Starting phenix.real_space_refine on Sun Jun 29 05:39:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xob_33343/06_2025/7xob_33343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xob_33343/06_2025/7xob_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_33343/06_2025/7xob_33343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xob_33343/06_2025/7xob_33343.map" model { file = "/net/cci-nas-00/data/ceres_data/7xob_33343/06_2025/7xob_33343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xob_33343/06_2025/7xob_33343.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34108 Number of models: 1 Model: "" Number of chains: 9 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, 'GLN:plan1': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 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, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: E Time building chain proxies: 23.11, per 1000 atoms: 0.68 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: 8.32 Conformation dependent library (CDL) restraints added in 4.6 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: 3.96 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: 14.19 Time building geometry restraints manager: 10.04 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 1146 or resid 1301 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 1146 or resid 1301 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: 7.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.340 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 82.240 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.000 ------------------------------------------------------------------------------- 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 : 8.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.039 0.001 TRP B 104 HIS 0.008 0.001 HIS B 207 PHE 0.069 0.002 PHE B 92 TYR 0.062 0.001 TYR B 37 ARG 0.017 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.02031 ( 37) link_NAG-ASN : angle 8.02105 ( 111) hydrogen bonds : bond 0.16866 ( 1335) hydrogen bonds : angle 6.28804 ( 3699) SS BOND : bond 0.14852 ( 40) SS BOND : angle 6.36389 ( 80) covalent geometry : bond 0.00523 (34941) covalent geometry : angle 0.91622 (47532) *********************** 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 : 3.579 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: 0.7455 (mmm160) REVERT: A 543 PHE cc_start: 0.8287 (m-10) cc_final: 0.7970 (m-80) REVERT: A 547 THR cc_start: 0.8006 (p) cc_final: 0.7793 (p) REVERT: A 551 VAL cc_start: 0.8022 (t) cc_final: 0.7689 (m) REVERT: A 569 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8170 (tp) REVERT: A 610 VAL cc_start: 0.7896 (t) cc_final: 0.7653 (t) REVERT: A 692 ILE cc_start: 0.7976 (mm) cc_final: 0.7656 (mt) REVERT: A 737 ASP cc_start: 0.6872 (t0) cc_final: 0.6151 (t70) REVERT: A 774 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7236 (mp10) REVERT: A 819 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6927 (mt-10) REVERT: A 820 ASP cc_start: 0.6815 (t0) cc_final: 0.6583 (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: 0.7706 (tt) REVERT: A 949 GLN cc_start: 0.7729 (tp40) cc_final: 0.7512 (mm-40) REVERT: A 1019 ARG cc_start: 0.6932 (ttm110) cc_final: 0.6450 (ttp80) REVERT: A 1091 ARG cc_start: 0.7183 (mtt90) cc_final: 0.6964 (mtt90) REVERT: A 1122 VAL cc_start: 0.8323 (p) cc_final: 0.8045 (m) REVERT: A 1136 THR cc_start: 0.7856 (t) cc_final: 0.7571 (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: 0.6695 (mp0) REVERT: B 317 ASN cc_start: 0.7161 (m110) cc_final: 0.6594 (m110) REVERT: B 340 GLU cc_start: 0.7219 (tp30) cc_final: 0.6665 (tp30) REVERT: B 615 VAL cc_start: 0.8265 (p) cc_final: 0.8032 (p) REVERT: B 645 THR cc_start: 0.8366 (p) cc_final: 0.7167 (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: 0.7236 (mp10) REVERT: B 981 LEU cc_start: 0.7542 (mm) cc_final: 0.7166 (mm) REVERT: B 994 ASP cc_start: 0.7474 (t0) cc_final: 0.7096 (t0) REVERT: D 39 LEU cc_start: 0.4606 (mt) cc_final: 0.4352 (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: 0.6853 (mtt180) REVERT: C 309 GLU cc_start: 0.5827 (mm-30) cc_final: 0.5547 (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: 0.7960 (ptp-170) REVERT: C 584 ILE cc_start: 0.7905 (tp) cc_final: 0.7571 (mm) 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: 0.7305 (t80) REVERT: C 772 VAL cc_start: 0.8023 (p) cc_final: 0.7723 (m) REVERT: C 816 SER cc_start: 0.8499 (p) cc_final: 0.8298 (p) REVERT: C 819 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7385 (mt-10) REVERT: C 1018 ILE cc_start: 0.7030 (mm) cc_final: 0.6806 (mm) REVERT: C 1128 VAL cc_start: 0.8708 (m) cc_final: 0.8499 (p) outliers start: 21 outliers final: 2 residues processed: 908 average time/residue: 0.4992 time to fit residues: 729.2879 Evaluate side-chains 742 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 737 time to evaluate : 3.424 ------------------------------------------------------------------------------- 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 358 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 216 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 247 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 277 ASN D 345 HIS D 417 HIS D 472 GLN D 493 HIS C 125 ASN C 164 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 978 ASN C1135 ASN E 42 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN E 98 GLN E 113 ASN E 188 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4525 r_free = 0.4525 target = 0.214495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.161146 restraints weight = 55589.435| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.96 r_work: 0.3744 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 35018 Z= 0.222 Angle : 0.736 13.816 47723 Z= 0.368 Chirality : 0.050 0.857 5374 Planarity : 0.005 0.059 6098 Dihedral : 6.655 108.193 5363 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.93 % Allowed : 15.38 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.12), residues: 4202 helix: 0.11 (0.14), residues: 1370 sheet: -1.09 (0.19), residues: 590 loop : -2.53 (0.11), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 461 HIS 0.012 0.001 HIS B1064 PHE 0.039 0.002 PHE E 315 TYR 0.026 0.002 TYR C1138 ARG 0.012 0.001 ARG E 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00792 ( 37) link_NAG-ASN : angle 3.48553 ( 111) hydrogen bonds : bond 0.04260 ( 1335) hydrogen bonds : angle 5.04369 ( 3699) SS BOND : bond 0.00946 ( 40) SS BOND : angle 1.92475 ( 80) covalent geometry : bond 0.00511 (34941) covalent geometry : angle 0.71386 (47532) *********************** 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 948 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 840 time to evaluate : 3.599 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: A 275 PHE cc_start: 0.8200 (m-80) cc_final: 0.7903 (m-80) REVERT: A 377 PHE cc_start: 0.8583 (t80) cc_final: 0.8170 (t80) REVERT: A 378 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7823 (ttpp) REVERT: A 543 PHE cc_start: 0.8499 (m-10) cc_final: 0.8299 (m-80) REVERT: A 551 VAL cc_start: 0.8650 (t) cc_final: 0.8360 (m) REVERT: A 576 VAL cc_start: 0.8764 (p) cc_final: 0.8424 (t) REVERT: A 580 GLN cc_start: 0.8069 (mm110) cc_final: 0.7618 (mt0) REVERT: A 654 GLU cc_start: 0.7764 (tt0) cc_final: 0.7559 (tt0) REVERT: A 710 ASN cc_start: 0.7914 (p0) cc_final: 0.7692 (p0) REVERT: A 790 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7959 (mtmm) REVERT: A 796 TYR cc_start: 0.7584 (t80) cc_final: 0.7381 (t80) REVERT: A 819 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 820 ASP cc_start: 0.7821 (t0) cc_final: 0.7351 (m-30) REVERT: A 900 MET cc_start: 0.8276 (mtm) cc_final: 0.7951 (mtp) REVERT: A 934 ILE cc_start: 0.8433 (tt) cc_final: 0.8100 (tp) REVERT: A 1003 SER cc_start: 0.8999 (p) cc_final: 0.8695 (t) REVERT: A 1105 THR cc_start: 0.8192 (t) cc_final: 0.7969 (p) REVERT: A 1130 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8314 (mt) REVERT: B 29 THR cc_start: 0.6798 (t) cc_final: 0.5035 (p) REVERT: B 40 ASP cc_start: 0.8063 (m-30) cc_final: 0.7786 (m-30) REVERT: B 70 VAL cc_start: 0.4128 (OUTLIER) cc_final: 0.3663 (p) REVERT: B 309 GLU cc_start: 0.7766 (mp0) cc_final: 0.7518 (mp0) REVERT: B 340 GLU cc_start: 0.7624 (tp30) cc_final: 0.7114 (tp30) REVERT: B 347 PHE cc_start: 0.7373 (m-80) cc_final: 0.6718 (m-10) REVERT: B 360 ASN cc_start: 0.8190 (m-40) cc_final: 0.7885 (m-40) REVERT: B 361 CYS cc_start: 0.7910 (OUTLIER) cc_final: 0.6978 (p) REVERT: B 436 TRP cc_start: 0.7569 (p90) cc_final: 0.7311 (p90) REVERT: B 658 ASN cc_start: 0.7864 (p0) cc_final: 0.7270 (p0) REVERT: B 698 SER cc_start: 0.8752 (t) cc_final: 0.8384 (p) REVERT: B 703 ASN cc_start: 0.7850 (t0) cc_final: 0.7487 (m-40) REVERT: B 710 ASN cc_start: 0.8064 (p0) cc_final: 0.7762 (p0) REVERT: B 774 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7765 (mp10) REVERT: B 934 ILE cc_start: 0.7933 (tt) cc_final: 0.7598 (tt) REVERT: B 994 ASP cc_start: 0.8034 (t70) cc_final: 0.7722 (t0) REVERT: B 1073 LYS cc_start: 0.8273 (mtpt) cc_final: 0.8001 (mtpp) REVERT: B 1104 VAL cc_start: 0.8812 (t) cc_final: 0.8589 (p) REVERT: B 1119 ASN cc_start: 0.8053 (p0) cc_final: 0.7814 (p0) REVERT: B 1125 ASN cc_start: 0.7963 (p0) cc_final: 0.7738 (p0) REVERT: B 1127 ASP cc_start: 0.7728 (t0) cc_final: 0.7143 (t0) REVERT: D 61 LYS cc_start: 0.8535 (mttt) cc_final: 0.8128 (mttt) REVERT: D 225 ASP cc_start: 0.7395 (m-30) cc_final: 0.7109 (m-30) REVERT: D 246 ARG cc_start: 0.0573 (mtm110) cc_final: 0.0292 (mmp-170) REVERT: D 249 MET cc_start: 0.4865 (mmm) cc_final: 0.3272 (mmm) REVERT: D 256 ILE cc_start: 0.3499 (mt) cc_final: 0.3158 (mt) REVERT: D 327 PHE cc_start: 0.7448 (t80) cc_final: 0.7198 (t80) REVERT: D 334 THR cc_start: 0.5401 (t) cc_final: 0.4878 (p) REVERT: D 380 GLN cc_start: 0.4977 (mm-40) cc_final: 0.4751 (mm-40) REVERT: D 381 TYR cc_start: 0.8006 (t80) cc_final: 0.7506 (t80) REVERT: D 385 TYR cc_start: 0.7133 (p90) cc_final: 0.5930 (p90) REVERT: D 400 PHE cc_start: 0.4166 (m-80) cc_final: 0.3713 (m-80) REVERT: D 444 LEU cc_start: 0.4731 (mt) cc_final: 0.4335 (mm) REVERT: D 557 MET cc_start: 0.7400 (tmm) cc_final: 0.6793 (tmm) REVERT: C 42 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7984 (p) REVERT: C 47 VAL cc_start: 0.8393 (p) cc_final: 0.8164 (t) REVERT: C 307 THR cc_start: 0.7550 (p) cc_final: 0.7258 (p) REVERT: C 317 ASN cc_start: 0.7804 (m-40) cc_final: 0.7524 (m-40) REVERT: C 346 ARG cc_start: 0.7603 (ttm110) cc_final: 0.7329 (ttm110) REVERT: C 542 ASN cc_start: 0.8307 (t0) cc_final: 0.7828 (t0) REVERT: C 543 PHE cc_start: 0.8376 (m-10) cc_final: 0.7993 (m-10) REVERT: C 558 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7561 (mmmm) REVERT: C 576 VAL cc_start: 0.8755 (p) cc_final: 0.8517 (t) REVERT: C 580 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: C 644 GLN cc_start: 0.7413 (tp40) cc_final: 0.7165 (tp40) REVERT: C 654 GLU cc_start: 0.7867 (tt0) cc_final: 0.7598 (tt0) REVERT: C 703 ASN cc_start: 0.7660 (t0) cc_final: 0.7452 (t0) REVERT: C 718 PHE cc_start: 0.7968 (p90) cc_final: 0.7558 (p90) REVERT: C 772 VAL cc_start: 0.8428 (p) cc_final: 0.8150 (m) REVERT: C 820 ASP cc_start: 0.7928 (t0) cc_final: 0.7676 (m-30) REVERT: C 947 LYS cc_start: 0.8364 (mttt) cc_final: 0.8138 (mttp) REVERT: C 954 HIS cc_start: 0.7458 (m170) cc_final: 0.7255 (m-70) REVERT: C 979 ASP cc_start: 0.7683 (t70) cc_final: 0.7366 (m-30) REVERT: C 1010 GLN cc_start: 0.7661 (mt0) cc_final: 0.7434 (mm-40) REVERT: C 1128 VAL cc_start: 0.8770 (m) cc_final: 0.8471 (p) REVERT: E 40 SER cc_start: 0.7798 (t) cc_final: 0.7270 (p) REVERT: E 61 LYS cc_start: 0.8093 (mttt) cc_final: 0.7712 (mttt) REVERT: E 64 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5771 (mm-30) REVERT: E 75 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6541 (pp20) REVERT: E 381 TYR cc_start: 0.5704 (t80) cc_final: 0.5367 (t80) REVERT: E 562 ASN cc_start: 0.6635 (t0) cc_final: 0.6400 (t0) REVERT: E 568 LYS cc_start: 0.7579 (tptp) cc_final: 0.7322 (mmtp) REVERT: E 609 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5967 (pm20) outliers start: 108 outliers final: 48 residues processed: 905 average time/residue: 0.4652 time to fit residues: 681.8216 Evaluate side-chains 821 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 766 time to evaluate : 3.927 ------------------------------------------------------------------------------- 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 659 SER 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 D residue 468 ILE 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 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 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 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 210 optimal weight: 8.9990 chunk 245 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 331 optimal weight: 0.4980 chunk 295 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 304 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 373 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 901 GLN C 925 ASN E 30 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS E 325 GLN E 397 ASN E 522 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.209672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155773 restraints weight = 54995.800| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.80 r_work: 0.3625 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 35018 Z= 0.252 Angle : 0.714 14.379 47723 Z= 0.361 Chirality : 0.049 0.582 5374 Planarity : 0.005 0.061 6098 Dihedral : 5.705 96.199 5355 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.80 % Allowed : 17.36 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.12), residues: 4202 helix: 0.33 (0.14), residues: 1423 sheet: -0.93 (0.19), residues: 637 loop : -2.24 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 203 HIS 0.011 0.001 HIS B1064 PHE 0.034 0.002 PHE B 565 TYR 0.029 0.002 TYR B 204 ARG 0.009 0.001 ARG D 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00811 ( 37) link_NAG-ASN : angle 3.38145 ( 111) hydrogen bonds : bond 0.04399 ( 1335) hydrogen bonds : angle 5.06666 ( 3699) SS BOND : bond 0.00570 ( 40) SS BOND : angle 2.41970 ( 80) covalent geometry : bond 0.00583 (34941) covalent geometry : angle 0.68971 (47532) *********************** 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 982 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 842 time to evaluate : 3.505 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: A 41 LYS cc_start: 0.5813 (ttmt) cc_final: 0.5014 (mtpt) REVERT: A 43 PHE cc_start: 0.7263 (t80) cc_final: 0.6854 (t80) REVERT: A 130 VAL cc_start: 0.6998 (OUTLIER) cc_final: 0.6581 (t) REVERT: A 204 TYR cc_start: 0.7346 (m-80) cc_final: 0.6873 (m-80) REVERT: A 207 HIS cc_start: 0.7448 (m-70) cc_final: 0.7159 (m-70) REVERT: A 377 PHE cc_start: 0.8848 (t80) cc_final: 0.8458 (t80) REVERT: A 378 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8231 (ttpp) REVERT: A 524 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7276 (m) REVERT: A 580 GLN cc_start: 0.8169 (mm110) cc_final: 0.7847 (mt0) REVERT: A 583 GLU cc_start: 0.7748 (tp30) cc_final: 0.6761 (tp30) REVERT: A 654 GLU cc_start: 0.8174 (tt0) cc_final: 0.7943 (tt0) REVERT: A 710 ASN cc_start: 0.8346 (p0) cc_final: 0.8120 (p0) REVERT: A 725 GLU cc_start: 0.8325 (tt0) cc_final: 0.8082 (tt0) REVERT: A 790 LYS cc_start: 0.8535 (mtpt) cc_final: 0.7959 (mtmm) REVERT: A 820 ASP cc_start: 0.7942 (t0) cc_final: 0.7540 (m-30) REVERT: A 821 LEU cc_start: 0.8703 (tp) cc_final: 0.8423 (tt) REVERT: A 900 MET cc_start: 0.8478 (mtm) cc_final: 0.8152 (mtp) REVERT: A 934 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8362 (tp) REVERT: A 957 GLN cc_start: 0.8301 (tt0) cc_final: 0.8040 (tt0) REVERT: A 1003 SER cc_start: 0.9058 (p) cc_final: 0.8809 (t) REVERT: A 1105 THR cc_start: 0.8497 (t) cc_final: 0.8289 (p) REVERT: A 1136 THR cc_start: 0.8632 (t) cc_final: 0.8390 (p) REVERT: B 29 THR cc_start: 0.7314 (t) cc_final: 0.5261 (p) REVERT: B 51 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8534 (p) REVERT: B 196 ASN cc_start: 0.7764 (t0) cc_final: 0.7530 (t0) REVERT: B 298 GLU cc_start: 0.8051 (tp30) cc_final: 0.7671 (tt0) REVERT: B 340 GLU cc_start: 0.8044 (tp30) cc_final: 0.7616 (tp30) REVERT: B 347 PHE cc_start: 0.8018 (m-80) cc_final: 0.7598 (m-10) REVERT: B 385 THR cc_start: 0.8725 (m) cc_final: 0.8448 (t) REVERT: B 398 ASP cc_start: 0.8207 (m-30) cc_final: 0.7980 (m-30) REVERT: B 514 SER cc_start: 0.8585 (t) cc_final: 0.8186 (p) REVERT: B 619 GLU cc_start: 0.7550 (mp0) cc_final: 0.7169 (mp0) REVERT: B 698 SER cc_start: 0.8946 (t) cc_final: 0.8604 (p) REVERT: B 702 GLU cc_start: 0.7660 (tp30) cc_final: 0.7460 (tp30) REVERT: B 703 ASN cc_start: 0.8269 (t0) cc_final: 0.7940 (t0) REVERT: B 710 ASN cc_start: 0.8344 (p0) cc_final: 0.8058 (p0) REVERT: B 719 THR cc_start: 0.8610 (t) cc_final: 0.8311 (p) REVERT: B 747 THR cc_start: 0.8286 (p) cc_final: 0.7824 (p) REVERT: B 751 ASN cc_start: 0.8440 (m-40) cc_final: 0.8154 (m-40) REVERT: B 825 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8054 (mttm) REVERT: B 934 ILE cc_start: 0.8179 (tt) cc_final: 0.7900 (tt) REVERT: B 950 ASP cc_start: 0.8117 (m-30) cc_final: 0.7899 (m-30) REVERT: B 994 ASP cc_start: 0.8267 (t70) cc_final: 0.8013 (t0) REVERT: B 1017 GLU cc_start: 0.8034 (tp30) cc_final: 0.7736 (tp30) REVERT: B 1073 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8042 (mtpp) REVERT: B 1125 ASN cc_start: 0.8107 (p0) cc_final: 0.7866 (p0) REVERT: B 1127 ASP cc_start: 0.8210 (t0) cc_final: 0.7880 (t0) REVERT: D 26 LYS cc_start: 0.7500 (mttt) cc_final: 0.7125 (mttt) REVERT: D 33 ASN cc_start: 0.7219 (t0) cc_final: 0.6681 (t0) REVERT: D 38 ASP cc_start: 0.7604 (t0) cc_final: 0.7401 (t0) REVERT: D 39 LEU cc_start: 0.8119 (mt) cc_final: 0.7885 (mt) REVERT: D 58 ASN cc_start: 0.7347 (m110) cc_final: 0.5396 (m110) REVERT: D 61 LYS cc_start: 0.8658 (mttt) cc_final: 0.8277 (mttt) REVERT: D 163 TRP cc_start: 0.4232 (p-90) cc_final: 0.3363 (p-90) REVERT: D 246 ARG cc_start: 0.0701 (mtm110) cc_final: 0.0394 (mmp-170) REVERT: D 249 MET cc_start: 0.5349 (mmm) cc_final: 0.3549 (mmm) REVERT: D 256 ILE cc_start: 0.3523 (mt) cc_final: 0.3319 (mt) REVERT: D 315 PHE cc_start: 0.5432 (OUTLIER) cc_final: 0.5212 (t80) REVERT: D 322 HIS cc_start: 0.5444 (OUTLIER) cc_final: 0.4866 (m90) REVERT: D 327 PHE cc_start: 0.7742 (t80) cc_final: 0.7503 (t80) REVERT: D 335 GLU cc_start: 0.6049 (tm-30) cc_final: 0.5025 (mp0) REVERT: D 381 TYR cc_start: 0.8087 (t80) cc_final: 0.7439 (t80) REVERT: D 400 PHE cc_start: 0.4247 (m-80) cc_final: 0.3906 (m-80) REVERT: D 456 LEU cc_start: 0.6727 (pp) cc_final: 0.6509 (pp) REVERT: D 510 TYR cc_start: 0.6778 (m-80) cc_final: 0.6555 (m-80) REVERT: D 515 TYR cc_start: 0.5665 (m-80) cc_final: 0.5225 (m-80) REVERT: D 557 MET cc_start: 0.7548 (tmm) cc_final: 0.7071 (tmm) REVERT: C 58 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7810 (m-10) REVERT: C 339 ASP cc_start: 0.7980 (p0) cc_final: 0.7622 (p0) REVERT: C 346 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7659 (ttm110) REVERT: C 529 LYS cc_start: 0.6072 (mtmt) cc_final: 0.5790 (mtmt) REVERT: C 542 ASN cc_start: 0.8302 (t0) cc_final: 0.7941 (t0) REVERT: C 558 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7942 (mmmm) REVERT: C 576 VAL cc_start: 0.8821 (p) cc_final: 0.8617 (t) REVERT: C 607 GLN cc_start: 0.8308 (tt0) cc_final: 0.8058 (mt0) REVERT: C 610 VAL cc_start: 0.8501 (t) cc_final: 0.8225 (m) REVERT: C 654 GLU cc_start: 0.8454 (tt0) cc_final: 0.8212 (tt0) REVERT: C 663 ASP cc_start: 0.7789 (t0) cc_final: 0.7541 (t0) REVERT: C 708 SER cc_start: 0.8473 (m) cc_final: 0.8017 (p) REVERT: C 710 ASN cc_start: 0.8055 (p0) cc_final: 0.7827 (p0) REVERT: C 723 THR cc_start: 0.8472 (m) cc_final: 0.8092 (p) REVERT: C 772 VAL cc_start: 0.8459 (p) cc_final: 0.8252 (t) REVERT: C 779 GLN cc_start: 0.8183 (mt0) cc_final: 0.7982 (mt0) REVERT: C 820 ASP cc_start: 0.8093 (t0) cc_final: 0.7837 (m-30) REVERT: C 947 LYS cc_start: 0.8524 (mttt) cc_final: 0.8299 (mttp) REVERT: C 949 GLN cc_start: 0.8292 (mt0) cc_final: 0.8085 (mm-40) REVERT: C 1128 VAL cc_start: 0.8744 (m) cc_final: 0.8486 (p) REVERT: C 1136 THR cc_start: 0.8558 (t) cc_final: 0.8190 (p) REVERT: E 61 LYS cc_start: 0.8109 (mttt) cc_final: 0.7742 (mttt) REVERT: E 64 GLU cc_start: 0.6146 (mm-30) cc_final: 0.5786 (mm-30) REVERT: E 75 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6730 (pp20) REVERT: E 366 MET cc_start: 0.3063 (mmm) cc_final: 0.2437 (mmp) REVERT: E 462 MET cc_start: 0.3940 (mtm) cc_final: 0.3705 (ttm) REVERT: E 562 ASN cc_start: 0.7241 (t0) cc_final: 0.6888 (t0) outliers start: 140 outliers final: 73 residues processed: 917 average time/residue: 0.4850 time to fit residues: 722.0742 Evaluate side-chains 874 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 793 time to evaluate : 3.275 ------------------------------------------------------------------------------- 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 130 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 302 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 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 659 SER 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 1122 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 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 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 973 ILE 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 1111 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 322 HIS 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 C residue 42 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 109 THR 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 390 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 738 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 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 552 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 151 optimal weight: 0.0070 chunk 18 optimal weight: 5.9990 chunk 322 optimal weight: 1.9990 chunk 357 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 228 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 334 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 367 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 658 ASN B1005 GLN D 96 GLN D 380 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN E 221 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 = 0.4442 r_free = 0.4442 target = 0.205100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150740 restraints weight = 54607.751| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.50 r_work: 0.3631 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4920 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= 0.158 Angle : 0.633 15.596 47723 Z= 0.314 Chirality : 0.045 0.277 5374 Planarity : 0.004 0.057 6098 Dihedral : 5.619 86.645 5354 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.61 % Allowed : 18.88 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 4202 helix: 0.60 (0.14), residues: 1413 sheet: -0.61 (0.19), residues: 644 loop : -2.06 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 461 HIS 0.009 0.001 HIS E 493 PHE 0.025 0.002 PHE B 201 TYR 0.021 0.001 TYR E 41 ARG 0.011 0.001 ARG D 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 37) link_NAG-ASN : angle 2.95686 ( 111) hydrogen bonds : bond 0.03672 ( 1335) hydrogen bonds : angle 4.94482 ( 3699) SS BOND : bond 0.00476 ( 40) SS BOND : angle 2.46213 ( 80) covalent geometry : bond 0.00369 (34941) covalent geometry : angle 0.60959 (47532) *********************** 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 915 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 782 time to evaluate : 3.447 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 204 TYR cc_start: 0.7388 (m-80) cc_final: 0.6858 (m-80) REVERT: A 239 GLN cc_start: 0.7981 (mp10) cc_final: 0.7707 (mp10) REVERT: A 240 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7855 (t) REVERT: A 270 LEU cc_start: 0.8375 (mt) cc_final: 0.8143 (mt) REVERT: A 377 PHE cc_start: 0.8730 (t80) cc_final: 0.8368 (t80) REVERT: A 378 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8224 (ttpp) REVERT: A 388 ASN cc_start: 0.8109 (t0) cc_final: 0.7898 (t0) REVERT: A 440 LYS cc_start: 0.8455 (mmmm) cc_final: 0.8242 (mmmm) REVERT: A 524 VAL cc_start: 0.7473 (OUTLIER) cc_final: 0.7215 (m) REVERT: A 576 VAL cc_start: 0.8905 (p) cc_final: 0.8689 (t) REVERT: A 580 GLN cc_start: 0.8155 (mm110) cc_final: 0.7862 (mt0) REVERT: A 654 GLU cc_start: 0.8144 (tt0) cc_final: 0.7935 (tt0) REVERT: A 710 ASN cc_start: 0.8322 (p0) cc_final: 0.8092 (p0) REVERT: A 790 LYS cc_start: 0.8468 (mtpt) cc_final: 0.7886 (mtmm) REVERT: A 900 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8074 (mtp) REVERT: A 934 ILE cc_start: 0.8663 (tt) cc_final: 0.8429 (tp) REVERT: A 957 GLN cc_start: 0.8248 (tt0) cc_final: 0.7988 (tt0) REVERT: A 1003 SER cc_start: 0.9026 (p) cc_final: 0.8792 (t) REVERT: A 1084 ASP cc_start: 0.8115 (t0) cc_final: 0.7574 (t0) REVERT: A 1105 THR cc_start: 0.8503 (t) cc_final: 0.8205 (p) REVERT: A 1136 THR cc_start: 0.8623 (t) cc_final: 0.8409 (p) REVERT: B 51 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8512 (p) REVERT: B 129 LYS cc_start: 0.7454 (mmtt) cc_final: 0.6957 (mtmm) REVERT: B 142 ASP cc_start: 0.6573 (p0) cc_final: 0.6176 (p0) REVERT: B 196 ASN cc_start: 0.7761 (t0) cc_final: 0.7513 (t0) REVERT: B 340 GLU cc_start: 0.7953 (tp30) cc_final: 0.7556 (tp30) REVERT: B 347 PHE cc_start: 0.7947 (m-80) cc_final: 0.7563 (m-10) REVERT: B 361 CYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7180 (p) REVERT: B 385 THR cc_start: 0.8645 (m) cc_final: 0.8410 (t) REVERT: B 396 TYR cc_start: 0.8197 (m-80) cc_final: 0.7990 (m-10) REVERT: B 543 PHE cc_start: 0.8018 (m-80) cc_final: 0.7632 (m-80) REVERT: B 619 GLU cc_start: 0.7181 (mp0) cc_final: 0.6870 (mp0) REVERT: B 651 ILE cc_start: 0.8627 (pt) cc_final: 0.8245 (mp) REVERT: B 698 SER cc_start: 0.8875 (t) cc_final: 0.8543 (p) REVERT: B 702 GLU cc_start: 0.7686 (tp30) cc_final: 0.7482 (tp30) REVERT: B 703 ASN cc_start: 0.8192 (t0) cc_final: 0.7872 (t0) REVERT: B 710 ASN cc_start: 0.8389 (p0) cc_final: 0.8107 (p0) REVERT: B 719 THR cc_start: 0.8604 (t) cc_final: 0.8360 (p) REVERT: B 747 THR cc_start: 0.8331 (p) cc_final: 0.7876 (p) REVERT: B 751 ASN cc_start: 0.8423 (m-40) cc_final: 0.8128 (m-40) REVERT: B 934 ILE cc_start: 0.8156 (tt) cc_final: 0.7869 (tt) REVERT: B 935 GLN cc_start: 0.7958 (tt0) cc_final: 0.7377 (mt0) REVERT: B 950 ASP cc_start: 0.7966 (m-30) cc_final: 0.7742 (m-30) REVERT: B 994 ASP cc_start: 0.8191 (t70) cc_final: 0.7910 (t0) REVERT: B 1017 GLU cc_start: 0.7892 (tp30) cc_final: 0.7624 (tp30) REVERT: B 1028 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8074 (mttm) REVERT: B 1125 ASN cc_start: 0.8093 (p0) cc_final: 0.7823 (p0) REVERT: B 1127 ASP cc_start: 0.8082 (t0) cc_final: 0.7554 (t0) REVERT: D 22 GLU cc_start: 0.6892 (tp30) cc_final: 0.6500 (tp30) REVERT: D 26 LYS cc_start: 0.7486 (mttt) cc_final: 0.7201 (mttt) REVERT: D 39 LEU cc_start: 0.8115 (mt) cc_final: 0.7838 (mt) REVERT: D 42 GLN cc_start: 0.7144 (mt0) cc_final: 0.6794 (mt0) REVERT: D 58 ASN cc_start: 0.6942 (m110) cc_final: 0.5496 (m110) REVERT: D 61 LYS cc_start: 0.8624 (mttt) cc_final: 0.8396 (ptpt) REVERT: D 152 MET cc_start: 0.4099 (OUTLIER) cc_final: 0.3893 (ptt) REVERT: D 163 TRP cc_start: 0.4223 (p-90) cc_final: 0.3344 (p-90) REVERT: D 246 ARG cc_start: 0.0743 (mtm110) cc_final: 0.0501 (mmm160) REVERT: D 310 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6799 (mm-30) REVERT: D 322 HIS cc_start: 0.5448 (OUTLIER) cc_final: 0.4501 (m90) REVERT: D 376 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6102 (ppp) REVERT: D 381 TYR cc_start: 0.8054 (t80) cc_final: 0.7841 (t80) REVERT: D 400 PHE cc_start: 0.4262 (m-80) cc_final: 0.3780 (m-80) REVERT: D 408 MET cc_start: 0.6503 (mmt) cc_final: 0.6017 (ttm) REVERT: D 456 LEU cc_start: 0.6638 (pp) cc_final: 0.6401 (pp) REVERT: D 510 TYR cc_start: 0.6938 (m-80) cc_final: 0.6691 (m-80) REVERT: D 515 TYR cc_start: 0.5649 (m-80) cc_final: 0.5424 (m-80) REVERT: D 557 MET cc_start: 0.7604 (tmm) cc_final: 0.7131 (tmm) REVERT: D 568 LYS cc_start: 0.7904 (tttm) cc_final: 0.7491 (tptt) REVERT: C 339 ASP cc_start: 0.8013 (p0) cc_final: 0.7733 (p0) REVERT: C 346 ARG cc_start: 0.7979 (ttm110) cc_final: 0.7730 (ttm110) REVERT: C 453 TYR cc_start: 0.7009 (p90) cc_final: 0.6738 (p90) REVERT: C 516 GLU cc_start: 0.6386 (tt0) cc_final: 0.6110 (tt0) REVERT: C 542 ASN cc_start: 0.8288 (t0) cc_final: 0.7836 (t0) REVERT: C 558 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8062 (mmmm) REVERT: C 610 VAL cc_start: 0.8418 (t) cc_final: 0.8172 (m) REVERT: C 654 GLU cc_start: 0.8389 (tt0) cc_final: 0.8167 (tt0) REVERT: C 656 VAL cc_start: 0.8546 (t) cc_final: 0.8279 (m) REVERT: C 708 SER cc_start: 0.8399 (m) cc_final: 0.7957 (p) REVERT: C 710 ASN cc_start: 0.8101 (p0) cc_final: 0.7863 (p0) REVERT: C 820 ASP cc_start: 0.8030 (t0) cc_final: 0.7811 (m-30) REVERT: C 947 LYS cc_start: 0.8423 (mttt) cc_final: 0.8206 (mttp) REVERT: C 949 GLN cc_start: 0.8214 (mt0) cc_final: 0.8011 (mm-40) REVERT: C 1128 VAL cc_start: 0.8725 (m) cc_final: 0.8450 (p) REVERT: C 1130 ILE cc_start: 0.8508 (pt) cc_final: 0.8161 (mt) REVERT: C 1136 THR cc_start: 0.8536 (t) cc_final: 0.8194 (p) REVERT: E 61 LYS cc_start: 0.8139 (mttt) cc_final: 0.7757 (mttt) REVERT: E 64 GLU cc_start: 0.6124 (mm-30) cc_final: 0.5763 (mm-30) REVERT: E 75 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6769 (pp20) REVERT: E 94 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7714 (pttt) REVERT: E 190 MET cc_start: 0.1614 (ptt) cc_final: 0.1012 (mtt) REVERT: E 313 LYS cc_start: 0.7393 (ttmm) cc_final: 0.7117 (mtmm) REVERT: E 521 TYR cc_start: 0.6200 (m-10) cc_final: 0.5930 (m-10) REVERT: E 549 GLU cc_start: 0.4245 (mm-30) cc_final: 0.3708 (mp0) REVERT: E 568 LYS cc_start: 0.7276 (mmmt) cc_final: 0.7006 (mmmm) outliers start: 133 outliers final: 73 residues processed: 858 average time/residue: 0.4624 time to fit residues: 642.3336 Evaluate side-chains 834 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 750 time to evaluate : 3.585 ------------------------------------------------------------------------------- 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 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 615 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 763 LEU 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 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET 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 226 LEU 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 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 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL 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 D residue 103 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 376 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 90 VAL 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 615 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN 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 283 VAL Chi-restraints excluded: chain E residue 343 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 366 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 142 optimal weight: 0.0060 chunk 341 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 306 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 379 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 D 401 HIS D 586 ASN C 641 ASN ** E 51 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.203812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149908 restraints weight = 54352.303| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.77 r_work: 0.3607 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 35018 Z= 0.154 Angle : 0.627 13.129 47723 Z= 0.314 Chirality : 0.045 0.333 5374 Planarity : 0.004 0.105 6098 Dihedral : 5.479 83.631 5354 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.83 % Allowed : 19.75 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4202 helix: 0.72 (0.14), residues: 1405 sheet: -0.41 (0.19), residues: 636 loop : -1.89 (0.12), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 461 HIS 0.009 0.001 HIS E 493 PHE 0.027 0.002 PHE B 201 TYR 0.018 0.001 TYR B1067 ARG 0.012 0.001 ARG D 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 37) link_NAG-ASN : angle 2.84725 ( 111) hydrogen bonds : bond 0.03661 ( 1335) hydrogen bonds : angle 4.85104 ( 3699) SS BOND : bond 0.00437 ( 40) SS BOND : angle 2.27608 ( 80) covalent geometry : bond 0.00357 (34941) covalent geometry : angle 0.60541 (47532) *********************** 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 912 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 771 time to evaluate : 3.695 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: 0.7473 (m-80) cc_final: 0.6969 (m-80) REVERT: A 235 ILE cc_start: 0.6076 (mt) cc_final: 0.5786 (mt) REVERT: A 239 GLN cc_start: 0.8029 (mp10) cc_final: 0.7802 (mp10) REVERT: A 240 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7857 (t) REVERT: A 377 PHE cc_start: 0.8778 (t80) cc_final: 0.8438 (t80) REVERT: A 378 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8200 (ttpp) REVERT: A 388 ASN cc_start: 0.8155 (t0) cc_final: 0.7863 (t0) REVERT: A 524 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7115 (m) REVERT: A 554 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7015 (mm-30) REVERT: A 576 VAL cc_start: 0.8917 (p) cc_final: 0.8703 (t) REVERT: A 580 GLN cc_start: 0.8205 (mm110) cc_final: 0.7880 (mt0) REVERT: A 583 GLU cc_start: 0.7694 (tp30) cc_final: 0.7415 (tp30) REVERT: A 654 GLU cc_start: 0.8169 (tt0) cc_final: 0.7956 (tt0) REVERT: A 710 ASN cc_start: 0.8370 (p0) cc_final: 0.8144 (p0) REVERT: A 790 LYS cc_start: 0.8459 (mtpt) cc_final: 0.7917 (mtmm) REVERT: A 820 ASP cc_start: 0.7872 (t0) cc_final: 0.7561 (m-30) REVERT: A 900 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8091 (mtp) REVERT: A 934 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8381 (tp) REVERT: A 957 GLN cc_start: 0.8268 (tt0) cc_final: 0.7983 (tt0) REVERT: A 1003 SER cc_start: 0.9015 (p) cc_final: 0.8774 (t) REVERT: A 1028 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8156 (mttm) REVERT: A 1105 THR cc_start: 0.8516 (t) cc_final: 0.8222 (p) REVERT: A 1120 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8221 (p) REVERT: A 1127 ASP cc_start: 0.7701 (t0) cc_final: 0.7372 (t0) REVERT: B 29 THR cc_start: 0.7345 (t) cc_final: 0.5019 (p) REVERT: B 51 THR cc_start: 0.8737 (t) cc_final: 0.8500 (p) REVERT: B 298 GLU cc_start: 0.8005 (tp30) cc_final: 0.7740 (tp30) REVERT: B 340 GLU cc_start: 0.8055 (tp30) cc_final: 0.7681 (tp30) REVERT: B 347 PHE cc_start: 0.7972 (m-80) cc_final: 0.7634 (m-10) REVERT: B 361 CYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7245 (p) REVERT: B 385 THR cc_start: 0.8676 (m) cc_final: 0.8433 (t) REVERT: B 386 LYS cc_start: 0.8144 (mttt) cc_final: 0.7940 (mttp) REVERT: B 430 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8821 (p) REVERT: B 453 TYR cc_start: 0.8169 (p90) cc_final: 0.7630 (p90) REVERT: B 543 PHE cc_start: 0.8111 (m-80) cc_final: 0.7753 (m-80) REVERT: B 619 GLU cc_start: 0.7208 (mp0) cc_final: 0.6953 (mp0) REVERT: B 651 ILE cc_start: 0.8647 (pt) cc_final: 0.8291 (mp) REVERT: B 698 SER cc_start: 0.8866 (t) cc_final: 0.8537 (p) REVERT: B 702 GLU cc_start: 0.7767 (tp30) cc_final: 0.7524 (tp30) REVERT: B 703 ASN cc_start: 0.8234 (t0) cc_final: 0.7879 (t0) REVERT: B 710 ASN cc_start: 0.8408 (p0) cc_final: 0.8114 (p0) REVERT: B 719 THR cc_start: 0.8635 (t) cc_final: 0.8404 (p) REVERT: B 730 SER cc_start: 0.8796 (t) cc_final: 0.8475 (m) REVERT: B 751 ASN cc_start: 0.8465 (m-40) cc_final: 0.8174 (m-40) REVERT: B 934 ILE cc_start: 0.8115 (tt) cc_final: 0.7823 (tt) REVERT: B 935 GLN cc_start: 0.7979 (tt0) cc_final: 0.7288 (mt0) REVERT: B 950 ASP cc_start: 0.8026 (m-30) cc_final: 0.7802 (m-30) REVERT: B 980 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8226 (mt) REVERT: B 994 ASP cc_start: 0.8251 (t70) cc_final: 0.7985 (t0) REVERT: B 1017 GLU cc_start: 0.7929 (tp30) cc_final: 0.7644 (tp30) REVERT: B 1028 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8239 (mttm) REVERT: B 1125 ASN cc_start: 0.8127 (p0) cc_final: 0.7887 (p0) REVERT: B 1127 ASP cc_start: 0.8147 (t0) cc_final: 0.7690 (t0) REVERT: D 22 GLU cc_start: 0.6943 (tp30) cc_final: 0.6437 (mm-30) REVERT: D 39 LEU cc_start: 0.8135 (mt) cc_final: 0.7886 (mt) REVERT: D 42 GLN cc_start: 0.7189 (mt0) cc_final: 0.6886 (mt0) REVERT: D 61 LYS cc_start: 0.8658 (mttt) cc_final: 0.8403 (ptpt) REVERT: D 97 LEU cc_start: 0.8186 (tp) cc_final: 0.7656 (mm) REVERT: D 163 TRP cc_start: 0.4312 (p-90) cc_final: 0.3386 (p-90) REVERT: D 225 ASP cc_start: 0.7618 (m-30) cc_final: 0.7391 (m-30) REVERT: D 246 ARG cc_start: 0.0753 (mtm110) cc_final: 0.0525 (mmm160) REVERT: D 249 MET cc_start: 0.5914 (tpp) cc_final: 0.4223 (mmm) REVERT: D 298 MET cc_start: 0.6593 (ttm) cc_final: 0.6265 (ttm) REVERT: D 322 HIS cc_start: 0.5624 (OUTLIER) cc_final: 0.4649 (m90) REVERT: D 365 THR cc_start: 0.7218 (p) cc_final: 0.6928 (t) REVERT: D 366 MET cc_start: 0.5096 (mmm) cc_final: 0.4217 (mmm) REVERT: D 381 TYR cc_start: 0.8502 (t80) cc_final: 0.7574 (t80) REVERT: D 385 TYR cc_start: 0.7065 (p90) cc_final: 0.5787 (p90) REVERT: D 400 PHE cc_start: 0.4246 (m-80) cc_final: 0.3756 (m-80) REVERT: D 557 MET cc_start: 0.7642 (tmm) cc_final: 0.7206 (tmm) REVERT: C 339 ASP cc_start: 0.8013 (p0) cc_final: 0.7732 (p0) REVERT: C 453 TYR cc_start: 0.7048 (p90) cc_final: 0.6559 (p90) REVERT: C 495 TYR cc_start: 0.6284 (m-80) cc_final: 0.5072 (m-10) REVERT: C 516 GLU cc_start: 0.6535 (tt0) cc_final: 0.6262 (tt0) REVERT: C 542 ASN cc_start: 0.8261 (t0) cc_final: 0.7773 (t0) REVERT: C 558 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8065 (mmmm) REVERT: C 607 GLN cc_start: 0.8489 (mt0) cc_final: 0.8231 (mt0) REVERT: C 654 GLU cc_start: 0.8442 (tt0) cc_final: 0.8202 (tt0) REVERT: C 708 SER cc_start: 0.8393 (m) cc_final: 0.7941 (p) REVERT: C 710 ASN cc_start: 0.8106 (p0) cc_final: 0.7871 (p0) REVERT: C 820 ASP cc_start: 0.8044 (t0) cc_final: 0.7837 (m-30) REVERT: C 947 LYS cc_start: 0.8423 (mttt) cc_final: 0.8201 (mttp) REVERT: C 949 GLN cc_start: 0.8220 (mt0) cc_final: 0.7977 (mm-40) REVERT: C 1128 VAL cc_start: 0.8725 (m) cc_final: 0.8444 (p) REVERT: C 1130 ILE cc_start: 0.8488 (pt) cc_final: 0.8176 (mt) REVERT: C 1136 THR cc_start: 0.8571 (t) cc_final: 0.8250 (p) REVERT: E 61 LYS cc_start: 0.8148 (mttt) cc_final: 0.7788 (mttt) REVERT: E 64 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5823 (mm-30) REVERT: E 94 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7731 (pttt) REVERT: E 113 ASN cc_start: 0.7043 (p0) cc_final: 0.6749 (p0) REVERT: E 169 ARG cc_start: 0.2499 (ttp80) cc_final: 0.1405 (ttp-110) REVERT: E 228 ARG cc_start: 0.6491 (tmm160) cc_final: 0.6101 (ttp80) REVERT: E 270 MET cc_start: 0.0332 (ptm) cc_final: 0.0102 (ptt) REVERT: E 313 LYS cc_start: 0.7444 (ttmm) cc_final: 0.7152 (mtmm) REVERT: E 366 MET cc_start: 0.3028 (mmm) cc_final: 0.2599 (mmp) REVERT: E 480 MET cc_start: 0.7084 (mtp) cc_final: 0.6765 (mtp) REVERT: E 510 TYR cc_start: 0.5698 (m-80) cc_final: 0.5443 (m-10) REVERT: E 526 GLN cc_start: 0.7725 (tp40) cc_final: 0.7414 (tp40) REVERT: E 549 GLU cc_start: 0.4314 (mm-30) cc_final: 0.3781 (mp0) REVERT: E 579 MET cc_start: 0.4297 (mtm) cc_final: 0.3804 (mmm) outliers start: 141 outliers final: 90 residues processed: 861 average time/residue: 0.4819 time to fit residues: 671.0811 Evaluate side-chains 853 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 750 time to evaluate : 3.471 ------------------------------------------------------------------------------- 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 401 VAL 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 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 659 SER 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 791 THR Chi-restraints excluded: chain A residue 859 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 1050 MET 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 226 LEU 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 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 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU 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 D residue 233 ILE 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 450 LEU Chi-restraints excluded: chain D residue 586 ASN 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 203 ILE 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 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 615 VAL Chi-restraints excluded: chain C residue 670 ILE 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 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 32 optimal weight: 0.0980 chunk 223 optimal weight: 8.9990 chunk 182 optimal weight: 0.5980 chunk 264 optimal weight: 0.5980 chunk 222 optimal weight: 0.6980 chunk 356 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 219 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 381 optimal weight: 7.9990 chunk 316 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 414 GLN B 658 ASN B1002 GLN D 101 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 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 = 0.4431 r_free = 0.4431 target = 0.203171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149123 restraints weight = 54516.685| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.49 r_work: 0.3619 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35018 Z= 0.136 Angle : 0.627 17.032 47723 Z= 0.315 Chirality : 0.045 0.400 5374 Planarity : 0.004 0.083 6098 Dihedral : 5.338 80.233 5354 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.80 % Allowed : 20.27 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4202 helix: 0.85 (0.14), residues: 1401 sheet: -0.39 (0.19), residues: 674 loop : -1.83 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 461 HIS 0.007 0.001 HIS E 493 PHE 0.033 0.002 PHE D 72 TYR 0.018 0.001 TYR B1067 ARG 0.009 0.000 ARG D 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 37) link_NAG-ASN : angle 2.74552 ( 111) hydrogen bonds : bond 0.03560 ( 1335) hydrogen bonds : angle 4.78460 ( 3699) SS BOND : bond 0.00571 ( 40) SS BOND : angle 2.86495 ( 80) covalent geometry : bond 0.00315 (34941) covalent geometry : angle 0.60279 (47532) *********************** 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 921 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 781 time to evaluate : 3.737 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 41 LYS cc_start: 0.6003 (ttmt) cc_final: 0.5748 (mtpt) REVERT: A 203 ILE cc_start: 0.8648 (pt) cc_final: 0.8275 (mt) REVERT: A 204 TYR cc_start: 0.7490 (m-80) cc_final: 0.6998 (m-80) REVERT: A 235 ILE cc_start: 0.6131 (mt) cc_final: 0.5860 (mt) REVERT: A 239 GLN cc_start: 0.7989 (mp10) cc_final: 0.7752 (mp10) REVERT: A 240 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7806 (t) REVERT: A 377 PHE cc_start: 0.8712 (t80) cc_final: 0.8384 (t80) REVERT: A 378 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8163 (ttpp) REVERT: A 388 ASN cc_start: 0.8047 (t0) cc_final: 0.7761 (t0) REVERT: A 524 VAL cc_start: 0.7335 (OUTLIER) cc_final: 0.7082 (m) REVERT: A 554 GLU cc_start: 0.7732 (mm-30) cc_final: 0.6932 (mm-30) REVERT: A 562 PHE cc_start: 0.8532 (p90) cc_final: 0.8325 (p90) REVERT: A 576 VAL cc_start: 0.8880 (p) cc_final: 0.8674 (t) REVERT: A 580 GLN cc_start: 0.8141 (mm110) cc_final: 0.7862 (mt0) REVERT: A 583 GLU cc_start: 0.7683 (tp30) cc_final: 0.7461 (tp30) REVERT: A 654 GLU cc_start: 0.8087 (tt0) cc_final: 0.7885 (tt0) REVERT: A 710 ASN cc_start: 0.8365 (p0) cc_final: 0.8143 (p0) REVERT: A 754 LEU cc_start: 0.8770 (mt) cc_final: 0.8556 (mp) REVERT: A 790 LYS cc_start: 0.8446 (mtpt) cc_final: 0.7888 (mtmm) REVERT: A 820 ASP cc_start: 0.7841 (t0) cc_final: 0.7546 (m-30) REVERT: A 900 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8090 (mtp) REVERT: A 934 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8371 (tp) REVERT: A 957 GLN cc_start: 0.8226 (tt0) cc_final: 0.7952 (tt0) REVERT: A 1003 SER cc_start: 0.8974 (p) cc_final: 0.8751 (t) REVERT: A 1105 THR cc_start: 0.8497 (t) cc_final: 0.8215 (p) REVERT: A 1120 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8243 (p) REVERT: A 1127 ASP cc_start: 0.7723 (t0) cc_final: 0.7337 (t0) REVERT: B 29 THR cc_start: 0.7361 (t) cc_final: 0.5005 (p) REVERT: B 65 PHE cc_start: 0.7810 (m-10) cc_final: 0.7531 (m-80) REVERT: B 129 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6990 (mtmm) REVERT: B 170 TYR cc_start: 0.6161 (m-80) cc_final: 0.5739 (m-80) REVERT: B 237 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6782 (mmt180) REVERT: B 340 GLU cc_start: 0.8031 (tp30) cc_final: 0.7714 (tp30) REVERT: B 347 PHE cc_start: 0.7969 (m-80) cc_final: 0.7688 (m-10) REVERT: B 361 CYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7239 (p) REVERT: B 385 THR cc_start: 0.8628 (m) cc_final: 0.8382 (t) REVERT: B 386 LYS cc_start: 0.8120 (mttt) cc_final: 0.7882 (mttp) REVERT: B 430 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8782 (p) REVERT: B 453 TYR cc_start: 0.8145 (p90) cc_final: 0.7592 (p90) REVERT: B 462 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8509 (mmmm) REVERT: B 515 PHE cc_start: 0.8368 (m-10) cc_final: 0.8153 (m-80) REVERT: B 619 GLU cc_start: 0.7005 (mp0) cc_final: 0.6711 (mp0) REVERT: B 651 ILE cc_start: 0.8599 (pt) cc_final: 0.8266 (mp) REVERT: B 698 SER cc_start: 0.8847 (t) cc_final: 0.8533 (p) REVERT: B 702 GLU cc_start: 0.7720 (tp30) cc_final: 0.7446 (tp30) REVERT: B 703 ASN cc_start: 0.8207 (t0) cc_final: 0.7838 (t0) REVERT: B 710 ASN cc_start: 0.8365 (p0) cc_final: 0.8098 (p0) REVERT: B 719 THR cc_start: 0.8613 (t) cc_final: 0.8394 (p) REVERT: B 730 SER cc_start: 0.8792 (t) cc_final: 0.8464 (m) REVERT: B 751 ASN cc_start: 0.8430 (m-40) cc_final: 0.8138 (m-40) REVERT: B 907 ASN cc_start: 0.8394 (t0) cc_final: 0.8059 (t0) REVERT: B 935 GLN cc_start: 0.8021 (tt0) cc_final: 0.7308 (mt0) REVERT: B 950 ASP cc_start: 0.7970 (m-30) cc_final: 0.7761 (m-30) REVERT: B 980 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8224 (mt) REVERT: B 994 ASP cc_start: 0.8157 (t70) cc_final: 0.7898 (t0) REVERT: B 1017 GLU cc_start: 0.7940 (tp30) cc_final: 0.7649 (tp30) REVERT: B 1028 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8229 (mttm) REVERT: B 1125 ASN cc_start: 0.8047 (p0) cc_final: 0.7818 (p0) REVERT: B 1127 ASP cc_start: 0.8118 (t0) cc_final: 0.7690 (t0) REVERT: D 22 GLU cc_start: 0.6978 (tp30) cc_final: 0.6434 (mm-30) REVERT: D 39 LEU cc_start: 0.8154 (mt) cc_final: 0.7895 (mt) REVERT: D 42 GLN cc_start: 0.7240 (mt0) cc_final: 0.6933 (mt0) REVERT: D 58 ASN cc_start: 0.7070 (m110) cc_final: 0.6577 (m110) REVERT: D 61 LYS cc_start: 0.8658 (mttt) cc_final: 0.8421 (ptpt) REVERT: D 152 MET cc_start: 0.4160 (OUTLIER) cc_final: 0.3930 (ptt) REVERT: D 225 ASP cc_start: 0.7593 (m-30) cc_final: 0.7284 (m-30) REVERT: D 249 MET cc_start: 0.5824 (tpp) cc_final: 0.3937 (mtt) REVERT: D 298 MET cc_start: 0.6580 (ttm) cc_final: 0.6238 (ttm) REVERT: D 308 PHE cc_start: 0.8125 (m-80) cc_final: 0.7887 (m-80) REVERT: D 327 PHE cc_start: 0.7754 (t80) cc_final: 0.7504 (m-80) REVERT: D 365 THR cc_start: 0.7199 (p) cc_final: 0.6919 (t) REVERT: D 366 MET cc_start: 0.5228 (mmm) cc_final: 0.4286 (mmm) REVERT: D 381 TYR cc_start: 0.8557 (t80) cc_final: 0.7722 (t80) REVERT: D 385 TYR cc_start: 0.7095 (p90) cc_final: 0.6394 (p90) REVERT: D 400 PHE cc_start: 0.4238 (m-80) cc_final: 0.3753 (m-80) REVERT: D 477 TRP cc_start: 0.6993 (t-100) cc_final: 0.6522 (t-100) REVERT: D 557 MET cc_start: 0.7691 (tmm) cc_final: 0.7304 (tmm) REVERT: D 568 LYS cc_start: 0.7836 (tttm) cc_final: 0.7403 (tptt) REVERT: D 586 ASN cc_start: 0.6356 (OUTLIER) cc_final: 0.5554 (t0) REVERT: C 339 ASP cc_start: 0.7973 (p0) cc_final: 0.7696 (p0) REVERT: C 346 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7779 (ttm170) REVERT: C 453 TYR cc_start: 0.7110 (p90) cc_final: 0.6592 (p90) REVERT: C 495 TYR cc_start: 0.6291 (m-80) cc_final: 0.4870 (m-10) REVERT: C 516 GLU cc_start: 0.6550 (tt0) cc_final: 0.6295 (tt0) REVERT: C 542 ASN cc_start: 0.8239 (t0) cc_final: 0.7813 (t0) REVERT: C 558 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8013 (mmmm) REVERT: C 654 GLU cc_start: 0.8369 (tt0) cc_final: 0.8073 (tt0) REVERT: C 708 SER cc_start: 0.8369 (m) cc_final: 0.7926 (p) REVERT: C 710 ASN cc_start: 0.8106 (p0) cc_final: 0.7878 (p0) REVERT: C 947 LYS cc_start: 0.8390 (mttt) cc_final: 0.8166 (mtmm) REVERT: C 1128 VAL cc_start: 0.8701 (m) cc_final: 0.8410 (p) REVERT: C 1130 ILE cc_start: 0.8463 (pt) cc_final: 0.8176 (mt) REVERT: C 1136 THR cc_start: 0.8519 (t) cc_final: 0.8222 (p) REVERT: E 41 TYR cc_start: 0.7540 (t80) cc_final: 0.6465 (t80) REVERT: E 61 LYS cc_start: 0.8138 (mttt) cc_final: 0.7775 (mttt) REVERT: E 64 GLU cc_start: 0.6201 (mm-30) cc_final: 0.5843 (mm-30) REVERT: E 75 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6946 (pp20) REVERT: E 94 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7751 (pttt) REVERT: E 113 ASN cc_start: 0.6959 (p0) cc_final: 0.6691 (p0) REVERT: E 152 MET cc_start: 0.0618 (ptm) cc_final: 0.0401 (ptm) REVERT: E 183 TYR cc_start: 0.2473 (OUTLIER) cc_final: 0.1077 (t80) REVERT: E 190 MET cc_start: 0.1689 (ptt) cc_final: 0.1191 (mtt) REVERT: E 228 ARG cc_start: 0.6477 (tmm160) cc_final: 0.6177 (ttp80) REVERT: E 278 LEU cc_start: 0.0267 (OUTLIER) cc_final: -0.0088 (tp) REVERT: E 313 LYS cc_start: 0.7433 (ttmm) cc_final: 0.7133 (mtmm) REVERT: E 349 TRP cc_start: 0.5541 (m100) cc_final: 0.5142 (m100) REVERT: E 355 ASP cc_start: 0.3967 (t0) cc_final: 0.3576 (t0) REVERT: E 381 TYR cc_start: 0.6030 (t80) cc_final: 0.5530 (t80) REVERT: E 476 LYS cc_start: 0.5528 (tptt) cc_final: 0.5183 (pttm) REVERT: E 480 MET cc_start: 0.7485 (mtp) cc_final: 0.6554 (mtp) REVERT: E 510 TYR cc_start: 0.5641 (m-80) cc_final: 0.5394 (m-10) REVERT: E 526 GLN cc_start: 0.7714 (tp40) cc_final: 0.7379 (tp40) REVERT: E 549 GLU cc_start: 0.4260 (mm-30) cc_final: 0.3402 (mp0) REVERT: E 579 MET cc_start: 0.4371 (mtm) cc_final: 0.3987 (mmm) outliers start: 140 outliers final: 97 residues processed: 863 average time/residue: 0.4767 time to fit residues: 661.4002 Evaluate side-chains 874 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 761 time to evaluate : 3.554 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 358 ILE 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 401 VAL 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 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 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 791 THR Chi-restraints excluded: chain A residue 859 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 975 SER Chi-restraints excluded: chain A residue 1050 MET 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 226 LEU 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 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 402 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 430 THR 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 785 VAL Chi-restraints excluded: chain B residue 859 THR 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 980 ILE 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 D residue 142 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 586 ASN 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 203 ILE 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 740 MET 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 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 81 GLN Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 183 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 364 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 0.1980 chunk 177 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 295 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 586 ASN C 69 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 394 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.202273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147846 restraints weight = 54203.490| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.50 r_work: 0.3589 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35018 Z= 0.177 Angle : 0.659 23.275 47723 Z= 0.330 Chirality : 0.046 0.446 5374 Planarity : 0.004 0.055 6098 Dihedral : 5.372 76.042 5354 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.57 % Favored : 95.41 % Rotamer: Outliers : 3.96 % Allowed : 20.62 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4202 helix: 0.78 (0.14), residues: 1404 sheet: -0.25 (0.19), residues: 666 loop : -1.76 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 461 HIS 0.006 0.001 HIS C1101 PHE 0.025 0.002 PHE B 201 TYR 0.019 0.002 TYR E 454 ARG 0.007 0.001 ARG D 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00759 ( 37) link_NAG-ASN : angle 2.81988 ( 111) hydrogen bonds : bond 0.03768 ( 1335) hydrogen bonds : angle 4.82557 ( 3699) SS BOND : bond 0.00728 ( 40) SS BOND : angle 2.95194 ( 80) covalent geometry : bond 0.00411 (34941) covalent geometry : angle 0.63501 (47532) *********************** 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 926 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 780 time to evaluate : 3.940 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: A 41 LYS cc_start: 0.6283 (ttmt) cc_final: 0.6017 (mtpt) REVERT: A 129 LYS cc_start: 0.7495 (mmtt) cc_final: 0.7065 (mmtt) REVERT: A 203 ILE cc_start: 0.8623 (pt) cc_final: 0.8254 (mt) REVERT: A 204 TYR cc_start: 0.7521 (m-80) cc_final: 0.7073 (m-80) REVERT: A 239 GLN cc_start: 0.7971 (mp10) cc_final: 0.7701 (mp10) REVERT: A 240 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7871 (t) REVERT: A 360 ASN cc_start: 0.7441 (m-40) cc_final: 0.7187 (m-40) REVERT: A 377 PHE cc_start: 0.8735 (t80) cc_final: 0.8449 (t80) REVERT: A 378 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8191 (ttpp) REVERT: A 388 ASN cc_start: 0.8091 (t0) cc_final: 0.7836 (t0) REVERT: A 524 VAL cc_start: 0.7262 (OUTLIER) cc_final: 0.7017 (m) REVERT: A 554 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 580 GLN cc_start: 0.8168 (mm110) cc_final: 0.7875 (mt0) REVERT: A 710 ASN cc_start: 0.8431 (p0) cc_final: 0.8205 (p0) REVERT: A 725 GLU cc_start: 0.8259 (tt0) cc_final: 0.8036 (tt0) REVERT: A 804 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8072 (mm-40) REVERT: A 900 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: A 934 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8421 (tp) REVERT: A 957 GLN cc_start: 0.8228 (tt0) cc_final: 0.7938 (tt0) REVERT: A 1003 SER cc_start: 0.8978 (p) cc_final: 0.8725 (t) REVERT: A 1005 GLN cc_start: 0.8103 (mt0) cc_final: 0.7857 (mt0) REVERT: A 1084 ASP cc_start: 0.8161 (t0) cc_final: 0.7672 (t0) REVERT: A 1105 THR cc_start: 0.8497 (t) cc_final: 0.8237 (p) REVERT: A 1120 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 1127 ASP cc_start: 0.7842 (t0) cc_final: 0.7455 (t0) REVERT: B 29 THR cc_start: 0.7470 (t) cc_final: 0.5135 (p) REVERT: B 51 THR cc_start: 0.8729 (t) cc_final: 0.8465 (p) REVERT: B 65 PHE cc_start: 0.7776 (m-10) cc_final: 0.7471 (m-80) REVERT: B 129 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7168 (mtmm) REVERT: B 237 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6801 (mmt180) REVERT: B 340 GLU cc_start: 0.8030 (tp30) cc_final: 0.7778 (tp30) REVERT: B 347 PHE cc_start: 0.8073 (m-80) cc_final: 0.7870 (m-10) REVERT: B 361 CYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7287 (p) REVERT: B 385 THR cc_start: 0.8637 (m) cc_final: 0.8408 (t) REVERT: B 453 TYR cc_start: 0.8186 (p90) cc_final: 0.7523 (p90) REVERT: B 462 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8490 (mmmm) REVERT: B 543 PHE cc_start: 0.8301 (m-80) cc_final: 0.8047 (m-80) REVERT: B 619 GLU cc_start: 0.7059 (mp0) cc_final: 0.6786 (mp0) REVERT: B 658 ASN cc_start: 0.8179 (p0) cc_final: 0.7542 (p0) REVERT: B 698 SER cc_start: 0.8818 (t) cc_final: 0.8416 (p) REVERT: B 703 ASN cc_start: 0.8201 (t0) cc_final: 0.7830 (t0) REVERT: B 710 ASN cc_start: 0.8425 (p0) cc_final: 0.8111 (p0) REVERT: B 719 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8383 (p) REVERT: B 730 SER cc_start: 0.8749 (t) cc_final: 0.8458 (m) REVERT: B 751 ASN cc_start: 0.8372 (m-40) cc_final: 0.8064 (m-40) REVERT: B 788 ILE cc_start: 0.8560 (mt) cc_final: 0.8342 (mm) REVERT: B 907 ASN cc_start: 0.8414 (t0) cc_final: 0.8085 (t0) REVERT: B 950 ASP cc_start: 0.7971 (m-30) cc_final: 0.7749 (m-30) REVERT: B 960 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8218 (m-40) REVERT: B 970 PHE cc_start: 0.8338 (m-10) cc_final: 0.8118 (m-10) REVERT: B 1017 GLU cc_start: 0.7920 (tp30) cc_final: 0.7608 (tp30) REVERT: B 1028 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8220 (mttm) REVERT: B 1127 ASP cc_start: 0.8112 (t0) cc_final: 0.7910 (t0) REVERT: D 22 GLU cc_start: 0.6912 (tp30) cc_final: 0.6359 (mm-30) REVERT: D 39 LEU cc_start: 0.8208 (mt) cc_final: 0.7954 (mt) REVERT: D 42 GLN cc_start: 0.7294 (mt0) cc_final: 0.7001 (mt0) REVERT: D 61 LYS cc_start: 0.8673 (mttt) cc_final: 0.8299 (mttt) REVERT: D 97 LEU cc_start: 0.8207 (tp) cc_final: 0.7681 (mm) REVERT: D 249 MET cc_start: 0.5742 (tpp) cc_final: 0.3763 (mtt) REVERT: D 298 MET cc_start: 0.6592 (ttm) cc_final: 0.6276 (ttm) REVERT: D 327 PHE cc_start: 0.7829 (t80) cc_final: 0.7565 (m-80) REVERT: D 365 THR cc_start: 0.7241 (p) cc_final: 0.6929 (t) REVERT: D 366 MET cc_start: 0.5178 (mmm) cc_final: 0.4361 (mmm) REVERT: D 376 MET cc_start: 0.5696 (ptt) cc_final: 0.5485 (ppp) REVERT: D 381 TYR cc_start: 0.8587 (t80) cc_final: 0.8142 (t80) REVERT: D 385 TYR cc_start: 0.7137 (p90) cc_final: 0.6812 (p90) REVERT: D 400 PHE cc_start: 0.4384 (m-80) cc_final: 0.3996 (m-80) REVERT: D 440 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6171 (pp) REVERT: D 477 TRP cc_start: 0.7062 (t-100) cc_final: 0.6329 (t-100) REVERT: D 557 MET cc_start: 0.7756 (tmm) cc_final: 0.7371 (tmm) REVERT: D 568 LYS cc_start: 0.7869 (tttm) cc_final: 0.7426 (tptt) REVERT: C 346 ARG cc_start: 0.8092 (ttm170) cc_final: 0.7783 (ttm110) REVERT: C 453 TYR cc_start: 0.7157 (p90) cc_final: 0.6585 (p90) REVERT: C 495 TYR cc_start: 0.6391 (m-80) cc_final: 0.4902 (m-10) REVERT: C 516 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: C 542 ASN cc_start: 0.8279 (t0) cc_final: 0.7889 (t0) REVERT: C 558 LYS cc_start: 0.8383 (mtmt) cc_final: 0.7987 (mmmm) REVERT: C 654 GLU cc_start: 0.8359 (tt0) cc_final: 0.8096 (tt0) REVERT: C 691 SER cc_start: 0.8743 (p) cc_final: 0.8378 (m) REVERT: C 708 SER cc_start: 0.8367 (m) cc_final: 0.7947 (p) REVERT: C 947 LYS cc_start: 0.8420 (mttt) cc_final: 0.8176 (mtmm) REVERT: C 1029 MET cc_start: 0.8307 (ttm) cc_final: 0.7761 (ttm) REVERT: C 1128 VAL cc_start: 0.8704 (m) cc_final: 0.8406 (p) REVERT: C 1130 ILE cc_start: 0.8463 (pt) cc_final: 0.8234 (mt) REVERT: C 1136 THR cc_start: 0.8543 (t) cc_final: 0.8255 (p) REVERT: E 41 TYR cc_start: 0.7647 (t80) cc_final: 0.6638 (t80) REVERT: E 61 LYS cc_start: 0.8147 (mttt) cc_final: 0.7789 (mttt) REVERT: E 64 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5897 (mm-30) REVERT: E 75 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6987 (pp20) REVERT: E 94 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7786 (pttt) REVERT: E 113 ASN cc_start: 0.6897 (p0) cc_final: 0.6596 (p0) REVERT: E 183 TYR cc_start: 0.2490 (OUTLIER) cc_final: 0.2027 (t80) REVERT: E 190 MET cc_start: 0.1651 (ptt) cc_final: 0.1135 (mtt) REVERT: E 207 TYR cc_start: 0.4037 (m-80) cc_final: 0.3695 (m-80) REVERT: E 278 LEU cc_start: 0.0226 (OUTLIER) cc_final: -0.0145 (tp) REVERT: E 313 LYS cc_start: 0.7471 (ttmm) cc_final: 0.7157 (mtmm) REVERT: E 327 PHE cc_start: 0.7856 (t80) cc_final: 0.7105 (t80) REVERT: E 349 TRP cc_start: 0.5533 (m100) cc_final: 0.5119 (m100) REVERT: E 355 ASP cc_start: 0.4439 (t0) cc_final: 0.3947 (t0) REVERT: E 366 MET cc_start: 0.2592 (mmm) cc_final: 0.1931 (mmp) REVERT: E 480 MET cc_start: 0.7444 (mtp) cc_final: 0.6792 (mtp) REVERT: E 510 TYR cc_start: 0.5746 (m-80) cc_final: 0.5512 (m-10) REVERT: E 526 GLN cc_start: 0.7706 (tp40) cc_final: 0.7391 (tp40) REVERT: E 549 GLU cc_start: 0.4445 (mm-30) cc_final: 0.3889 (mp0) REVERT: E 579 MET cc_start: 0.4428 (mtm) cc_final: 0.3815 (mmm) outliers start: 146 outliers final: 101 residues processed: 865 average time/residue: 0.5690 time to fit residues: 796.3324 Evaluate side-chains 873 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 756 time to evaluate : 3.510 ------------------------------------------------------------------------------- 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 358 ILE 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 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 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 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 1050 MET 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 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 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 719 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 960 ASN 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 1028 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 586 ASN 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 203 ILE 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 379 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 516 GLU 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 670 ILE 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 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 183 TYR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 83 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 69 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 374 optimal weight: 7.9990 chunk 285 optimal weight: 0.6980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 506 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN D 586 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 856 ASN C1054 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.201420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.146869 restraints weight = 53835.891| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.49 r_work: 0.3562 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35018 Z= 0.186 Angle : 0.678 22.439 47723 Z= 0.339 Chirality : 0.047 0.449 5374 Planarity : 0.005 0.061 6098 Dihedral : 5.255 73.912 5354 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 4.04 % Allowed : 20.78 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4202 helix: 0.82 (0.14), residues: 1403 sheet: -0.17 (0.19), residues: 630 loop : -1.71 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 461 HIS 0.006 0.001 HIS C1101 PHE 0.030 0.002 PHE D 512 TYR 0.018 0.002 TYR B1067 ARG 0.009 0.001 ARG D 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 37) link_NAG-ASN : angle 3.29303 ( 111) hydrogen bonds : bond 0.03792 ( 1335) hydrogen bonds : angle 4.83045 ( 3699) SS BOND : bond 0.00559 ( 40) SS BOND : angle 2.94994 ( 80) covalent geometry : bond 0.00432 (34941) covalent geometry : angle 0.64886 (47532) *********************** 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 931 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 782 time to evaluate : 3.683 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: 0.7468 (mmtt) cc_final: 0.7060 (mmtt) REVERT: A 196 ASN cc_start: 0.6482 (p0) cc_final: 0.6192 (p0) REVERT: A 203 ILE cc_start: 0.8642 (pt) cc_final: 0.8240 (mt) REVERT: A 204 TYR cc_start: 0.7516 (m-80) cc_final: 0.7100 (m-80) REVERT: A 239 GLN cc_start: 0.7970 (mp10) cc_final: 0.7702 (mp10) REVERT: A 240 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7875 (t) REVERT: A 360 ASN cc_start: 0.7462 (m-40) cc_final: 0.7196 (m-40) REVERT: A 377 PHE cc_start: 0.8764 (t80) cc_final: 0.8491 (t80) REVERT: A 378 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8165 (ttpp) REVERT: A 388 ASN cc_start: 0.8107 (t0) cc_final: 0.7838 (t0) REVERT: A 524 VAL cc_start: 0.7258 (OUTLIER) cc_final: 0.7016 (m) REVERT: A 580 GLN cc_start: 0.8141 (mm110) cc_final: 0.7929 (mt0) REVERT: A 710 ASN cc_start: 0.8471 (p0) cc_final: 0.8259 (p0) REVERT: A 725 GLU cc_start: 0.8259 (tt0) cc_final: 0.8021 (tt0) REVERT: A 790 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8152 (mtmm) REVERT: A 791 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7866 (p) REVERT: A 820 ASP cc_start: 0.7822 (t0) cc_final: 0.7549 (m-30) REVERT: A 900 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8145 (mtp) REVERT: A 934 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8407 (tp) REVERT: A 957 GLN cc_start: 0.8241 (tt0) cc_final: 0.7964 (tt0) REVERT: A 1003 SER cc_start: 0.8967 (p) cc_final: 0.8709 (t) REVERT: A 1005 GLN cc_start: 0.8130 (mt0) cc_final: 0.7890 (mt0) REVERT: A 1084 ASP cc_start: 0.8179 (t0) cc_final: 0.7759 (t0) REVERT: A 1105 THR cc_start: 0.8495 (t) cc_final: 0.8233 (p) REVERT: A 1120 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8289 (p) REVERT: A 1127 ASP cc_start: 0.7847 (t0) cc_final: 0.7410 (t0) REVERT: A 1139 ASP cc_start: 0.8106 (t0) cc_final: 0.7889 (t0) REVERT: B 51 THR cc_start: 0.8718 (t) cc_final: 0.8459 (p) REVERT: B 52 GLN cc_start: 0.8340 (tp40) cc_final: 0.8095 (tp40) REVERT: B 65 PHE cc_start: 0.7750 (m-10) cc_final: 0.7491 (m-80) REVERT: B 129 LYS cc_start: 0.7757 (mmtt) cc_final: 0.7417 (mtmm) REVERT: B 159 VAL cc_start: 0.6630 (OUTLIER) cc_final: 0.6366 (m) REVERT: B 170 TYR cc_start: 0.6497 (m-80) cc_final: 0.6209 (m-80) REVERT: B 237 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6851 (mmt180) REVERT: B 298 GLU cc_start: 0.7970 (tp30) cc_final: 0.7450 (tp30) REVERT: B 340 GLU cc_start: 0.8088 (tp30) cc_final: 0.7825 (tp30) REVERT: B 361 CYS cc_start: 0.8006 (OUTLIER) cc_final: 0.6975 (p) REVERT: B 385 THR cc_start: 0.8649 (m) cc_final: 0.8435 (t) REVERT: B 430 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8792 (p) REVERT: B 462 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8449 (mmmm) REVERT: B 524 VAL cc_start: 0.8357 (m) cc_final: 0.7884 (p) REVERT: B 543 PHE cc_start: 0.8312 (m-80) cc_final: 0.8098 (m-80) REVERT: B 619 GLU cc_start: 0.7100 (mp0) cc_final: 0.6803 (mp0) REVERT: B 651 ILE cc_start: 0.8576 (pt) cc_final: 0.8275 (mp) REVERT: B 698 SER cc_start: 0.8845 (t) cc_final: 0.8436 (p) REVERT: B 703 ASN cc_start: 0.8202 (t0) cc_final: 0.7833 (t0) REVERT: B 710 ASN cc_start: 0.8450 (p0) cc_final: 0.8127 (p0) REVERT: B 730 SER cc_start: 0.8782 (t) cc_final: 0.8474 (m) REVERT: B 751 ASN cc_start: 0.8398 (m-40) cc_final: 0.8081 (m-40) REVERT: B 788 ILE cc_start: 0.8563 (mt) cc_final: 0.8350 (mm) REVERT: B 907 ASN cc_start: 0.8417 (t0) cc_final: 0.8108 (t0) REVERT: B 950 ASP cc_start: 0.8016 (m-30) cc_final: 0.7807 (m-30) REVERT: B 960 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8237 (m-40) REVERT: B 1017 GLU cc_start: 0.7950 (tp30) cc_final: 0.7651 (tp30) REVERT: B 1028 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8211 (mttm) REVERT: D 22 GLU cc_start: 0.6940 (tp30) cc_final: 0.6575 (mm-30) REVERT: D 39 LEU cc_start: 0.8244 (mt) cc_final: 0.7993 (mt) REVERT: D 42 GLN cc_start: 0.7333 (mt0) cc_final: 0.7122 (mt0) REVERT: D 58 ASN cc_start: 0.7247 (m110) cc_final: 0.5824 (m-40) REVERT: D 61 LYS cc_start: 0.8702 (mttt) cc_final: 0.8341 (mttt) REVERT: D 69 TRP cc_start: 0.7714 (t60) cc_final: 0.7448 (t60) REVERT: D 97 LEU cc_start: 0.8235 (tp) cc_final: 0.7735 (mm) REVERT: D 327 PHE cc_start: 0.7823 (t80) cc_final: 0.7591 (m-80) REVERT: D 365 THR cc_start: 0.7146 (p) cc_final: 0.6879 (t) REVERT: D 366 MET cc_start: 0.5190 (mmm) cc_final: 0.4964 (mmm) REVERT: D 376 MET cc_start: 0.5757 (ptt) cc_final: 0.5204 (ppp) REVERT: D 381 TYR cc_start: 0.8549 (t80) cc_final: 0.8032 (t80) REVERT: D 385 TYR cc_start: 0.7064 (p90) cc_final: 0.6579 (p90) REVERT: D 388 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7125 (mm-40) REVERT: D 400 PHE cc_start: 0.4409 (m-80) cc_final: 0.4026 (m-80) REVERT: D 408 MET cc_start: 0.6425 (mmt) cc_final: 0.6216 (mmt) REVERT: D 440 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6166 (pp) REVERT: D 557 MET cc_start: 0.7736 (tmm) cc_final: 0.7373 (tmm) REVERT: D 568 LYS cc_start: 0.7886 (tttm) cc_final: 0.7441 (tptt) REVERT: D 586 ASN cc_start: 0.6591 (m110) cc_final: 0.5957 (t0) REVERT: C 88 ASP cc_start: 0.6594 (t0) cc_final: 0.6288 (t70) REVERT: C 346 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7783 (ttm110) REVERT: C 453 TYR cc_start: 0.7253 (p90) cc_final: 0.6783 (p90) REVERT: C 516 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: C 542 ASN cc_start: 0.8287 (t0) cc_final: 0.7912 (t0) REVERT: C 558 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8007 (mmmm) REVERT: C 654 GLU cc_start: 0.8316 (tt0) cc_final: 0.8085 (tt0) REVERT: C 691 SER cc_start: 0.8742 (p) cc_final: 0.8374 (m) REVERT: C 708 SER cc_start: 0.8391 (m) cc_final: 0.7958 (p) REVERT: C 723 THR cc_start: 0.8492 (m) cc_final: 0.8108 (p) REVERT: C 737 ASP cc_start: 0.7917 (t0) cc_final: 0.7706 (t0) REVERT: C 821 LEU cc_start: 0.8553 (tp) cc_final: 0.8247 (tt) REVERT: C 947 LYS cc_start: 0.8399 (mttt) cc_final: 0.8152 (mtmm) REVERT: C 1084 ASP cc_start: 0.8203 (m-30) cc_final: 0.7949 (t0) REVERT: C 1128 VAL cc_start: 0.8699 (m) cc_final: 0.8393 (p) REVERT: C 1130 ILE cc_start: 0.8450 (pt) cc_final: 0.8244 (mt) REVERT: C 1136 THR cc_start: 0.8529 (t) cc_final: 0.8269 (p) REVERT: E 41 TYR cc_start: 0.7647 (t80) cc_final: 0.6715 (t80) REVERT: E 61 LYS cc_start: 0.8136 (mttt) cc_final: 0.7785 (mttt) REVERT: E 64 GLU cc_start: 0.6273 (mm-30) cc_final: 0.5873 (mm-30) REVERT: E 75 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7021 (pp20) REVERT: E 94 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7771 (pttt) REVERT: E 113 ASN cc_start: 0.6868 (p0) cc_final: 0.6582 (p0) REVERT: E 169 ARG cc_start: 0.3167 (ttp80) cc_final: 0.2509 (ttp80) REVERT: E 183 TYR cc_start: 0.2473 (OUTLIER) cc_final: 0.1007 (t80) REVERT: E 190 MET cc_start: 0.1704 (ptt) cc_final: 0.1198 (mtt) REVERT: E 207 TYR cc_start: 0.4060 (m-80) cc_final: 0.3704 (m-80) REVERT: E 228 ARG cc_start: 0.6574 (ttp80) cc_final: 0.6227 (ttp80) REVERT: E 278 LEU cc_start: 0.0269 (OUTLIER) cc_final: -0.0104 (tp) REVERT: E 313 LYS cc_start: 0.7517 (ttmm) cc_final: 0.7178 (mtmm) REVERT: E 327 PHE cc_start: 0.7908 (t80) cc_final: 0.7242 (t80) REVERT: E 349 TRP cc_start: 0.5416 (m100) cc_final: 0.5007 (m100) REVERT: E 366 MET cc_start: 0.2774 (mmm) cc_final: 0.1447 (mmp) REVERT: E 381 TYR cc_start: 0.5956 (t80) cc_final: 0.5651 (t80) REVERT: E 480 MET cc_start: 0.7463 (mtp) cc_final: 0.6801 (mtp) REVERT: E 510 TYR cc_start: 0.5720 (m-80) cc_final: 0.5505 (m-10) REVERT: E 526 GLN cc_start: 0.7709 (tp40) cc_final: 0.7365 (tp40) REVERT: E 549 GLU cc_start: 0.4656 (mm-30) cc_final: 0.3499 (pm20) REVERT: E 579 MET cc_start: 0.4373 (mtm) cc_final: 0.4051 (mmm) outliers start: 149 outliers final: 107 residues processed: 864 average time/residue: 0.4974 time to fit residues: 695.5156 Evaluate side-chains 893 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 768 time to evaluate : 3.774 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 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 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 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 761 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 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 1050 MET 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 226 LEU 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 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 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 602 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU 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 960 ASN 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 1028 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 343 VAL 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 203 ILE 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 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 670 ILE 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 820 ASP 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 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 323 MET Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 163 optimal weight: 0.0870 chunk 72 optimal weight: 0.8980 chunk 322 optimal weight: 2.9990 chunk 392 optimal weight: 0.3980 chunk 156 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 350 optimal weight: 0.3980 chunk 394 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN B 460 ASN B 895 GLN ** C 173 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.202151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148001 restraints weight = 54401.539| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.49 r_work: 0.3600 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35018 Z= 0.130 Angle : 0.664 21.468 47723 Z= 0.328 Chirality : 0.046 0.668 5374 Planarity : 0.005 0.095 6098 Dihedral : 5.257 71.900 5354 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 3.31 % Allowed : 21.57 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4202 helix: 0.92 (0.15), residues: 1401 sheet: -0.11 (0.19), residues: 640 loop : -1.63 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 461 HIS 0.005 0.001 HIS C1101 PHE 0.025 0.001 PHE B 201 TYR 0.017 0.001 TYR B1067 ARG 0.013 0.001 ARG D 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 37) link_NAG-ASN : angle 3.54185 ( 111) hydrogen bonds : bond 0.03512 ( 1335) hydrogen bonds : angle 4.77062 ( 3699) SS BOND : bond 0.00701 ( 40) SS BOND : angle 2.70766 ( 80) covalent geometry : bond 0.00295 (34941) covalent geometry : angle 0.63315 (47532) *********************** 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 892 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 770 time to evaluate : 3.942 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: A 41 LYS cc_start: 0.6872 (mtpt) cc_final: 0.6649 (mtpt) REVERT: A 129 LYS cc_start: 0.7371 (mmtt) cc_final: 0.7042 (mmtt) REVERT: A 196 ASN cc_start: 0.6272 (p0) cc_final: 0.5979 (p0) REVERT: A 203 ILE cc_start: 0.8671 (pt) cc_final: 0.8251 (mt) REVERT: A 204 TYR cc_start: 0.7475 (m-80) cc_final: 0.7045 (m-80) REVERT: A 239 GLN cc_start: 0.7992 (mp10) cc_final: 0.7718 (mp10) REVERT: A 240 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7859 (t) REVERT: A 360 ASN cc_start: 0.7454 (m-40) cc_final: 0.7190 (m-40) REVERT: A 377 PHE cc_start: 0.8718 (t80) cc_final: 0.8457 (t80) REVERT: A 378 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8184 (ttpp) REVERT: A 388 ASN cc_start: 0.8033 (t0) cc_final: 0.7790 (t0) REVERT: A 524 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.6994 (m) REVERT: A 710 ASN cc_start: 0.8470 (p0) cc_final: 0.8268 (p0) REVERT: A 725 GLU cc_start: 0.8232 (tt0) cc_final: 0.7990 (tt0) REVERT: A 790 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8136 (mtmm) REVERT: A 791 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7836 (p) REVERT: A 804 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8161 (mm-40) REVERT: A 820 ASP cc_start: 0.7744 (t0) cc_final: 0.7455 (m-30) REVERT: A 900 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8093 (mtp) REVERT: A 934 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8391 (tp) REVERT: A 957 GLN cc_start: 0.8240 (tt0) cc_final: 0.7990 (tt0) REVERT: A 984 LEU cc_start: 0.8785 (mt) cc_final: 0.8515 (mt) REVERT: A 1003 SER cc_start: 0.8959 (p) cc_final: 0.8674 (t) REVERT: A 1084 ASP cc_start: 0.8142 (t0) cc_final: 0.7624 (t0) REVERT: A 1105 THR cc_start: 0.8465 (t) cc_final: 0.8235 (p) REVERT: A 1120 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 1127 ASP cc_start: 0.7809 (t0) cc_final: 0.7346 (t0) REVERT: A 1139 ASP cc_start: 0.8081 (t0) cc_final: 0.7877 (t0) REVERT: B 29 THR cc_start: 0.7309 (t) cc_final: 0.5192 (p) REVERT: B 65 PHE cc_start: 0.7692 (m-10) cc_final: 0.7474 (m-80) REVERT: B 129 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7247 (mtmm) REVERT: B 159 VAL cc_start: 0.6648 (OUTLIER) cc_final: 0.6405 (m) REVERT: B 237 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6866 (mmp-170) REVERT: B 340 GLU cc_start: 0.8060 (tp30) cc_final: 0.7831 (tp30) REVERT: B 347 PHE cc_start: 0.7512 (m-10) cc_final: 0.7304 (m-10) REVERT: B 361 CYS cc_start: 0.7863 (OUTLIER) cc_final: 0.6974 (p) REVERT: B 385 THR cc_start: 0.8637 (m) cc_final: 0.8423 (t) REVERT: B 386 LYS cc_start: 0.8037 (mttp) cc_final: 0.7631 (mttp) REVERT: B 430 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8796 (p) REVERT: B 462 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8415 (mmmm) REVERT: B 524 VAL cc_start: 0.8279 (m) cc_final: 0.7787 (p) REVERT: B 543 PHE cc_start: 0.8313 (m-80) cc_final: 0.8110 (m-80) REVERT: B 651 ILE cc_start: 0.8554 (pt) cc_final: 0.8248 (mp) REVERT: B 658 ASN cc_start: 0.8125 (p0) cc_final: 0.7639 (p0) REVERT: B 660 TYR cc_start: 0.8555 (m-80) cc_final: 0.8304 (m-80) REVERT: B 698 SER cc_start: 0.8806 (t) cc_final: 0.8409 (p) REVERT: B 703 ASN cc_start: 0.8184 (t0) cc_final: 0.7802 (t0) REVERT: B 710 ASN cc_start: 0.8414 (p0) cc_final: 0.8139 (p0) REVERT: B 730 SER cc_start: 0.8791 (t) cc_final: 0.8477 (m) REVERT: B 751 ASN cc_start: 0.8369 (m-40) cc_final: 0.8088 (m-40) REVERT: B 788 ILE cc_start: 0.8561 (mt) cc_final: 0.8351 (mm) REVERT: B 907 ASN cc_start: 0.8406 (t0) cc_final: 0.8082 (t0) REVERT: B 960 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8227 (m-40) REVERT: B 1017 GLU cc_start: 0.7930 (tp30) cc_final: 0.7623 (tp30) REVERT: B 1028 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8203 (mttm) REVERT: D 22 GLU cc_start: 0.6898 (tp30) cc_final: 0.6518 (mm-30) REVERT: D 39 LEU cc_start: 0.8233 (mt) cc_final: 0.7981 (mt) REVERT: D 42 GLN cc_start: 0.7294 (mt0) cc_final: 0.7091 (mt0) REVERT: D 58 ASN cc_start: 0.7173 (m110) cc_final: 0.5706 (m110) REVERT: D 69 TRP cc_start: 0.7643 (t60) cc_final: 0.7382 (t60) REVERT: D 97 LEU cc_start: 0.8170 (tp) cc_final: 0.7641 (mm) REVERT: D 127 TYR cc_start: 0.4948 (t80) cc_final: 0.4266 (t80) REVERT: D 365 THR cc_start: 0.7040 (p) cc_final: 0.6804 (t) REVERT: D 381 TYR cc_start: 0.8558 (t80) cc_final: 0.8049 (t80) REVERT: D 388 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7113 (mm-40) REVERT: D 400 PHE cc_start: 0.4464 (m-80) cc_final: 0.4055 (m-80) REVERT: D 408 MET cc_start: 0.6411 (mmt) cc_final: 0.6149 (mmt) REVERT: D 440 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6229 (pp) REVERT: D 460 ARG cc_start: 0.6144 (tpt170) cc_final: 0.5799 (tpp80) REVERT: D 515 TYR cc_start: 0.5448 (m-80) cc_final: 0.4729 (m-80) REVERT: D 557 MET cc_start: 0.7769 (tmm) cc_final: 0.7421 (tmm) REVERT: D 568 LYS cc_start: 0.7842 (tttm) cc_final: 0.7423 (tptt) REVERT: D 586 ASN cc_start: 0.6542 (m110) cc_final: 0.5942 (t0) REVERT: C 88 ASP cc_start: 0.6644 (t0) cc_final: 0.6323 (t70) REVERT: C 281 GLU cc_start: 0.7662 (pm20) cc_final: 0.7298 (pp20) REVERT: C 334 ASN cc_start: 0.8241 (m-40) cc_final: 0.7770 (t0) REVERT: C 346 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7718 (ttm110) REVERT: C 453 TYR cc_start: 0.7311 (p90) cc_final: 0.6886 (p90) REVERT: C 498 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7514 (mtt90) REVERT: C 516 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6470 (tt0) REVERT: C 542 ASN cc_start: 0.8227 (t0) cc_final: 0.7818 (t0) REVERT: C 558 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7948 (mmmm) REVERT: C 654 GLU cc_start: 0.8252 (tt0) cc_final: 0.7996 (tt0) REVERT: C 691 SER cc_start: 0.8734 (p) cc_final: 0.8366 (m) REVERT: C 708 SER cc_start: 0.8365 (m) cc_final: 0.7979 (p) REVERT: C 821 LEU cc_start: 0.8558 (tp) cc_final: 0.8258 (tt) REVERT: C 947 LYS cc_start: 0.8352 (mttt) cc_final: 0.8147 (mttp) REVERT: C 997 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8166 (mt) REVERT: C 1128 VAL cc_start: 0.8692 (m) cc_final: 0.8399 (p) REVERT: C 1130 ILE cc_start: 0.8440 (pt) cc_final: 0.8240 (mt) REVERT: C 1136 THR cc_start: 0.8522 (t) cc_final: 0.8267 (p) REVERT: E 41 TYR cc_start: 0.7560 (t80) cc_final: 0.6531 (t80) REVERT: E 61 LYS cc_start: 0.8117 (mttt) cc_final: 0.7749 (mttt) REVERT: E 64 GLU cc_start: 0.6221 (mm-30) cc_final: 0.5817 (mm-30) REVERT: E 75 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6956 (pp20) REVERT: E 94 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7770 (pttt) REVERT: E 113 ASN cc_start: 0.6850 (p0) cc_final: 0.6550 (p0) REVERT: E 169 ARG cc_start: 0.3195 (ttp80) cc_final: 0.2775 (ttp80) REVERT: E 183 TYR cc_start: 0.2465 (OUTLIER) cc_final: 0.1024 (t80) REVERT: E 190 MET cc_start: 0.1808 (ptt) cc_final: 0.1280 (mtt) REVERT: E 207 TYR cc_start: 0.4079 (m-80) cc_final: 0.3756 (m-80) REVERT: E 228 ARG cc_start: 0.6552 (ttp80) cc_final: 0.6084 (ttp80) REVERT: E 278 LEU cc_start: 0.0191 (OUTLIER) cc_final: -0.0164 (tp) REVERT: E 313 LYS cc_start: 0.7573 (ttmm) cc_final: 0.7226 (mtmm) REVERT: E 327 PHE cc_start: 0.7827 (t80) cc_final: 0.7343 (t80) REVERT: E 349 TRP cc_start: 0.5436 (m100) cc_final: 0.4995 (m100) REVERT: E 366 MET cc_start: 0.2855 (mmm) cc_final: 0.1537 (mmp) REVERT: E 381 TYR cc_start: 0.6061 (t80) cc_final: 0.5756 (t80) REVERT: E 480 MET cc_start: 0.7387 (mtp) cc_final: 0.6777 (mtp) REVERT: E 510 TYR cc_start: 0.5832 (m-80) cc_final: 0.5609 (m-10) REVERT: E 526 GLN cc_start: 0.7732 (tp40) cc_final: 0.7385 (tp40) REVERT: E 549 GLU cc_start: 0.4576 (mm-30) cc_final: 0.3343 (pm20) REVERT: E 552 GLN cc_start: 0.5626 (pp30) cc_final: 0.5151 (pp30) REVERT: E 579 MET cc_start: 0.4411 (mtm) cc_final: 0.3843 (mmm) outliers start: 122 outliers final: 86 residues processed: 840 average time/residue: 0.6396 time to fit residues: 875.9297 Evaluate side-chains 854 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 749 time to evaluate : 6.802 ------------------------------------------------------------------------------- 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 130 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 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE 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 599 THR Chi-restraints excluded: chain A residue 723 THR 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 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 1050 MET 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 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 785 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE 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 C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL 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 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 670 ILE 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 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 183 TYR 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 323 MET Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 208 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 399 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** A 564 GLN A 644 GLN B 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN D 277 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.198286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143226 restraints weight = 53479.995| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.85 r_work: 0.3508 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 35018 Z= 0.257 Angle : 0.748 21.108 47723 Z= 0.376 Chirality : 0.049 0.371 5374 Planarity : 0.005 0.076 6098 Dihedral : 5.443 68.796 5354 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.52 % Favored : 94.46 % Rotamer: Outliers : 3.47 % Allowed : 21.92 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 4202 helix: 0.70 (0.14), residues: 1417 sheet: -0.09 (0.19), residues: 625 loop : -1.68 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 461 HIS 0.008 0.001 HIS B1064 PHE 0.035 0.002 PHE B 392 TYR 0.022 0.002 TYR A 365 ARG 0.010 0.001 ARG D 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00807 ( 37) link_NAG-ASN : angle 3.62809 ( 111) hydrogen bonds : bond 0.04332 ( 1335) hydrogen bonds : angle 4.94341 ( 3699) SS BOND : bond 0.00562 ( 40) SS BOND : angle 3.18123 ( 80) covalent geometry : bond 0.00598 (34941) covalent geometry : angle 0.71693 (47532) ********************** 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 923 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 795 time to evaluate : 3.624 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 106 PHE cc_start: 0.8353 (m-80) cc_final: 0.7748 (m-80) REVERT: A 129 LYS cc_start: 0.7629 (mmtt) cc_final: 0.7237 (mmtt) REVERT: A 196 ASN cc_start: 0.6648 (p0) cc_final: 0.6367 (p0) REVERT: A 203 ILE cc_start: 0.8614 (pt) cc_final: 0.8211 (mt) REVERT: A 204 TYR cc_start: 0.7528 (m-80) cc_final: 0.7083 (m-80) REVERT: A 235 ILE cc_start: 0.6949 (tp) cc_final: 0.5899 (mt) REVERT: A 239 GLN cc_start: 0.7957 (mp10) cc_final: 0.7638 (mp10) REVERT: A 240 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7865 (t) REVERT: A 353 TRP cc_start: 0.7640 (p-90) cc_final: 0.7434 (p-90) REVERT: A 360 ASN cc_start: 0.7485 (m-40) cc_final: 0.7248 (m-40) REVERT: A 377 PHE cc_start: 0.8826 (t80) cc_final: 0.8567 (t80) REVERT: A 378 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8157 (ttpp) REVERT: A 388 ASN cc_start: 0.8200 (t0) cc_final: 0.7938 (t0) REVERT: A 524 VAL cc_start: 0.7217 (OUTLIER) cc_final: 0.6941 (m) REVERT: A 586 ASP cc_start: 0.7831 (m-30) cc_final: 0.7621 (m-30) REVERT: A 592 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7869 (t80) REVERT: A 725 GLU cc_start: 0.8324 (tt0) cc_final: 0.8107 (tt0) REVERT: A 820 ASP cc_start: 0.7979 (t0) cc_final: 0.7711 (m-30) REVERT: A 900 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8129 (mtp) REVERT: A 934 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 957 GLN cc_start: 0.8284 (tt0) cc_final: 0.7979 (tt0) REVERT: A 984 LEU cc_start: 0.8863 (mt) cc_final: 0.8531 (mt) REVERT: A 994 ASP cc_start: 0.8209 (t0) cc_final: 0.7925 (t0) REVERT: A 1003 SER cc_start: 0.9016 (p) cc_final: 0.8724 (t) REVERT: A 1084 ASP cc_start: 0.8297 (t0) cc_final: 0.7899 (t0) REVERT: A 1105 THR cc_start: 0.8469 (t) cc_final: 0.8250 (p) REVERT: A 1120 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8273 (p) REVERT: A 1127 ASP cc_start: 0.8042 (t0) cc_final: 0.7628 (t0) REVERT: A 1139 ASP cc_start: 0.8164 (t0) cc_final: 0.7940 (t0) REVERT: B 129 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7509 (mtmm) REVERT: B 159 VAL cc_start: 0.7081 (OUTLIER) cc_final: 0.6877 (m) REVERT: B 170 TYR cc_start: 0.6717 (m-80) cc_final: 0.6495 (m-80) REVERT: B 237 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7033 (mmt180) REVERT: B 298 GLU cc_start: 0.7984 (tp30) cc_final: 0.7602 (tp30) REVERT: B 340 GLU cc_start: 0.8251 (tp30) cc_final: 0.8041 (tp30) REVERT: B 385 THR cc_start: 0.8710 (m) cc_final: 0.8484 (t) REVERT: B 386 LYS cc_start: 0.8147 (mttp) cc_final: 0.7684 (mttp) REVERT: B 462 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8525 (mmmm) REVERT: B 514 SER cc_start: 0.8626 (t) cc_final: 0.8203 (p) REVERT: B 651 ILE cc_start: 0.8594 (pt) cc_final: 0.8300 (mp) REVERT: B 658 ASN cc_start: 0.8213 (p0) cc_final: 0.7745 (p0) REVERT: B 698 SER cc_start: 0.8871 (t) cc_final: 0.8446 (p) REVERT: B 710 ASN cc_start: 0.8564 (p0) cc_final: 0.8194 (p0) REVERT: B 730 SER cc_start: 0.8769 (t) cc_final: 0.8473 (m) REVERT: B 751 ASN cc_start: 0.8443 (m-40) cc_final: 0.8149 (m-40) REVERT: B 788 ILE cc_start: 0.8587 (mt) cc_final: 0.8387 (mm) REVERT: B 868 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7792 (mm-30) REVERT: B 907 ASN cc_start: 0.8460 (t0) cc_final: 0.8157 (t0) REVERT: B 960 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: B 980 ILE cc_start: 0.8367 (mt) cc_final: 0.8159 (mt) REVERT: B 1017 GLU cc_start: 0.8026 (tp30) cc_final: 0.7698 (tp30) REVERT: B 1028 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8252 (mttm) REVERT: B 1107 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7761 (mtt180) REVERT: D 22 GLU cc_start: 0.6986 (tp30) cc_final: 0.6501 (mm-30) REVERT: D 39 LEU cc_start: 0.8266 (mt) cc_final: 0.8035 (mt) REVERT: D 69 TRP cc_start: 0.7799 (t60) cc_final: 0.7558 (t60) REVERT: D 97 LEU cc_start: 0.8235 (tp) cc_final: 0.7707 (mm) REVERT: D 127 TYR cc_start: 0.4945 (t80) cc_final: 0.4339 (t80) REVERT: D 249 MET cc_start: 0.6103 (tpp) cc_final: 0.4028 (mtt) REVERT: D 327 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: D 365 THR cc_start: 0.6768 (p) cc_final: 0.6447 (t) REVERT: D 376 MET cc_start: 0.5561 (ptt) cc_final: 0.5229 (ppp) REVERT: D 381 TYR cc_start: 0.8546 (t80) cc_final: 0.7951 (t80) REVERT: D 388 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7228 (mm-40) REVERT: D 408 MET cc_start: 0.6340 (mmt) cc_final: 0.6114 (mmt) REVERT: D 440 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6224 (pp) REVERT: D 455 MET cc_start: 0.7557 (ptm) cc_final: 0.7226 (mtm) REVERT: D 460 ARG cc_start: 0.6143 (tpt170) cc_final: 0.5890 (tpp80) REVERT: D 477 TRP cc_start: 0.7105 (t-100) cc_final: 0.6339 (t-100) REVERT: D 481 LYS cc_start: 0.3028 (tttm) cc_final: 0.2738 (tttm) REVERT: D 515 TYR cc_start: 0.5455 (m-80) cc_final: 0.4750 (m-80) REVERT: D 557 MET cc_start: 0.7808 (tmm) cc_final: 0.7540 (tmm) REVERT: D 568 LYS cc_start: 0.7879 (tttm) cc_final: 0.7454 (tptt) REVERT: C 88 ASP cc_start: 0.6770 (t0) cc_final: 0.6427 (t0) REVERT: C 339 ASP cc_start: 0.8128 (p0) cc_final: 0.7806 (p0) REVERT: C 346 ARG cc_start: 0.8142 (ttm170) cc_final: 0.7823 (ttm110) REVERT: C 498 ARG cc_start: 0.8229 (mtt90) cc_final: 0.7658 (mtt90) REVERT: C 516 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6658 (tt0) REVERT: C 558 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7956 (mmmm) REVERT: C 654 GLU cc_start: 0.8481 (tt0) cc_final: 0.8198 (tt0) REVERT: C 691 SER cc_start: 0.8734 (p) cc_final: 0.8419 (m) REVERT: C 708 SER cc_start: 0.8544 (m) cc_final: 0.8191 (p) REVERT: C 723 THR cc_start: 0.8498 (m) cc_final: 0.8134 (p) REVERT: C 821 LEU cc_start: 0.8567 (tp) cc_final: 0.8258 (tt) REVERT: C 947 LYS cc_start: 0.8471 (mttt) cc_final: 0.8265 (mttp) REVERT: C 997 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8253 (mt) REVERT: C 1084 ASP cc_start: 0.8313 (m-30) cc_final: 0.8079 (t0) REVERT: C 1128 VAL cc_start: 0.8706 (m) cc_final: 0.8392 (p) REVERT: C 1136 THR cc_start: 0.8622 (t) cc_final: 0.8335 (p) REVERT: E 41 TYR cc_start: 0.7685 (t80) cc_final: 0.6670 (t80) REVERT: E 61 LYS cc_start: 0.8185 (mttt) cc_final: 0.7808 (mttt) REVERT: E 64 GLU cc_start: 0.6380 (mm-30) cc_final: 0.5956 (mm-30) REVERT: E 76 GLN cc_start: 0.8741 (mm110) cc_final: 0.8265 (mm110) REVERT: E 94 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7861 (pttt) REVERT: E 113 ASN cc_start: 0.7009 (p0) cc_final: 0.6686 (p0) REVERT: E 183 TYR cc_start: 0.2497 (OUTLIER) cc_final: 0.2103 (t80) REVERT: E 187 LYS cc_start: 0.5306 (mtpp) cc_final: 0.4902 (mttm) REVERT: E 190 MET cc_start: 0.1732 (ptt) cc_final: 0.1313 (mtt) REVERT: E 207 TYR cc_start: 0.4267 (m-80) cc_final: 0.3908 (m-80) REVERT: E 228 ARG cc_start: 0.6640 (ttp80) cc_final: 0.6165 (ttp80) REVERT: E 278 LEU cc_start: 0.0161 (OUTLIER) cc_final: -0.0190 (tp) REVERT: E 327 PHE cc_start: 0.7835 (t80) cc_final: 0.7177 (t80) REVERT: E 366 MET cc_start: 0.3127 (mmm) cc_final: 0.1749 (mmp) REVERT: E 480 MET cc_start: 0.7388 (mtp) cc_final: 0.6771 (mtp) REVERT: E 510 TYR cc_start: 0.5903 (m-80) cc_final: 0.5694 (m-10) REVERT: E 526 GLN cc_start: 0.7706 (tp40) cc_final: 0.7438 (tp40) REVERT: E 549 GLU cc_start: 0.4967 (mm-30) cc_final: 0.4056 (mp0) REVERT: E 579 MET cc_start: 0.4382 (mtm) cc_final: 0.3830 (mmm) outliers start: 128 outliers final: 94 residues processed: 870 average time/residue: 0.4895 time to fit residues: 686.7771 Evaluate side-chains 885 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 773 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 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 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE 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 588 THR Chi-restraints excluded: chain A residue 592 PHE 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 761 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 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 1050 MET 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 A residue 1136 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 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 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 785 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 960 ASN 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 1028 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain D residue 343 VAL 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 90 VAL 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 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 649 CYS Chi-restraints excluded: chain C residue 670 ILE 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 183 TYR 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 315 PHE Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 352 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 297 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 381 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 230 optimal weight: 0.0770 chunk 24 optimal weight: 0.0980 chunk 280 optimal weight: 2.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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** A 564 GLN A 644 GLN B 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** D 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN ** 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 = 0.4431 r_free = 0.4431 target = 0.202659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148812 restraints weight = 53344.588| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.53 r_work: 0.3613 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35018 Z= 0.133 Angle : 0.678 21.352 47723 Z= 0.336 Chirality : 0.045 0.357 5374 Planarity : 0.004 0.057 6098 Dihedral : 5.188 66.998 5354 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 3.17 % Allowed : 22.57 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4202 helix: 0.85 (0.14), residues: 1419 sheet: -0.16 (0.19), residues: 669 loop : -1.60 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP D 461 HIS 0.006 0.001 HIS D 493 PHE 0.032 0.001 PHE D 72 TYR 0.019 0.001 TYR A 655 ARG 0.014 0.001 ARG D 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 37) link_NAG-ASN : angle 3.39169 ( 111) hydrogen bonds : bond 0.03622 ( 1335) hydrogen bonds : angle 4.83763 ( 3699) SS BOND : bond 0.00477 ( 40) SS BOND : angle 2.72130 ( 80) covalent geometry : bond 0.00304 (34941) covalent geometry : angle 0.64999 (47532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28727.89 seconds wall clock time: 502 minutes 32.69 seconds (30152.69 seconds total)