: C 558 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8085 (mmmm) REVERT: C 607 GLN cc_start: 0.8543 (mt0) cc_final: 0.8331 (mt0) REVERT: C 654 GLU cc_start: 0.8415 (tt0) cc_final: 0.8188 (tt0) REVERT: C 708 SER cc_start: 0.8371 (m) cc_final: 0.7907 (p) REVERT: C 710 ASN cc_start: 0.8097 (p0) cc_final: 0.7873 (p0) REVERT: C 820 ASP cc_start: 0.8024 (t0) cc_final: 0.7801 (m-30) REVERT: C 947 LYS cc_start: 0.8457 (mttt) cc_final: 0.8249 (mttp) REVERT: C 949 GLN cc_start: 0.8205 (mt0) cc_final: 0.7988 (mm-40) REVERT: C 980 ILE cc_start: 0.8193 (mm) cc_final: 0.7843 (mt) REVERT: C 1029 MET cc_start: 0.8243 (ttm) cc_final: 0.7767 (ttm) REVERT: C 1128 VAL cc_start: 0.8729 (m) cc_final: 0.8429 (p) REVERT: C 1130 ILE cc_start: 0.8490 (pt) cc_final: 0.8158 (mt) REVERT: C 1136 THR cc_start: 0.8549 (t) cc_final: 0.8207 (p) REVERT: E 58 ASN cc_start: 0.6351 (m-40) cc_final: 0.4418 (m110) REVERT: E 61 LYS cc_start: 0.8156 (mttt) cc_final: 0.7804 (mttt) REVERT: E 64 GLU cc_start: 0.6208 (mm-30) cc_final: 0.5852 (mm-30) REVERT: E 94 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7704 (pttt) REVERT: E 116 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6594 (tt) REVERT: E 190 MET cc_start: 0.1740 (ptt) cc_final: 0.1195 (mtt) REVERT: E 278 LEU cc_start: 0.0293 (OUTLIER) cc_final: -0.0060 (tp) REVERT: E 327 PHE cc_start: 0.7850 (t80) cc_final: 0.7408 (t80) REVERT: E 349 TRP cc_start: 0.5477 (m100) cc_final: 0.5161 (m100) REVERT: E 366 MET cc_start: 0.3126 (mmm) cc_final: 0.2602 (mmp) REVERT: E 510 TYR cc_start: 0.5687 (m-80) cc_final: 0.5474 (m-10) REVERT: E 526 GLN cc_start: 0.7783 (tp40) cc_final: 0.7463 (tp40) REVERT: E 579 MET cc_start: 0.4339 (mtm) cc_final: 0.3997 (mmm) outliers start: 145 outliers final: 93 residues processed: 871 average time/residue: 0.2007 time to fit residues: 284.9960 Evaluate side-chains 858 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 751 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 133 optimal weight: 0.7980 chunk 314 optimal weight: 0.9990 chunk 193 optimal weight: 0.4980 chunk 252 optimal weight: 20.0000 chunk 307 optimal weight: 0.5980 chunk 268 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 380 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 210 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C1054 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.205132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150688 restraints weight = 54393.072| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.50 r_work: 0.3617 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35018 Z= 0.142 Angle : 0.622 18.408 47723 Z= 0.312 Chirality : 0.045 0.422 5374 Planarity : 0.004 0.064 6098 Dihedral : 5.514 96.776 5354 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.91 % Allowed : 20.02 % Favored : 76.07 % 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: -0.94 (0.13), residues: 4202 helix: 0.88 (0.14), residues: 1411 sheet: -0.29 (0.19), residues: 639 loop : -1.82 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 460 TYR 0.019 0.001 TYR D 237 PHE 0.029 0.001 PHE D 327 TRP 0.016 0.001 TRP D 69 HIS 0.005 0.001 HIS E 493 Details of bonding type rmsd covalent geometry : bond 0.00331 (34941) covalent geometry : angle 0.59828 (47532) SS BOND : bond 0.00420 ( 40) SS BOND : angle 2.74145 ( 80) hydrogen bonds : bond 0.03542 ( 1335) hydrogen bonds : angle 4.76272 ( 3699) link_NAG-ASN : bond 0.00512 ( 37) link_NAG-ASN : angle 2.80240 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 770 time to evaluate : 1.090 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 203 ILE cc_start: 0.8612 (pt) cc_final: 0.8256 (mt) REVERT: A 204 TYR cc_start: 0.7439 (m-80) cc_final: 0.6930 (m-80) REVERT: A 235 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5516 (mt) REVERT: A 239 GLN cc_start: 0.7909 (mp10) cc_final: 0.7639 (mp10) REVERT: A 240 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7799 (t) REVERT: A 360 ASN cc_start: 0.7536 (m-40) cc_final: 0.7227 (m-40) REVERT: A 377 PHE cc_start: 0.8741 (t80) cc_final: 0.8429 (t80) REVERT: A 378 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8158 (ttpp) REVERT: A 388 ASN cc_start: 0.8019 (t0) cc_final: 0.7729 (t0) REVERT: A 524 VAL cc_start: 0.7353 (OUTLIER) cc_final: 0.7095 (m) REVERT: A 541 PHE cc_start: 0.8240 (p90) cc_final: 0.8032 (p90) REVERT: A 554 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7023 (mm-30) REVERT: A 562 PHE cc_start: 0.8506 (p90) cc_final: 0.8298 (p90) REVERT: A 576 VAL cc_start: 0.8919 (p) cc_final: 0.8704 (t) REVERT: A 580 GLN cc_start: 0.8169 (mm110) cc_final: 0.7853 (mt0) REVERT: A 583 GLU cc_start: 0.7706 (tp30) cc_final: 0.7497 (tp30) REVERT: A 592 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7695 (t80) REVERT: A 710 ASN cc_start: 0.8364 (p0) cc_final: 0.8144 (p0) REVERT: A 754 LEU cc_start: 0.8762 (mt) cc_final: 0.8556 (mp) REVERT: A 790 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8112 (mtmm) REVERT: A 804 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8121 (mm-40) REVERT: A 820 ASP cc_start: 0.7765 (t0) cc_final: 0.7351 (m-30) REVERT: A 900 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8109 (mtp) REVERT: A 934 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8389 (tp) REVERT: A 957 GLN cc_start: 0.8245 (tt0) cc_final: 0.7977 (tt0) REVERT: A 1003 SER cc_start: 0.8975 (p) cc_final: 0.8725 (t) REVERT: A 1005 GLN cc_start: 0.8283 (tp40) cc_final: 0.8063 (mt0) REVERT: A 1105 THR cc_start: 0.8531 (t) cc_final: 0.8257 (p) REVERT: A 1120 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 29 THR cc_start: 0.7305 (t) cc_final: 0.5042 (p) REVERT: B 65 PHE cc_start: 0.7803 (m-10) cc_final: 0.7519 (m-80) REVERT: B 118 LEU cc_start: 0.8355 (tp) cc_final: 0.8131 (tt) REVERT: B 129 LYS cc_start: 0.7347 (mmtt) cc_final: 0.6875 (mtmm) REVERT: B 170 TYR cc_start: 0.6167 (m-80) cc_final: 0.5663 (m-80) REVERT: B 237 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6742 (mmt180) REVERT: B 298 GLU cc_start: 0.7974 (tp30) cc_final: 0.7660 (tt0) REVERT: B 317 ASN cc_start: 0.8361 (m110) cc_final: 0.7994 (m-40) REVERT: B 340 GLU cc_start: 0.8047 (tp30) cc_final: 0.7715 (tp30) REVERT: B 347 PHE cc_start: 0.7937 (m-80) cc_final: 0.7638 (m-10) REVERT: B 360 ASN cc_start: 0.8424 (m-40) cc_final: 0.8166 (m-40) REVERT: B 361 CYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7261 (p) REVERT: B 385 THR cc_start: 0.8645 (m) cc_final: 0.8414 (t) REVERT: B 430 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8809 (p) REVERT: B 453 TYR cc_start: 0.8143 (p90) cc_final: 0.7612 (p90) REVERT: B 462 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8367 (mmmm) REVERT: B 514 SER cc_start: 0.8570 (t) cc_final: 0.8171 (p) REVERT: B 537 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8342 (ptmt) REVERT: B 543 PHE cc_start: 0.8094 (m-80) cc_final: 0.7823 (m-80) REVERT: B 651 ILE cc_start: 0.8590 (pt) cc_final: 0.8248 (mt) REVERT: B 698 SER cc_start: 0.8836 (t) cc_final: 0.8441 (p) REVERT: B 710 ASN cc_start: 0.8399 (p0) cc_final: 0.8132 (p0) REVERT: B 719 THR cc_start: 0.8631 (t) cc_final: 0.8413 (p) REVERT: B 730 SER cc_start: 0.8802 (t) cc_final: 0.8464 (m) REVERT: B 747 THR cc_start: 0.8365 (p) cc_final: 0.7877 (p) REVERT: B 751 ASN cc_start: 0.8414 (m-40) cc_final: 0.8121 (m-40) REVERT: B 781 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8132 (t) REVERT: B 994 ASP cc_start: 0.8150 (t70) cc_final: 0.7891 (t0) REVERT: B 1017 GLU cc_start: 0.7908 (tp30) cc_final: 0.7602 (tp30) REVERT: B 1084 ASP cc_start: 0.7994 (t0) cc_final: 0.7593 (t0) REVERT: B 1127 ASP cc_start: 0.8058 (t0) cc_final: 0.7829 (t0) REVERT: D 22 GLU cc_start: 0.6944 (tp30) cc_final: 0.6636 (tp30) REVERT: D 27 THR cc_start: 0.7961 (p) cc_final: 0.7742 (t) REVERT: D 42 GLN cc_start: 0.7205 (mt0) cc_final: 0.6837 (mt0) REVERT: D 61 LYS cc_start: 0.8637 (mttt) cc_final: 0.8425 (ptpt) REVERT: D 94 LYS cc_start: 0.8231 (tttt) cc_final: 0.7921 (tttt) REVERT: D 225 ASP cc_start: 0.7482 (m-30) cc_final: 0.7281 (m-30) REVERT: D 249 MET cc_start: 0.5875 (tpt) cc_final: 0.4562 (tpt) REVERT: D 298 MET cc_start: 0.6581 (ttm) cc_final: 0.6244 (ttm) REVERT: D 308 PHE cc_start: 0.8090 (m-80) cc_final: 0.7823 (m-80) REVERT: D 365 THR cc_start: 0.7172 (p) cc_final: 0.6880 (t) REVERT: D 366 MET cc_start: 0.5233 (mmm) cc_final: 0.4371 (mmm) REVERT: D 381 TYR cc_start: 0.8424 (t80) cc_final: 0.7757 (t80) REVERT: D 400 PHE cc_start: 0.4610 (m-80) cc_final: 0.4017 (m-80) REVERT: D 455 MET cc_start: 0.7605 (ptp) cc_final: 0.7303 (ptp) REVERT: D 557 MET cc_start: 0.7681 (tmm) cc_final: 0.7226 (tmm) REVERT: D 568 LYS cc_start: 0.7998 (tttm) cc_final: 0.7562 (tptt) REVERT: D 586 ASN cc_start: 0.6391 (m-40) cc_final: 0.6018 (t0) REVERT: C 34 ARG cc_start: 0.7256 (mtp85) cc_final: 0.6928 (mtt90) REVERT: C 317 ASN cc_start: 0.8236 (m-40) cc_final: 0.7960 (m-40) REVERT: C 339 ASP cc_start: 0.7945 (p0) cc_final: 0.7662 (p0) REVERT: C 453 TYR cc_start: 0.7041 (p90) cc_final: 0.6615 (p90) REVERT: C 495 TYR cc_start: 0.6305 (m-80) cc_final: 0.5167 (m-10) REVERT: C 516 GLU cc_start: 0.6549 (tt0) cc_final: 0.6279 (tt0) REVERT: C 542 ASN cc_start: 0.8273 (t0) cc_final: 0.7871 (t0) REVERT: C 558 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8026 (mmmm) REVERT: C 583 GLU cc_start: 0.7452 (tp30) cc_final: 0.7226 (tp30) REVERT: C 607 GLN cc_start: 0.8551 (mt0) cc_final: 0.8347 (mt0) REVERT: C 654 GLU cc_start: 0.8356 (tt0) cc_final: 0.8097 (tt0) REVERT: C 708 SER cc_start: 0.8358 (m) cc_final: 0.7909 (p) REVERT: C 710 ASN cc_start: 0.8077 (p0) cc_final: 0.7854 (p0) REVERT: C 820 ASP cc_start: 0.8030 (t0) cc_final: 0.7818 (m-30) REVERT: C 947 LYS cc_start: 0.8465 (mttt) cc_final: 0.8248 (mttp) REVERT: C 980 ILE cc_start: 0.8277 (mm) cc_final: 0.7949 (mt) REVERT: C 1029 MET cc_start: 0.8194 (ttm) cc_final: 0.7796 (ttm) REVERT: C 1128 VAL cc_start: 0.8700 (m) cc_final: 0.8405 (p) REVERT: C 1130 ILE cc_start: 0.8470 (pt) cc_final: 0.8179 (mt) REVERT: C 1136 THR cc_start: 0.8522 (t) cc_final: 0.8202 (p) REVERT: E 41 TYR cc_start: 0.7604 (t80) cc_final: 0.6604 (t80) REVERT: E 61 LYS cc_start: 0.8138 (mttt) cc_final: 0.7774 (mttt) REVERT: E 64 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5850 (mm-30) REVERT: E 94 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7748 (pttt) REVERT: E 116 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6692 (tt) REVERT: E 169 ARG cc_start: 0.2359 (ttp80) cc_final: 0.0605 (ptm160) REVERT: E 190 MET cc_start: 0.1696 (ptt) cc_final: 0.1197 (mtt) REVERT: E 278 LEU cc_start: 0.0256 (OUTLIER) cc_final: -0.0098 (tp) REVERT: E 305 GLU cc_start: 0.6353 (pt0) cc_final: 0.6016 (pm20) REVERT: E 306 ARG cc_start: 0.5009 (mmm160) cc_final: 0.4641 (tpm170) REVERT: E 327 PHE cc_start: 0.7889 (t80) cc_final: 0.7382 (t80) REVERT: E 349 TRP cc_start: 0.5485 (m100) cc_final: 0.5168 (m100) REVERT: E 381 TYR cc_start: 0.6004 (t80) cc_final: 0.5516 (t80) REVERT: E 510 TYR cc_start: 0.5669 (m-80) cc_final: 0.5450 (m-10) REVERT: E 512 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.5872 (t80) REVERT: E 526 GLN cc_start: 0.7739 (tp40) cc_final: 0.7405 (tp40) REVERT: E 579 MET cc_start: 0.4356 (mtm) cc_final: 0.4059 (mmm) outliers start: 144 outliers final: 98 residues processed: 855 average time/residue: 0.2019 time to fit residues: 279.9263 Evaluate side-chains 864 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 750 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 187 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 321 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 73 optimal weight: 0.0010 chunk 289 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 419 optimal weight: 7.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 388 ASN C 641 ASN C1054 GLN E 24 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 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 = 0.4420 r_free = 0.4420 target = 0.202996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148151 restraints weight = 54483.533| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.51 r_work: 0.3586 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35018 Z= 0.185 Angle : 0.657 23.467 47723 Z= 0.330 Chirality : 0.046 0.359 5374 Planarity : 0.004 0.068 6098 Dihedral : 5.505 97.279 5354 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.96 % Allowed : 20.32 % Favored : 75.72 % 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: -0.87 (0.13), residues: 4202 helix: 0.87 (0.14), residues: 1412 sheet: -0.24 (0.20), residues: 632 loop : -1.73 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 460 TYR 0.031 0.002 TYR E 207 PHE 0.033 0.002 PHE D 72 TRP 0.017 0.001 TRP D 69 HIS 0.014 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00426 (34941) covalent geometry : angle 0.62965 (47532) SS BOND : bond 0.00573 ( 40) SS BOND : angle 2.97976 ( 80) hydrogen bonds : bond 0.03782 ( 1335) hydrogen bonds : angle 4.80393 ( 3699) link_NAG-ASN : bond 0.00514 ( 37) link_NAG-ASN : angle 3.10026 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 782 time to evaluate : 1.197 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: A 41 LYS cc_start: 0.6206 (ttmt) cc_final: 0.5756 (mtpt) REVERT: A 203 ILE cc_start: 0.8600 (pt) cc_final: 0.8230 (mt) REVERT: A 204 TYR cc_start: 0.7466 (m-80) cc_final: 0.7003 (m-80) REVERT: A 235 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.6098 (mt) REVERT: A 239 GLN cc_start: 0.7866 (mp10) cc_final: 0.7642 (mp10) REVERT: A 240 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7843 (t) REVERT: A 360 ASN cc_start: 0.7470 (m-40) cc_final: 0.7196 (m-40) REVERT: A 377 PHE cc_start: 0.8750 (t80) cc_final: 0.8472 (t80) REVERT: A 378 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8197 (ttpp) REVERT: A 524 VAL cc_start: 0.7303 (OUTLIER) cc_final: 0.7032 (m) REVERT: A 541 PHE cc_start: 0.8252 (p90) cc_final: 0.8007 (p90) REVERT: A 576 VAL cc_start: 0.8940 (p) cc_final: 0.8718 (t) REVERT: A 580 GLN cc_start: 0.8161 (mm110) cc_final: 0.7864 (mt0) REVERT: A 592 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7733 (t80) REVERT: A 710 ASN cc_start: 0.8454 (p0) cc_final: 0.8237 (p0) REVERT: A 725 GLU cc_start: 0.8237 (tt0) cc_final: 0.7978 (tt0) REVERT: A 737 ASP cc_start: 0.7842 (m-30) cc_final: 0.7594 (m-30) REVERT: A 775 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: A 820 ASP cc_start: 0.7775 (t0) cc_final: 0.7368 (m-30) REVERT: A 900 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8119 (mtp) REVERT: A 934 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 957 GLN cc_start: 0.8235 (tt0) cc_final: 0.7954 (tt0) REVERT: A 1003 SER cc_start: 0.8954 (p) cc_final: 0.8699 (t) REVERT: A 1028 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8072 (mtpp) REVERT: A 1105 THR cc_start: 0.8497 (t) cc_final: 0.8226 (p) REVERT: A 1120 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 1127 ASP cc_start: 0.7677 (t0) cc_final: 0.7471 (t0) REVERT: B 65 PHE cc_start: 0.7772 (m-10) cc_final: 0.7459 (m-80) REVERT: B 237 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6820 (mmt180) REVERT: B 298 GLU cc_start: 0.7975 (tp30) cc_final: 0.7429 (tp30) REVERT: B 340 GLU cc_start: 0.8099 (tp30) cc_final: 0.7827 (tp30) REVERT: B 360 ASN cc_start: 0.8483 (m-40) cc_final: 0.8209 (m-40) REVERT: B 361 CYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7179 (p) REVERT: B 385 THR cc_start: 0.8675 (m) cc_final: 0.8465 (t) REVERT: B 430 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8798 (p) REVERT: B 462 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8461 (mmmm) REVERT: B 514 SER cc_start: 0.8560 (t) cc_final: 0.8165 (p) REVERT: B 698 SER cc_start: 0.8810 (t) cc_final: 0.8417 (p) REVERT: B 710 ASN cc_start: 0.8449 (p0) cc_final: 0.8163 (p0) REVERT: B 719 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8398 (p) REVERT: B 730 SER cc_start: 0.8780 (t) cc_final: 0.8479 (m) REVERT: B 747 THR cc_start: 0.8301 (p) cc_final: 0.7835 (p) REVERT: B 751 ASN cc_start: 0.8409 (m-40) cc_final: 0.8111 (m-40) REVERT: B 781 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8187 (t) REVERT: B 907 ASN cc_start: 0.8412 (t0) cc_final: 0.8082 (t0) REVERT: B 950 ASP cc_start: 0.8001 (m-30) cc_final: 0.7618 (m-30) REVERT: B 966 LEU cc_start: 0.9059 (mt) cc_final: 0.8798 (mt) REVERT: B 1017 GLU cc_start: 0.7941 (tp30) cc_final: 0.7616 (tp30) REVERT: B 1084 ASP cc_start: 0.8071 (t0) cc_final: 0.7655 (t0) REVERT: B 1127 ASP cc_start: 0.8087 (t0) cc_final: 0.7884 (t0) REVERT: D 22 GLU cc_start: 0.6942 (tp30) cc_final: 0.6644 (tp30) REVERT: D 23 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7709 (pt0) REVERT: D 61 LYS cc_start: 0.8614 (mttt) cc_final: 0.8374 (ptpt) REVERT: D 94 LYS cc_start: 0.8212 (tttt) cc_final: 0.7920 (tttt) REVERT: D 163 TRP cc_start: 0.4184 (p-90) cc_final: 0.3291 (p-90) REVERT: D 249 MET cc_start: 0.5562 (tpt) cc_final: 0.4851 (tpt) REVERT: D 298 MET cc_start: 0.6585 (ttm) cc_final: 0.6373 (ttm) REVERT: D 308 PHE cc_start: 0.8024 (m-80) cc_final: 0.7764 (m-80) REVERT: D 327 PHE cc_start: 0.7421 (m-80) cc_final: 0.6768 (m-80) REVERT: D 355 ASP cc_start: 0.6379 (t0) cc_final: 0.6099 (t0) REVERT: D 365 THR cc_start: 0.7108 (p) cc_final: 0.6785 (t) REVERT: D 366 MET cc_start: 0.5215 (mmm) cc_final: 0.4358 (mmm) REVERT: D 381 TYR cc_start: 0.8440 (t80) cc_final: 0.7744 (t80) REVERT: D 400 PHE cc_start: 0.4554 (m-80) cc_final: 0.3977 (m-80) REVERT: D 440 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6164 (pp) REVERT: D 455 MET cc_start: 0.7527 (ptp) cc_final: 0.7256 (ptp) REVERT: D 460 ARG cc_start: 0.6288 (tpt170) cc_final: 0.5875 (tpp80) REVERT: D 557 MET cc_start: 0.7737 (tmm) cc_final: 0.7291 (tmm) REVERT: D 568 LYS cc_start: 0.8026 (tttm) cc_final: 0.7495 (tptt) REVERT: D 586 ASN cc_start: 0.6423 (m-40) cc_final: 0.6027 (t0) REVERT: C 317 ASN cc_start: 0.8223 (m-40) cc_final: 0.7906 (m-40) REVERT: C 339 ASP cc_start: 0.8024 (p0) cc_final: 0.7774 (p0) REVERT: C 346 ARG cc_start: 0.8118 (ttm170) cc_final: 0.7803 (ttm110) REVERT: C 453 TYR cc_start: 0.7127 (p90) cc_final: 0.6619 (p90) REVERT: C 495 TYR cc_start: 0.6399 (m-80) cc_final: 0.5202 (m-10) REVERT: C 516 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6458 (tt0) REVERT: C 542 ASN cc_start: 0.8277 (t0) cc_final: 0.7864 (t0) REVERT: C 558 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8013 (mmmm) REVERT: C 578 ASP cc_start: 0.8098 (t0) cc_final: 0.7849 (t0) REVERT: C 642 VAL cc_start: 0.9011 (t) cc_final: 0.8783 (p) REVERT: C 654 GLU cc_start: 0.8406 (tt0) cc_final: 0.8103 (tt0) REVERT: C 691 SER cc_start: 0.8795 (p) cc_final: 0.8298 (m) REVERT: C 708 SER cc_start: 0.8365 (m) cc_final: 0.7935 (p) REVERT: C 820 ASP cc_start: 0.8037 (t0) cc_final: 0.7828 (m-30) REVERT: C 947 LYS cc_start: 0.8429 (mttt) cc_final: 0.8217 (mttp) REVERT: C 1128 VAL cc_start: 0.8704 (m) cc_final: 0.8406 (p) REVERT: C 1130 ILE cc_start: 0.8458 (pt) cc_final: 0.8223 (mt) REVERT: C 1136 THR cc_start: 0.8540 (t) cc_final: 0.8226 (p) REVERT: E 41 TYR cc_start: 0.7697 (t80) cc_final: 0.6709 (t80) REVERT: E 61 LYS cc_start: 0.8143 (mttt) cc_final: 0.7784 (mttt) REVERT: E 64 GLU cc_start: 0.6287 (mm-30) cc_final: 0.5899 (mm-30) REVERT: E 94 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7785 (pttt) REVERT: E 116 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6796 (tt) REVERT: E 169 ARG cc_start: 0.2344 (ttp80) cc_final: 0.0450 (ttt180) REVERT: E 183 TYR cc_start: 0.2482 (OUTLIER) cc_final: 0.0942 (t80) REVERT: E 190 MET cc_start: 0.1790 (ptt) cc_final: 0.1335 (mtt) REVERT: E 278 LEU cc_start: 0.0195 (OUTLIER) cc_final: -0.0178 (tp) REVERT: E 327 PHE cc_start: 0.7927 (t80) cc_final: 0.7392 (t80) REVERT: E 349 TRP cc_start: 0.5552 (m100) cc_final: 0.5187 (m100) REVERT: E 366 MET cc_start: 0.2597 (mmm) cc_final: 0.1935 (mmp) REVERT: E 476 LYS cc_start: 0.6650 (tptt) cc_final: 0.6330 (pttm) REVERT: E 480 MET cc_start: 0.7449 (mtp) cc_final: 0.6607 (mtp) REVERT: E 510 TYR cc_start: 0.5762 (m-80) cc_final: 0.5557 (m-10) REVERT: E 526 GLN cc_start: 0.7709 (tp40) cc_final: 0.7363 (tp40) REVERT: E 579 MET cc_start: 0.4268 (mtm) cc_final: 0.4030 (mmm) outliers start: 146 outliers final: 94 residues processed: 871 average time/residue: 0.2058 time to fit residues: 289.1425 Evaluate side-chains 880 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 764 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 234 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 303 optimal weight: 0.3980 chunk 411 optimal weight: 20.0000 chunk 394 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 272 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 385 optimal weight: 9.9990 chunk 389 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B1002 GLN D 42 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 309 GLN C 394 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.202231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147432 restraints weight = 53928.589| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.50 r_work: 0.3567 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35018 Z= 0.167 Angle : 0.664 21.568 47723 Z= 0.332 Chirality : 0.047 0.813 5374 Planarity : 0.004 0.051 6098 Dihedral : 5.504 99.566 5354 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.80 % Allowed : 20.73 % Favored : 75.47 % 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: -0.81 (0.13), residues: 4202 helix: 0.88 (0.14), residues: 1402 sheet: -0.10 (0.20), residues: 626 loop : -1.68 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 228 TYR 0.023 0.002 TYR E 207 PHE 0.027 0.002 PHE D 72 TRP 0.026 0.001 TRP D 328 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00387 (34941) covalent geometry : angle 0.63824 (47532) SS BOND : bond 0.00553 ( 40) SS BOND : angle 2.87770 ( 80) hydrogen bonds : bond 0.03746 ( 1335) hydrogen bonds : angle 4.81907 ( 3699) link_NAG-ASN : bond 0.00599 ( 37) link_NAG-ASN : angle 3.03500 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 785 time to evaluate : 1.047 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: A 129 LYS cc_start: 0.7471 (mmtt) cc_final: 0.7054 (mmtt) REVERT: A 196 ASN cc_start: 0.6432 (p0) cc_final: 0.6040 (p0) REVERT: A 203 ILE cc_start: 0.8615 (pt) cc_final: 0.8230 (mt) REVERT: A 204 TYR cc_start: 0.7475 (m-80) cc_final: 0.7044 (m-80) REVERT: A 239 GLN cc_start: 0.7887 (mp10) cc_final: 0.7656 (mp10) REVERT: A 240 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7844 (t) REVERT: A 360 ASN cc_start: 0.7454 (m-40) cc_final: 0.7196 (m-40) REVERT: A 377 PHE cc_start: 0.8768 (t80) cc_final: 0.8509 (t80) REVERT: A 378 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8178 (ttpp) REVERT: A 524 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.7005 (m) REVERT: A 541 PHE cc_start: 0.8261 (p90) cc_final: 0.8014 (p90) REVERT: A 710 ASN cc_start: 0.8469 (p0) cc_final: 0.8262 (p0) REVERT: A 725 GLU cc_start: 0.8298 (tt0) cc_final: 0.8063 (tt0) REVERT: A 775 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: A 820 ASP cc_start: 0.7760 (t0) cc_final: 0.7362 (m-30) REVERT: A 900 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8105 (mtp) REVERT: A 934 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8418 (tp) REVERT: A 957 GLN cc_start: 0.8261 (tt0) cc_final: 0.7972 (tt0) REVERT: A 1003 SER cc_start: 0.8928 (p) cc_final: 0.8682 (t) REVERT: A 1005 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7767 (mp10) REVERT: A 1028 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8008 (mtpp) REVERT: A 1105 THR cc_start: 0.8493 (t) cc_final: 0.8237 (p) REVERT: A 1120 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8292 (p) REVERT: A 1127 ASP cc_start: 0.7677 (t0) cc_final: 0.7393 (t0) REVERT: A 1139 ASP cc_start: 0.8122 (t0) cc_final: 0.7910 (t0) REVERT: B 65 PHE cc_start: 0.7717 (m-10) cc_final: 0.7459 (m-80) REVERT: B 94 SER cc_start: 0.7876 (t) cc_final: 0.7232 (m) REVERT: B 95 THR cc_start: 0.8003 (t) cc_final: 0.7789 (t) REVERT: B 129 LYS cc_start: 0.7523 (mmtt) cc_final: 0.6995 (mtmm) REVERT: B 159 VAL cc_start: 0.6661 (OUTLIER) cc_final: 0.6414 (m) REVERT: B 237 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6885 (mmp-170) REVERT: B 298 GLU cc_start: 0.7978 (tp30) cc_final: 0.7423 (tp30) REVERT: B 340 GLU cc_start: 0.8148 (tp30) cc_final: 0.7880 (tp30) REVERT: B 347 PHE cc_start: 0.7602 (m-10) cc_final: 0.7387 (m-10) REVERT: B 360 ASN cc_start: 0.8502 (m-40) cc_final: 0.8253 (m-40) REVERT: B 361 CYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7242 (p) REVERT: B 386 LYS cc_start: 0.8071 (mttp) cc_final: 0.7711 (mttp) REVERT: B 430 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8776 (p) REVERT: B 462 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8451 (mmmm) REVERT: B 514 SER cc_start: 0.8562 (t) cc_final: 0.8154 (p) REVERT: B 543 PHE cc_start: 0.8287 (m-80) cc_final: 0.8082 (m-80) REVERT: B 651 ILE cc_start: 0.8538 (pt) cc_final: 0.8253 (mp) REVERT: B 710 ASN cc_start: 0.8463 (p0) cc_final: 0.8172 (p0) REVERT: B 730 SER cc_start: 0.8805 (t) cc_final: 0.8504 (m) REVERT: B 747 THR cc_start: 0.8309 (p) cc_final: 0.7827 (p) REVERT: B 751 ASN cc_start: 0.8416 (m-40) cc_final: 0.8105 (m-40) REVERT: B 781 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8191 (t) REVERT: B 788 ILE cc_start: 0.8563 (mt) cc_final: 0.8337 (mm) REVERT: B 907 ASN cc_start: 0.8405 (t0) cc_final: 0.8079 (t0) REVERT: B 966 LEU cc_start: 0.9056 (mt) cc_final: 0.8805 (mt) REVERT: B 1017 GLU cc_start: 0.7946 (tp30) cc_final: 0.7632 (tp30) REVERT: B 1084 ASP cc_start: 0.8075 (t0) cc_final: 0.7639 (t0) REVERT: B 1127 ASP cc_start: 0.8079 (t0) cc_final: 0.7793 (t0) REVERT: D 22 GLU cc_start: 0.7027 (tp30) cc_final: 0.6726 (tp30) REVERT: D 23 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: D 58 ASN cc_start: 0.7227 (m110) cc_final: 0.6032 (m-40) REVERT: D 61 LYS cc_start: 0.8660 (mttt) cc_final: 0.8432 (ptpt) REVERT: D 69 TRP cc_start: 0.7693 (t60) cc_final: 0.7385 (t60) REVERT: D 94 LYS cc_start: 0.8189 (tttt) cc_final: 0.7895 (tttt) REVERT: D 163 TRP cc_start: 0.4167 (p-90) cc_final: 0.3262 (p-90) REVERT: D 190 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.3161 (tpt) REVERT: D 246 ARG cc_start: 0.1451 (ptm160) cc_final: 0.1248 (mmm160) REVERT: D 249 MET cc_start: 0.5698 (tpt) cc_final: 0.4392 (mmp) REVERT: D 298 MET cc_start: 0.6568 (ttm) cc_final: 0.6266 (ttm) REVERT: D 308 PHE cc_start: 0.7890 (m-80) cc_final: 0.7596 (m-80) REVERT: D 313 LYS cc_start: 0.7610 (tptp) cc_final: 0.7177 (ptpt) REVERT: D 335 GLU cc_start: 0.6790 (pp20) cc_final: 0.4722 (mp0) REVERT: D 355 ASP cc_start: 0.6460 (t0) cc_final: 0.6109 (t0) REVERT: D 365 THR cc_start: 0.7037 (p) cc_final: 0.6770 (t) REVERT: D 366 MET cc_start: 0.5196 (mmm) cc_final: 0.4416 (mmm) REVERT: D 381 TYR cc_start: 0.8407 (t80) cc_final: 0.7649 (t80) REVERT: D 440 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6178 (pp) REVERT: D 455 MET cc_start: 0.7599 (ptp) cc_final: 0.7058 (mtp) REVERT: D 460 ARG cc_start: 0.6278 (tpt170) cc_final: 0.5912 (tpp80) REVERT: D 557 MET cc_start: 0.7717 (tmm) cc_final: 0.7293 (tmm) REVERT: D 568 LYS cc_start: 0.7953 (tttm) cc_final: 0.7561 (tptt) REVERT: D 586 ASN cc_start: 0.6393 (m-40) cc_final: 0.5980 (t0) REVERT: C 317 ASN cc_start: 0.8245 (m-40) cc_final: 0.7908 (m-40) REVERT: C 328 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7564 (mmm-85) REVERT: C 346 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7750 (ttm110) REVERT: C 453 TYR cc_start: 0.7245 (p90) cc_final: 0.6870 (p90) REVERT: C 516 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: C 542 ASN cc_start: 0.8271 (t0) cc_final: 0.7909 (t0) REVERT: C 558 LYS cc_start: 0.8439 (mtmt) cc_final: 0.7999 (mmmm) REVERT: C 654 GLU cc_start: 0.8303 (tt0) cc_final: 0.8033 (tt0) REVERT: C 691 SER cc_start: 0.8781 (p) cc_final: 0.8276 (m) REVERT: C 708 SER cc_start: 0.8350 (m) cc_final: 0.7918 (p) REVERT: C 947 LYS cc_start: 0.8405 (mttt) cc_final: 0.8163 (mtmm) REVERT: C 1128 VAL cc_start: 0.8697 (m) cc_final: 0.8399 (p) REVERT: C 1130 ILE cc_start: 0.8442 (pt) cc_final: 0.8217 (mt) REVERT: C 1136 THR cc_start: 0.8541 (t) cc_final: 0.8237 (p) REVERT: E 41 TYR cc_start: 0.7596 (t80) cc_final: 0.6661 (t80) REVERT: E 61 LYS cc_start: 0.8151 (mttt) cc_final: 0.7787 (mttt) REVERT: E 64 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5842 (mm-30) REVERT: E 94 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7752 (pttt) REVERT: E 116 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6827 (tt) REVERT: E 142 LEU cc_start: -0.0614 (OUTLIER) cc_final: -0.1229 (tp) REVERT: E 169 ARG cc_start: 0.2413 (ttp80) cc_final: 0.2154 (ttp80) REVERT: E 190 MET cc_start: 0.1847 (ptt) cc_final: 0.1380 (mtt) REVERT: E 278 LEU cc_start: 0.0246 (OUTLIER) cc_final: -0.0118 (tp) REVERT: E 305 GLU cc_start: 0.6495 (pt0) cc_final: 0.6187 (pm20) REVERT: E 327 PHE cc_start: 0.7893 (t80) cc_final: 0.7382 (t80) REVERT: E 349 TRP cc_start: 0.5487 (m100) cc_final: 0.5152 (m100) REVERT: E 366 MET cc_start: 0.2855 (mmm) cc_final: 0.1498 (mmp) REVERT: E 476 LYS cc_start: 0.6675 (tptt) cc_final: 0.6363 (pttm) REVERT: E 480 MET cc_start: 0.7335 (mtp) cc_final: 0.6510 (mtp) REVERT: E 510 TYR cc_start: 0.5749 (m-80) cc_final: 0.5526 (m-10) REVERT: E 526 GLN cc_start: 0.7707 (tp40) cc_final: 0.7353 (tp40) REVERT: E 579 MET cc_start: 0.4299 (mtm) cc_final: 0.4005 (mmm) outliers start: 140 outliers final: 100 residues processed: 859 average time/residue: 0.2036 time to fit residues: 283.4215 Evaluate side-chains 889 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 767 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 364 optimal weight: 0.8980 chunk 423 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 356 optimal weight: 0.6980 chunk 380 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS D 42 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 562 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.200513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145572 restraints weight = 53615.384| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.50 r_work: 0.3537 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35018 Z= 0.212 Angle : 0.702 21.124 47723 Z= 0.353 Chirality : 0.047 0.371 5374 Planarity : 0.005 0.052 6098 Dihedral : 5.635 104.946 5354 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.81 % Favored : 95.17 % Rotamer: Outliers : 3.88 % Allowed : 20.89 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 4202 helix: 0.84 (0.14), residues: 1402 sheet: -0.11 (0.20), residues: 630 loop : -1.70 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 306 TYR 0.019 0.002 TYR B1067 PHE 0.030 0.002 PHE C 92 TRP 0.022 0.002 TRP D 328 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00494 (34941) covalent geometry : angle 0.67549 (47532) SS BOND : bond 0.00534 ( 40) SS BOND : angle 2.96138 ( 80) hydrogen bonds : bond 0.04055 ( 1335) hydrogen bonds : angle 4.85594 ( 3699) link_NAG-ASN : bond 0.00493 ( 37) link_NAG-ASN : angle 3.16818 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 774 time to evaluate : 0.849 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: A 129 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7113 (mmtt) REVERT: A 196 ASN cc_start: 0.6472 (p0) cc_final: 0.6189 (p0) REVERT: A 203 ILE cc_start: 0.8605 (pt) cc_final: 0.8215 (mt) REVERT: A 204 TYR cc_start: 0.7510 (m-80) cc_final: 0.7046 (m-80) REVERT: A 239 GLN cc_start: 0.7832 (mp10) cc_final: 0.7546 (mp10) REVERT: A 240 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7870 (t) REVERT: A 360 ASN cc_start: 0.7461 (m-40) cc_final: 0.7251 (m-40) REVERT: A 377 PHE cc_start: 0.8791 (t80) cc_final: 0.8547 (t80) REVERT: A 378 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8180 (ttpp) REVERT: A 524 VAL cc_start: 0.7257 (OUTLIER) cc_final: 0.6995 (m) REVERT: A 541 PHE cc_start: 0.8269 (p90) cc_final: 0.8065 (p90) REVERT: A 583 GLU cc_start: 0.7708 (tp30) cc_final: 0.7497 (tp30) REVERT: A 584 ILE cc_start: 0.8374 (tp) cc_final: 0.8047 (mm) REVERT: A 710 ASN cc_start: 0.8541 (p0) cc_final: 0.8286 (p0) REVERT: A 725 GLU cc_start: 0.8328 (tt0) cc_final: 0.8074 (tt0) REVERT: A 775 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: A 820 ASP cc_start: 0.7783 (t0) cc_final: 0.7374 (m-30) REVERT: A 900 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: A 934 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8430 (tp) REVERT: A 957 GLN cc_start: 0.8249 (tt0) cc_final: 0.7972 (tt0) REVERT: A 1003 SER cc_start: 0.8927 (p) cc_final: 0.8701 (t) REVERT: A 1005 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: A 1105 THR cc_start: 0.8493 (t) cc_final: 0.8244 (p) REVERT: A 1120 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8302 (p) REVERT: A 1127 ASP cc_start: 0.7766 (t0) cc_final: 0.7446 (t0) REVERT: A 1139 ASP cc_start: 0.8115 (t0) cc_final: 0.7907 (t0) REVERT: B 51 THR cc_start: 0.8735 (t) cc_final: 0.8502 (p) REVERT: B 129 LYS cc_start: 0.7631 (mmtt) cc_final: 0.7174 (mtmm) REVERT: B 159 VAL cc_start: 0.6811 (OUTLIER) cc_final: 0.6580 (m) REVERT: B 237 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6992 (mmt180) REVERT: B 298 GLU cc_start: 0.7965 (tp30) cc_final: 0.7536 (tp30) REVERT: B 340 GLU cc_start: 0.8132 (tp30) cc_final: 0.7909 (tp30) REVERT: B 386 LYS cc_start: 0.8139 (mttp) cc_final: 0.7784 (mttp) REVERT: B 430 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8785 (p) REVERT: B 462 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8449 (mmmm) REVERT: B 514 SER cc_start: 0.8558 (t) cc_final: 0.8165 (p) REVERT: B 651 ILE cc_start: 0.8576 (pt) cc_final: 0.8264 (mp) REVERT: B 658 ASN cc_start: 0.8094 (p0) cc_final: 0.7859 (p0) REVERT: B 710 ASN cc_start: 0.8513 (p0) cc_final: 0.8189 (p0) REVERT: B 730 SER cc_start: 0.8771 (t) cc_final: 0.8494 (m) REVERT: B 747 THR cc_start: 0.8313 (p) cc_final: 0.7667 (m) REVERT: B 751 ASN cc_start: 0.8425 (m-40) cc_final: 0.8120 (m-40) REVERT: B 781 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8234 (t) REVERT: B 788 ILE cc_start: 0.8564 (mt) cc_final: 0.8340 (mm) REVERT: B 907 ASN cc_start: 0.8419 (t0) cc_final: 0.8103 (t0) REVERT: B 950 ASP cc_start: 0.7970 (m-30) cc_final: 0.7765 (m-30) REVERT: B 966 LEU cc_start: 0.9044 (mt) cc_final: 0.8791 (mt) REVERT: B 1017 GLU cc_start: 0.7927 (tp30) cc_final: 0.7594 (tp30) REVERT: B 1084 ASP cc_start: 0.8070 (t0) cc_final: 0.7629 (t0) REVERT: B 1127 ASP cc_start: 0.8065 (t0) cc_final: 0.7847 (t0) REVERT: D 22 GLU cc_start: 0.6944 (tp30) cc_final: 0.6627 (tp30) REVERT: D 23 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: D 58 ASN cc_start: 0.7314 (m110) cc_final: 0.6040 (m110) REVERT: D 61 LYS cc_start: 0.8666 (mttt) cc_final: 0.8450 (ptpt) REVERT: D 69 TRP cc_start: 0.7781 (t60) cc_final: 0.7481 (t60) REVERT: D 163 TRP cc_start: 0.4159 (p-90) cc_final: 0.3231 (p-90) REVERT: D 190 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.3314 (tpt) REVERT: D 246 ARG cc_start: 0.1391 (ptm160) cc_final: 0.1117 (mmm160) REVERT: D 249 MET cc_start: 0.5606 (tpt) cc_final: 0.4165 (mmp) REVERT: D 298 MET cc_start: 0.6764 (ttm) cc_final: 0.6452 (ttm) REVERT: D 313 LYS cc_start: 0.7576 (tptp) cc_final: 0.7132 (ptpt) REVERT: D 327 PHE cc_start: 0.7405 (m-80) cc_final: 0.7166 (m-80) REVERT: D 335 GLU cc_start: 0.6782 (pp20) cc_final: 0.4668 (mp0) REVERT: D 355 ASP cc_start: 0.6535 (t0) cc_final: 0.6140 (t0) REVERT: D 366 MET cc_start: 0.5053 (mmm) cc_final: 0.4543 (mmm) REVERT: D 381 TYR cc_start: 0.8374 (t80) cc_final: 0.7671 (t80) REVERT: D 388 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7180 (mm-40) REVERT: D 440 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6182 (pp) REVERT: D 455 MET cc_start: 0.7611 (ptp) cc_final: 0.7168 (mtp) REVERT: D 515 TYR cc_start: 0.5359 (m-80) cc_final: 0.4797 (m-80) REVERT: D 557 MET cc_start: 0.7728 (tmm) cc_final: 0.7339 (tmm) REVERT: D 568 LYS cc_start: 0.8010 (tttm) cc_final: 0.7545 (tptt) REVERT: C 88 ASP cc_start: 0.6404 (t0) cc_final: 0.5974 (t70) REVERT: C 281 GLU cc_start: 0.7643 (pp20) cc_final: 0.7136 (pp20) REVERT: C 317 ASN cc_start: 0.8225 (m-40) cc_final: 0.7895 (m-40) REVERT: C 339 ASP cc_start: 0.8119 (p0) cc_final: 0.7782 (p0) REVERT: C 346 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7701 (ttm110) REVERT: C 453 TYR cc_start: 0.7300 (p90) cc_final: 0.6805 (p90) REVERT: C 498 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7561 (mtt90) REVERT: C 516 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: C 542 ASN cc_start: 0.8279 (t0) cc_final: 0.7929 (t0) REVERT: C 558 LYS cc_start: 0.8427 (mtmt) cc_final: 0.7996 (mmmm) REVERT: C 654 GLU cc_start: 0.8470 (tt0) cc_final: 0.8177 (tt0) REVERT: C 691 SER cc_start: 0.8794 (p) cc_final: 0.8321 (m) REVERT: C 708 SER cc_start: 0.8429 (m) cc_final: 0.8029 (p) REVERT: C 723 THR cc_start: 0.8495 (m) cc_final: 0.8104 (p) REVERT: C 977 LEU cc_start: 0.8651 (mm) cc_final: 0.8448 (mt) REVERT: C 997 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8278 (mt) REVERT: C 1128 VAL cc_start: 0.8685 (m) cc_final: 0.8385 (p) REVERT: C 1136 THR cc_start: 0.8559 (t) cc_final: 0.8268 (p) REVERT: E 41 TYR cc_start: 0.7679 (t80) cc_final: 0.6692 (t80) REVERT: E 61 LYS cc_start: 0.8131 (mttt) cc_final: 0.7769 (mttt) REVERT: E 64 GLU cc_start: 0.6298 (mm-30) cc_final: 0.5877 (mm-30) REVERT: E 94 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7771 (pttt) REVERT: E 116 LEU cc_start: 0.6984 (tt) cc_final: 0.6710 (tt) REVERT: E 142 LEU cc_start: -0.0535 (OUTLIER) cc_final: -0.1164 (tp) REVERT: E 169 ARG cc_start: 0.2507 (ttp80) cc_final: 0.0826 (ttt180) REVERT: E 183 TYR cc_start: 0.2672 (OUTLIER) cc_final: 0.1186 (t80) REVERT: E 190 MET cc_start: 0.1758 (ptt) cc_final: 0.1323 (mtt) REVERT: E 278 LEU cc_start: 0.0213 (OUTLIER) cc_final: -0.0161 (tp) REVERT: E 305 GLU cc_start: 0.6390 (pt0) cc_final: 0.5984 (pm20) REVERT: E 310 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7130 (mt-10) REVERT: E 327 PHE cc_start: 0.7947 (t80) cc_final: 0.7414 (t80) REVERT: E 349 TRP cc_start: 0.5482 (m100) cc_final: 0.5139 (m100) REVERT: E 366 MET cc_start: 0.2927 (mmm) cc_final: 0.1586 (mmp) REVERT: E 381 TYR cc_start: 0.6091 (t80) cc_final: 0.5755 (t80) REVERT: E 476 LYS cc_start: 0.6706 (tptt) cc_final: 0.6375 (pttm) REVERT: E 480 MET cc_start: 0.7387 (mtp) cc_final: 0.6560 (mtp) REVERT: E 510 TYR cc_start: 0.5722 (m-80) cc_final: 0.5521 (m-10) REVERT: E 526 GLN cc_start: 0.7653 (tp40) cc_final: 0.7321 (tp40) REVERT: E 579 MET cc_start: 0.4207 (mtm) cc_final: 0.4001 (mmm) outliers start: 143 outliers final: 103 residues processed: 855 average time/residue: 0.2053 time to fit residues: 284.0527 Evaluate side-chains 882 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 758 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 106 optimal weight: 4.9990 chunk 363 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 323 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 376 optimal weight: 40.0000 chunk 133 optimal weight: 0.0370 chunk 139 optimal weight: 0.8980 chunk 234 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 607 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN C 207 HIS C 856 ASN C 907 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.202610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148296 restraints weight = 53943.834| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.49 r_work: 0.3577 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35018 Z= 0.137 Angle : 0.668 21.379 47723 Z= 0.333 Chirality : 0.046 0.737 5374 Planarity : 0.004 0.064 6098 Dihedral : 5.582 109.576 5354 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.31 % Favored : 95.67 % Rotamer: Outliers : 3.28 % Allowed : 22.03 % Favored : 74.69 % 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: -0.73 (0.13), residues: 4202 helix: 0.94 (0.14), residues: 1406 sheet: -0.13 (0.19), residues: 657 loop : -1.63 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 228 TYR 0.017 0.001 TYR B1067 PHE 0.028 0.001 PHE C 168 TRP 0.034 0.001 TRP A 353 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00312 (34941) covalent geometry : angle 0.64309 (47532) SS BOND : bond 0.00492 ( 40) SS BOND : angle 2.69340 ( 80) hydrogen bonds : bond 0.03579 ( 1335) hydrogen bonds : angle 4.82201 ( 3699) link_NAG-ASN : bond 0.00528 ( 37) link_NAG-ASN : angle 3.07620 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 771 time to evaluate : 1.187 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 196 ASN cc_start: 0.6277 (p0) cc_final: 0.6068 (p0) REVERT: A 203 ILE cc_start: 0.8618 (pt) cc_final: 0.8217 (mt) REVERT: A 204 TYR cc_start: 0.7492 (m-80) cc_final: 0.7057 (m-80) REVERT: A 239 GLN cc_start: 0.7804 (mp10) cc_final: 0.7584 (mp10) REVERT: A 360 ASN cc_start: 0.7476 (m-40) cc_final: 0.7274 (m-40) REVERT: A 377 PHE cc_start: 0.8767 (t80) cc_final: 0.8515 (t80) REVERT: A 378 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8151 (ttpp) REVERT: A 524 VAL cc_start: 0.7229 (OUTLIER) cc_final: 0.7003 (m) REVERT: A 584 ILE cc_start: 0.8296 (tp) cc_final: 0.8029 (mm) REVERT: A 710 ASN cc_start: 0.8505 (p0) cc_final: 0.8262 (p0) REVERT: A 725 GLU cc_start: 0.8263 (tt0) cc_final: 0.8030 (tt0) REVERT: A 804 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8148 (mm-40) REVERT: A 869 MET cc_start: 0.8630 (mtm) cc_final: 0.8411 (mtt) REVERT: A 900 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: A 934 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8379 (tp) REVERT: A 957 GLN cc_start: 0.8259 (tt0) cc_final: 0.8014 (tt0) REVERT: A 1003 SER cc_start: 0.8951 (p) cc_final: 0.8704 (t) REVERT: A 1005 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: A 1084 ASP cc_start: 0.8125 (t0) cc_final: 0.7599 (t0) REVERT: A 1105 THR cc_start: 0.8516 (t) cc_final: 0.8255 (p) REVERT: A 1120 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8281 (p) REVERT: A 1127 ASP cc_start: 0.7717 (t0) cc_final: 0.7364 (t0) REVERT: A 1139 ASP cc_start: 0.8048 (t0) cc_final: 0.7844 (t0) REVERT: B 129 LYS cc_start: 0.7664 (mmtt) cc_final: 0.7348 (mtmm) REVERT: B 159 VAL cc_start: 0.6950 (OUTLIER) cc_final: 0.6746 (m) REVERT: B 237 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6923 (mmp-170) REVERT: B 298 GLU cc_start: 0.7952 (tp30) cc_final: 0.7473 (tp30) REVERT: B 340 GLU cc_start: 0.8118 (tp30) cc_final: 0.7897 (tp30) REVERT: B 386 LYS cc_start: 0.8102 (mttp) cc_final: 0.7781 (mttp) REVERT: B 430 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8800 (p) REVERT: B 462 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8270 (mmmm) REVERT: B 463 PRO cc_start: 0.8973 (Cg_exo) cc_final: 0.8683 (Cg_endo) REVERT: B 514 SER cc_start: 0.8565 (t) cc_final: 0.8165 (p) REVERT: B 524 VAL cc_start: 0.8398 (m) cc_final: 0.7977 (p) REVERT: B 543 PHE cc_start: 0.8340 (m-80) cc_final: 0.8100 (m-80) REVERT: B 651 ILE cc_start: 0.8521 (pt) cc_final: 0.8218 (mp) REVERT: B 710 ASN cc_start: 0.8466 (p0) cc_final: 0.8192 (p0) REVERT: B 730 SER cc_start: 0.8813 (t) cc_final: 0.8514 (m) REVERT: B 747 THR cc_start: 0.8294 (p) cc_final: 0.7808 (p) REVERT: B 751 ASN cc_start: 0.8410 (m-40) cc_final: 0.8105 (m-40) REVERT: B 781 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8133 (t) REVERT: B 788 ILE cc_start: 0.8560 (mt) cc_final: 0.8341 (mm) REVERT: B 868 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 907 ASN cc_start: 0.8391 (t0) cc_final: 0.8042 (t0) REVERT: B 950 ASP cc_start: 0.7867 (m-30) cc_final: 0.7639 (m-30) REVERT: B 1017 GLU cc_start: 0.7922 (tp30) cc_final: 0.7611 (tp30) REVERT: B 1084 ASP cc_start: 0.8090 (t0) cc_final: 0.7640 (t0) REVERT: B 1127 ASP cc_start: 0.8041 (t0) cc_final: 0.7796 (t0) REVERT: D 22 GLU cc_start: 0.6965 (tp30) cc_final: 0.6632 (tp30) REVERT: D 23 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7570 (pt0) REVERT: D 69 TRP cc_start: 0.7700 (t60) cc_final: 0.7379 (t60) REVERT: D 163 TRP cc_start: 0.4130 (p-90) cc_final: 0.3206 (p-90) REVERT: D 249 MET cc_start: 0.5635 (tpt) cc_final: 0.4770 (tpt) REVERT: D 298 MET cc_start: 0.6682 (ttm) cc_final: 0.6361 (ttm) REVERT: D 313 LYS cc_start: 0.7532 (tptp) cc_final: 0.7054 (ptpt) REVERT: D 335 GLU cc_start: 0.6703 (pp20) cc_final: 0.4710 (mp0) REVERT: D 355 ASP cc_start: 0.6488 (t0) cc_final: 0.6104 (t0) REVERT: D 366 MET cc_start: 0.4907 (mmm) cc_final: 0.4450 (mmm) REVERT: D 381 TYR cc_start: 0.8403 (t80) cc_final: 0.7546 (t80) REVERT: D 385 TYR cc_start: 0.7096 (p90) cc_final: 0.6070 (p90) REVERT: D 388 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7151 (mm-40) REVERT: D 440 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6187 (pp) REVERT: D 476 LYS cc_start: 0.5927 (mttp) cc_final: 0.5529 (pttm) REVERT: D 557 MET cc_start: 0.7790 (tmm) cc_final: 0.7409 (tmm) REVERT: D 568 LYS cc_start: 0.7934 (tttm) cc_final: 0.7547 (tptt) REVERT: C 128 ILE cc_start: 0.7478 (mp) cc_final: 0.6752 (tt) REVERT: C 281 GLU cc_start: 0.7569 (pp20) cc_final: 0.7025 (pp20) REVERT: C 317 ASN cc_start: 0.8227 (m-40) cc_final: 0.7881 (m-40) REVERT: C 334 ASN cc_start: 0.8324 (m-40) cc_final: 0.7884 (t0) REVERT: C 346 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7808 (ttm110) REVERT: C 453 TYR cc_start: 0.7346 (p90) cc_final: 0.6897 (p90) REVERT: C 498 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7538 (mtt90) REVERT: C 516 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6565 (tt0) REVERT: C 542 ASN cc_start: 0.8231 (t0) cc_final: 0.7819 (t0) REVERT: C 558 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7945 (mmmm) REVERT: C 654 GLU cc_start: 0.8357 (tt0) cc_final: 0.8085 (tt0) REVERT: C 657 ASN cc_start: 0.7390 (m110) cc_final: 0.6952 (m-40) REVERT: C 691 SER cc_start: 0.8774 (p) cc_final: 0.8276 (m) REVERT: C 708 SER cc_start: 0.8432 (m) cc_final: 0.8035 (p) REVERT: C 997 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8153 (mt) REVERT: C 1029 MET cc_start: 0.8389 (tpp) cc_final: 0.8105 (ttm) REVERT: C 1107 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7530 (mtt180) REVERT: C 1128 VAL cc_start: 0.8681 (m) cc_final: 0.8385 (p) REVERT: C 1136 THR cc_start: 0.8531 (t) cc_final: 0.8252 (p) REVERT: E 41 TYR cc_start: 0.7512 (t80) cc_final: 0.6513 (t80) REVERT: E 61 LYS cc_start: 0.8144 (mttt) cc_final: 0.7774 (mttt) REVERT: E 64 GLU cc_start: 0.6263 (mm-30) cc_final: 0.5825 (mm-30) REVERT: E 69 TRP cc_start: 0.8014 (t60) cc_final: 0.7671 (t60) REVERT: E 94 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7769 (pttt) REVERT: E 142 LEU cc_start: -0.0671 (OUTLIER) cc_final: -0.1249 (tp) REVERT: E 152 MET cc_start: -0.0020 (ptp) cc_final: -0.0319 (ptp) REVERT: E 183 TYR cc_start: 0.2624 (OUTLIER) cc_final: 0.1031 (t80) REVERT: E 187 LYS cc_start: 0.5273 (mtpp) cc_final: 0.4935 (mttm) REVERT: E 278 LEU cc_start: 0.0098 (OUTLIER) cc_final: -0.0264 (tp) REVERT: E 305 GLU cc_start: 0.6379 (pt0) cc_final: 0.6021 (pm20) REVERT: E 310 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7149 (mt-10) REVERT: E 327 PHE cc_start: 0.7718 (t80) cc_final: 0.7490 (t80) REVERT: E 328 TRP cc_start: 0.6903 (m-90) cc_final: 0.4981 (m-90) REVERT: E 349 TRP cc_start: 0.5463 (m100) cc_final: 0.5128 (m100) REVERT: E 366 MET cc_start: 0.2992 (mmm) cc_final: 0.1696 (mmp) REVERT: E 381 TYR cc_start: 0.6061 (t80) cc_final: 0.5718 (t80) REVERT: E 462 MET cc_start: 0.3488 (ttp) cc_final: 0.3194 (ttp) REVERT: E 476 LYS cc_start: 0.6811 (tptt) cc_final: 0.6402 (ptpp) REVERT: E 480 MET cc_start: 0.7329 (mtp) cc_final: 0.6491 (mtp) REVERT: E 512 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.5609 (t80) REVERT: E 515 TYR cc_start: 0.6744 (m-80) cc_final: 0.6077 (m-80) REVERT: E 526 GLN cc_start: 0.7649 (tp40) cc_final: 0.7318 (tp40) outliers start: 121 outliers final: 92 residues processed: 841 average time/residue: 0.2035 time to fit residues: 275.2842 Evaluate side-chains 866 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 755 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 184 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 236 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 410 optimal weight: 2.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1135 ASN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 58 ASN D 96 GLN D 101 GLN D 309 GLN D 368 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 856 ASN E 24 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.199850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145471 restraints weight = 53781.039| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.79 r_work: 0.3534 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 35018 Z= 0.198 Angle : 0.706 21.203 47723 Z= 0.355 Chirality : 0.048 0.597 5374 Planarity : 0.005 0.060 6098 Dihedral : 5.593 107.365 5354 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 3.47 % Allowed : 22.06 % Favored : 74.47 % 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: -0.76 (0.13), residues: 4202 helix: 0.90 (0.14), residues: 1404 sheet: -0.17 (0.19), residues: 633 loop : -1.60 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 228 TYR 0.025 0.002 TYR B 660 PHE 0.032 0.002 PHE A 823 TRP 0.034 0.002 TRP A 353 HIS 0.015 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00463 (34941) covalent geometry : angle 0.68016 (47532) SS BOND : bond 0.00508 ( 40) SS BOND : angle 3.04057 ( 80) hydrogen bonds : bond 0.03982 ( 1335) hydrogen bonds : angle 4.84911 ( 3699) link_NAG-ASN : bond 0.00528 ( 37) link_NAG-ASN : angle 3.09719 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12276.71 seconds wall clock time: 209 minutes 31.80 seconds (12571.80 seconds total)