Starting phenix.real_space_refine on Tue Jun 24 00:05:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whj_32501/06_2025/7whj_32501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whj_32501/06_2025/7whj_32501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whj_32501/06_2025/7whj_32501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whj_32501/06_2025/7whj_32501.map" model { file = "/net/cci-nas-00/data/ceres_data/7whj_32501/06_2025/7whj_32501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whj_32501/06_2025/7whj_32501.cif" } resolution = 3.27 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 131 5.16 5 C 17739 2.51 5 N 4570 2.21 5 O 5348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27788 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8243 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 60, 'TRANS': 997} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8159 Classifications: {'peptide': 1047} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 988} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8094 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 980} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 905 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 905 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "F" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 15.32, per 1000 atoms: 0.55 Number of scatterers: 27788 At special positions: 0 Unit cell: (140.448, 172.368, 187.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 131 16.00 O 5348 8.00 N 4570 7.00 C 17739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG A1313 " - " ASN A 616 " " NAG A1314 " - " ASN A 122 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG B1313 " - " ASN B 616 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 616 " Time building additional restraints: 7.02 Conformation dependent library (CDL) restraints added in 3.6 seconds 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6548 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 59 sheets defined 20.6% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.603A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.674A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 853 through 857 removed outlier: 3.525A pdb=" N GLY A 857 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.006A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.706A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.606A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.871A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1147 removed outlier: 3.957A pdb=" N SER A1147 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.808A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.643A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.833A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.505A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.879A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.321A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.688A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.615A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.046A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 4.116A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.183A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.799A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.620A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.525A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.631A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.107A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.856A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.190A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'F' and resid 200 through 204 removed outlier: 3.917A pdb=" N GLY F 204 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 229 removed outlier: 3.788A pdb=" N THR F 229 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.225A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.798A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.112A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 227 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.532A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.775A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.207A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.075A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 5.884A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 719 removed outlier: 7.147A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 722 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.902A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.454A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ALA B 222 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS B 205 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 51 removed outlier: 6.912A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.658A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.838A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.040A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.615A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 538 through 541 removed outlier: 3.531A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.135A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.242A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.319A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 719 removed outlier: 6.569A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 722 through 728 Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.471A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.527A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C 263 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 187 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 206 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE C 199 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASP C 228 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS C 205 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA C 222 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.527A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C 263 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.127A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.700A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE7, first strand: chain 'C' and resid 135 through 140 removed outlier: 3.837A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.260A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.261A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.033A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 378 through 380 removed outlier: 3.858A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 538 through 539 removed outlier: 3.694A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.697A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.093A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.918A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.547A pdb=" N CYS D 22 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR D 79 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 35 through 37 removed outlier: 3.531A pdb=" N VAL D 37 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 91 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL D 114 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 93 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 22 through 23 removed outlier: 3.642A pdb=" N CYS E 22 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR E 79 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER E 70 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.577A pdb=" N ALA E 91 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL E 114 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 196 through 197 removed outlier: 3.528A pdb=" N THR F 188 " --> pdb=" O TYR F 197 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TRP F 185 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ARG F 176 " --> pdb=" O TRP F 185 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER F 187 " --> pdb=" O TRP F 174 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA F 235 " --> pdb=" O SER F 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL F 175 " --> pdb=" O TYR F 233 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 206 through 207 removed outlier: 3.816A pdb=" N THR F 207 " --> pdb=" O GLN F 220 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2298 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: 11.70 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8768 1.34 - 1.46: 5270 1.46 - 1.58: 14233 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 28441 Sorted by residual: bond pdb=" CA SER B 172 " pdb=" C SER B 172 " ideal model delta sigma weight residual 1.526 1.483 0.043 1.21e-02 6.83e+03 1.27e+01 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.21e+00 bond pdb=" CA ASN A 122 " pdb=" C ASN A 122 " ideal model delta sigma weight residual 1.521 1.545 -0.024 1.28e-02 6.10e+03 3.56e+00 bond pdb=" N SER B 172 " pdb=" CA SER B 172 " ideal model delta sigma weight residual 1.463 1.439 0.023 1.30e-02 5.92e+03 3.25e+00 bond pdb=" N ASN A 122 " pdb=" CA ASN A 122 " ideal model delta sigma weight residual 1.455 1.476 -0.021 1.18e-02 7.18e+03 3.19e+00 ... (remaining 28436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 37885 1.43 - 2.85: 719 2.85 - 4.28: 95 4.28 - 5.70: 23 5.70 - 7.13: 6 Bond angle restraints: 38728 Sorted by residual: angle pdb=" N LEU A 176 " pdb=" CA LEU A 176 " pdb=" C LEU A 176 " ideal model delta sigma weight residual 112.25 105.32 6.93 1.36e+00 5.41e-01 2.60e+01 angle pdb=" C ASN A 121 " pdb=" N ASN A 122 " pdb=" CA ASN A 122 " ideal model delta sigma weight residual 121.69 128.82 -7.13 1.85e+00 2.92e-01 1.48e+01 angle pdb=" N VAL A 171 " pdb=" CA VAL A 171 " pdb=" C VAL A 171 " ideal model delta sigma weight residual 108.17 113.31 -5.14 1.46e+00 4.69e-01 1.24e+01 angle pdb=" N LEU B 176 " pdb=" CA LEU B 176 " pdb=" C LEU B 176 " ideal model delta sigma weight residual 113.21 109.27 3.94 1.15e+00 7.56e-01 1.17e+01 angle pdb=" C GLN A 173 " pdb=" N PRO A 174 " pdb=" CA PRO A 174 " ideal model delta sigma weight residual 119.84 115.89 3.95 1.25e+00 6.40e-01 1.00e+01 ... (remaining 38723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 17024 23.10 - 46.20: 337 46.20 - 69.29: 49 69.29 - 92.39: 7 92.39 - 115.49: 23 Dihedral angle restraints: 17440 sinusoidal: 7254 harmonic: 10186 Sorted by residual: dihedral pdb=" CA GLN B 173 " pdb=" C GLN B 173 " pdb=" N PRO B 174 " pdb=" CA PRO B 174 " ideal model delta harmonic sigma weight residual -180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N ASN A 122 " pdb=" CA ASN A 122 " ideal model delta harmonic sigma weight residual -180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PRO C 213 " pdb=" C PRO C 213 " pdb=" N GLU C 214 " pdb=" CA GLU C 214 " ideal model delta harmonic sigma weight residual -180.00 -153.03 -26.97 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 17437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3969 0.071 - 0.141: 509 0.141 - 0.212: 9 0.212 - 0.282: 4 0.282 - 0.353: 1 Chirality restraints: 4492 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA ASN A 122 " pdb=" N ASN A 122 " pdb=" C ASN A 122 " pdb=" CB ASN A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C1 NAG A1314 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1314 " pdb=" O5 NAG A1314 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 4489 not shown) Planarity restraints: 4990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1314 " 0.311 2.00e-02 2.50e+03 2.62e-01 8.57e+02 pdb=" C7 NAG A1314 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A1314 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG A1314 " -0.449 2.00e-02 2.50e+03 pdb=" O7 NAG A1314 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 171 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C VAL B 171 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL B 171 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 172 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 173 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 174 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " 0.029 5.00e-02 4.00e+02 ... (remaining 4987 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2796 2.75 - 3.29: 27157 3.29 - 3.83: 45030 3.83 - 4.36: 51624 4.36 - 4.90: 90188 Nonbonded interactions: 216795 Sorted by model distance: nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD2 ASP C 111 " model vdw 2.236 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.238 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.255 3.040 ... (remaining 216790 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 26 through 177 or resid 182 through 244 or resid 262 throu \ gh 620 or resid 641 through 1147 or resid 1301 through 1313)) selection = (chain 'B' and (resid 26 through 177 or resid 182 through 244 or resid 262 throu \ gh 827 or resid 848 through 1147 or resid 1301 through 1313)) selection = (chain 'C' and (resid 26 through 620 or resid 641 through 827 or resid 848 throu \ gh 1147 or resid 1301 through 1313)) } 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 62.500 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28525 Z= 0.131 Angle : 0.486 9.562 38936 Z= 0.254 Chirality : 0.043 0.353 4492 Planarity : 0.005 0.262 4950 Dihedral : 10.206 115.489 10760 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 1.96 % Allowed : 5.24 % Favored : 92.80 % Cbeta Deviations : 0.00 % 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: -3.44 (0.12), residues: 3445 helix: 0.16 (0.20), residues: 665 sheet: -2.61 (0.17), residues: 684 loop : -3.17 (0.11), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 185 HIS 0.002 0.000 HIS C 954 PHE 0.011 0.001 PHE E 29 TYR 0.007 0.001 TYR C 265 ARG 0.002 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 40) link_NAG-ASN : angle 1.37837 ( 120) hydrogen bonds : bond 0.21957 ( 831) hydrogen bonds : angle 8.43086 ( 2298) SS BOND : bond 0.00117 ( 44) SS BOND : angle 0.55149 ( 88) covalent geometry : bond 0.00253 (28441) covalent geometry : angle 0.48056 (38728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 759 time to evaluate : 3.026 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: A 52 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 189 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6924 (mt-10) REVERT: A 239 GLN cc_start: 0.7248 (mt0) cc_final: 0.6759 (mm-40) REVERT: A 377 PHE cc_start: 0.6604 (t80) cc_final: 0.6208 (t80) REVERT: A 378 LYS cc_start: 0.7318 (ptpp) cc_final: 0.6668 (ptpp) REVERT: A 401 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.6903 (t) REVERT: A 451 TYR cc_start: 0.8064 (m-10) cc_final: 0.7724 (m-80) REVERT: A 556 ASN cc_start: 0.7950 (p0) cc_final: 0.7636 (p0) REVERT: A 714 ILE cc_start: 0.8224 (mm) cc_final: 0.8010 (mt) REVERT: A 773 GLU cc_start: 0.6594 (tt0) cc_final: 0.5935 (tt0) REVERT: A 779 GLN cc_start: 0.7639 (tp40) cc_final: 0.7259 (tp40) REVERT: A 780 GLU cc_start: 0.7088 (tp30) cc_final: 0.6801 (tp30) REVERT: A 934 ILE cc_start: 0.8358 (mm) cc_final: 0.8034 (tp) REVERT: A 997 ILE cc_start: 0.7137 (mt) cc_final: 0.6887 (tt) REVERT: A 1017 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6965 (tm-30) REVERT: A 1047 TYR cc_start: 0.7854 (m-10) cc_final: 0.7547 (m-80) REVERT: A 1086 LYS cc_start: 0.8028 (ptpt) cc_final: 0.7803 (mtmt) REVERT: B 129 LYS cc_start: 0.7768 (ptpt) cc_final: 0.7564 (ptpp) REVERT: B 237 ARG cc_start: 0.7139 (mtp-110) cc_final: 0.6869 (mtp-110) REVERT: B 286 THR cc_start: 0.7652 (p) cc_final: 0.6547 (t) REVERT: B 394 ASN cc_start: 0.7038 (t0) cc_final: 0.6820 (t0) REVERT: B 534 VAL cc_start: 0.8803 (p) cc_final: 0.8544 (m) REVERT: B 541 PHE cc_start: 0.6886 (p90) cc_final: 0.6512 (p90) REVERT: B 571 ASP cc_start: 0.7267 (t0) cc_final: 0.6891 (t70) REVERT: B 714 ILE cc_start: 0.8342 (mm) cc_final: 0.8056 (mt) REVERT: B 779 GLN cc_start: 0.7455 (tp40) cc_final: 0.7029 (tp40) REVERT: B 804 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7558 (mm-40) REVERT: B 894 LEU cc_start: 0.8479 (mt) cc_final: 0.8244 (mt) REVERT: B 969 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8518 (mtmm) REVERT: C 52 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7439 (tp40) REVERT: C 104 TRP cc_start: 0.8160 (m-90) cc_final: 0.7664 (m-90) REVERT: C 121 ASN cc_start: 0.6716 (t0) cc_final: 0.5597 (t0) REVERT: C 189 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7054 (mt-10) REVERT: C 236 THR cc_start: 0.8119 (p) cc_final: 0.7864 (t) REVERT: C 303 LEU cc_start: 0.8761 (mp) cc_final: 0.8469 (mt) REVERT: C 360 ASN cc_start: 0.8150 (t0) cc_final: 0.7937 (t0) REVERT: C 386 LYS cc_start: 0.7922 (pttt) cc_final: 0.7640 (pttt) REVERT: C 392 PHE cc_start: 0.7392 (m-80) cc_final: 0.7131 (m-80) REVERT: C 394 ASN cc_start: 0.7603 (p0) cc_final: 0.7348 (p0) REVERT: C 430 THR cc_start: 0.7231 (p) cc_final: 0.7010 (p) REVERT: C 509 ARG cc_start: 0.6714 (mtt180) cc_final: 0.6468 (mtt180) REVERT: C 533 LEU cc_start: 0.8107 (tp) cc_final: 0.7898 (tt) REVERT: C 556 ASN cc_start: 0.8399 (p0) cc_final: 0.8123 (p0) REVERT: C 574 ASP cc_start: 0.7841 (t70) cc_final: 0.7615 (t70) REVERT: C 660 TYR cc_start: 0.8148 (m-80) cc_final: 0.7748 (m-80) REVERT: C 733 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7912 (mtpt) REVERT: C 774 GLN cc_start: 0.6711 (mm-40) cc_final: 0.6316 (mm110) REVERT: C 777 ASN cc_start: 0.6061 (m-40) cc_final: 0.5430 (m-40) REVERT: C 780 GLU cc_start: 0.7295 (pt0) cc_final: 0.7056 (pt0) REVERT: C 854 LYS cc_start: 0.8125 (tmtt) cc_final: 0.7776 (tmtt) REVERT: C 933 LYS cc_start: 0.7424 (mtpp) cc_final: 0.7116 (mtpp) REVERT: C 947 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8080 (mtpt) REVERT: C 969 LYS cc_start: 0.8486 (mttp) cc_final: 0.8183 (mttp) REVERT: C 1023 ASN cc_start: 0.8031 (m-40) cc_final: 0.7754 (m-40) REVERT: F 172 MET cc_start: 0.7077 (mtp) cc_final: 0.6772 (mtm) REVERT: F 174 TRP cc_start: 0.7650 (m100) cc_final: 0.7407 (m100) REVERT: F 229 THR cc_start: 0.6979 (OUTLIER) cc_final: 0.6635 (m) REVERT: F 254 VAL cc_start: 0.7072 (OUTLIER) cc_final: 0.6863 (p) outliers start: 59 outliers final: 20 residues processed: 808 average time/residue: 0.4436 time to fit residues: 559.8889 Evaluate side-chains 635 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 612 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain F residue 160 CYS Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 0.9980 chunk 261 optimal weight: 0.0670 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 0.0980 chunk 139 optimal weight: 0.0060 chunk 270 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 313 optimal weight: 0.0270 overall best weight: 0.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 134 GLN A 205 HIS A 271 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 755 GLN A 762 GLN A 777 ASN A 853 GLN A 907 ASN A 935 GLN A 965 GLN A1048 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 99 ASN B 134 GLN B 409 GLN B 448 ASN B 450 ASN B 474 GLN B 540 ASN B 580 GLN B 613 GLN B 641 ASN B 853 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1101 HIS C 409 GLN C 448 ASN C 505 HIS C 506 GLN C 519 HIS C 751 ASN C1048 HIS C1135 ASN F 220 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134493 restraints weight = 42359.609| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.52 r_work: 0.3530 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28525 Z= 0.119 Angle : 0.629 21.735 38936 Z= 0.302 Chirality : 0.052 1.399 4492 Planarity : 0.004 0.042 4950 Dihedral : 7.922 86.885 4632 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.32 % Allowed : 11.55 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.65 (0.13), residues: 3445 helix: 1.14 (0.21), residues: 671 sheet: -2.01 (0.18), residues: 750 loop : -2.84 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 633 HIS 0.005 0.001 HIS C1088 PHE 0.033 0.001 PHE A 429 TYR 0.022 0.001 TYR C 170 ARG 0.008 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00872 ( 40) link_NAG-ASN : angle 4.09822 ( 120) hydrogen bonds : bond 0.04060 ( 831) hydrogen bonds : angle 6.03079 ( 2298) SS BOND : bond 0.00377 ( 44) SS BOND : angle 1.84511 ( 88) covalent geometry : bond 0.00259 (28441) covalent geometry : angle 0.58165 (38728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 628 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8167 (mtp85) REVERT: A 52 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 189 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 239 GLN cc_start: 0.8004 (mt0) cc_final: 0.7324 (mm-40) REVERT: A 401 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7326 (t) REVERT: A 406 GLU cc_start: 0.7395 (mp0) cc_final: 0.7123 (mp0) REVERT: A 409 GLN cc_start: 0.7219 (mt0) cc_final: 0.6990 (tt0) REVERT: A 451 TYR cc_start: 0.8247 (m-10) cc_final: 0.7951 (m-80) REVERT: A 556 ASN cc_start: 0.8139 (p0) cc_final: 0.7816 (p0) REVERT: A 586 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: A 773 GLU cc_start: 0.7226 (tt0) cc_final: 0.6599 (tt0) REVERT: A 779 GLN cc_start: 0.8113 (tp40) cc_final: 0.7722 (tp40) REVERT: A 780 GLU cc_start: 0.8132 (tp30) cc_final: 0.7565 (tp30) REVERT: A 820 ASP cc_start: 0.7794 (t70) cc_final: 0.7521 (t0) REVERT: A 868 GLU cc_start: 0.7647 (mp0) cc_final: 0.7241 (mp0) REVERT: A 934 ILE cc_start: 0.7887 (mm) cc_final: 0.7528 (tp) REVERT: A 983 ARG cc_start: 0.7057 (ttp80) cc_final: 0.6676 (ttp80) REVERT: A 997 ILE cc_start: 0.7469 (mt) cc_final: 0.7037 (tt) REVERT: A 1017 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 1047 TYR cc_start: 0.8190 (m-10) cc_final: 0.7907 (m-80) REVERT: A 1086 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7863 (mtmt) REVERT: B 41 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8520 (mmtm) REVERT: B 189 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7332 (mt-10) REVERT: B 237 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7438 (mtp-110) REVERT: B 355 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7456 (ttm-80) REVERT: B 394 ASN cc_start: 0.7875 (t0) cc_final: 0.7673 (t0) REVERT: B 534 VAL cc_start: 0.8876 (p) cc_final: 0.8647 (m) REVERT: B 541 PHE cc_start: 0.7000 (p90) cc_final: 0.6658 (p90) REVERT: B 571 ASP cc_start: 0.7622 (t0) cc_final: 0.7233 (t70) REVERT: B 574 ASP cc_start: 0.8152 (p0) cc_final: 0.7892 (p0) REVERT: B 674 TYR cc_start: 0.8667 (t80) cc_final: 0.8465 (t80) REVERT: B 767 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8197 (mt) REVERT: B 779 GLN cc_start: 0.7906 (tp40) cc_final: 0.7414 (tp40) REVERT: B 804 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7948 (mm-40) REVERT: B 902 MET cc_start: 0.8442 (tpt) cc_final: 0.8217 (mmt) REVERT: B 965 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8407 (mt0) REVERT: B 969 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8621 (mtmm) REVERT: B 977 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7300 (mt) REVERT: B 981 PHE cc_start: 0.8093 (m-10) cc_final: 0.7863 (m-80) REVERT: B 988 GLU cc_start: 0.8028 (tp30) cc_final: 0.7818 (tp30) REVERT: B 1074 ASN cc_start: 0.7094 (OUTLIER) cc_final: 0.6674 (p0) REVERT: B 1101 HIS cc_start: 0.8211 (m170) cc_final: 0.7980 (m-70) REVERT: C 52 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8006 (tp40) REVERT: C 84 LEU cc_start: 0.8245 (mt) cc_final: 0.8018 (mp) REVERT: C 188 ARG cc_start: 0.8640 (mmt90) cc_final: 0.8402 (mtt90) REVERT: C 189 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7980 (mt-10) REVERT: C 236 THR cc_start: 0.8526 (p) cc_final: 0.8244 (t) REVERT: C 267 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8060 (t) REVERT: C 303 LEU cc_start: 0.8719 (mp) cc_final: 0.8454 (mt) REVERT: C 327 VAL cc_start: 0.8140 (m) cc_final: 0.7857 (p) REVERT: C 394 ASN cc_start: 0.7978 (p0) cc_final: 0.7635 (p0) REVERT: C 406 GLU cc_start: 0.7951 (mp0) cc_final: 0.7490 (mp0) REVERT: C 430 THR cc_start: 0.7507 (p) cc_final: 0.7277 (p) REVERT: C 509 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7552 (mtt180) REVERT: C 556 ASN cc_start: 0.8518 (p0) cc_final: 0.8315 (p0) REVERT: C 660 TYR cc_start: 0.8585 (m-80) cc_final: 0.8337 (m-80) REVERT: C 774 GLN cc_start: 0.7165 (mm-40) cc_final: 0.6877 (mm-40) REVERT: C 819 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7216 (mt-10) REVERT: C 851 CYS cc_start: 0.8106 (m) cc_final: 0.7867 (m) REVERT: C 854 LYS cc_start: 0.7975 (tmtt) cc_final: 0.7487 (tmtt) REVERT: C 933 LYS cc_start: 0.7608 (mtpp) cc_final: 0.7124 (mttm) REVERT: C 947 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8269 (mttp) REVERT: C 969 LYS cc_start: 0.8836 (mttp) cc_final: 0.8484 (mttp) REVERT: C 970 PHE cc_start: 0.8418 (m-80) cc_final: 0.7893 (m-10) REVERT: C 984 LEU cc_start: 0.6803 (mp) cc_final: 0.6501 (mp) REVERT: C 1144 GLU cc_start: 0.7519 (mp0) cc_final: 0.7205 (mp0) REVERT: F 172 MET cc_start: 0.8389 (mtp) cc_final: 0.7847 (mtm) REVERT: F 174 TRP cc_start: 0.8151 (m100) cc_final: 0.7675 (m100) REVERT: F 219 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6953 (mt) REVERT: F 229 THR cc_start: 0.7450 (t) cc_final: 0.6964 (m) REVERT: F 254 VAL cc_start: 0.7176 (OUTLIER) cc_final: 0.6927 (p) outliers start: 70 outliers final: 40 residues processed: 677 average time/residue: 0.4129 time to fit residues: 440.2513 Evaluate side-chains 634 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 586 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 160 CYS Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 242 optimal weight: 2.9990 chunk 304 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 305 optimal weight: 0.0040 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 194 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 505 HIS B 644 GLN B 787 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 955 ASN C1005 GLN C1048 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126892 restraints weight = 41954.562| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.59 r_work: 0.3440 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 28525 Z= 0.199 Angle : 0.673 20.715 38936 Z= 0.330 Chirality : 0.050 0.833 4492 Planarity : 0.004 0.051 4950 Dihedral : 6.809 79.896 4630 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.92 % Allowed : 12.61 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.28 (0.14), residues: 3445 helix: 1.19 (0.21), residues: 683 sheet: -1.58 (0.18), residues: 748 loop : -2.60 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 248 HIS 0.009 0.001 HIS B 519 PHE 0.025 0.002 PHE A 429 TYR 0.020 0.002 TYR C 265 ARG 0.006 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 40) link_NAG-ASN : angle 3.63838 ( 120) hydrogen bonds : bond 0.04591 ( 831) hydrogen bonds : angle 5.50613 ( 2298) SS BOND : bond 0.00504 ( 44) SS BOND : angle 1.82318 ( 88) covalent geometry : bond 0.00458 (28441) covalent geometry : angle 0.63728 (38728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 647 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 79 PHE cc_start: 0.5160 (OUTLIER) cc_final: 0.4958 (t80) REVERT: A 451 TYR cc_start: 0.8171 (m-10) cc_final: 0.7911 (m-80) REVERT: A 556 ASN cc_start: 0.8174 (p0) cc_final: 0.7919 (p0) REVERT: A 773 GLU cc_start: 0.7307 (tt0) cc_final: 0.6931 (tt0) REVERT: A 780 GLU cc_start: 0.7871 (tp30) cc_final: 0.7353 (tp30) REVERT: A 804 GLN cc_start: 0.8325 (mt0) cc_final: 0.8040 (mt0) REVERT: A 820 ASP cc_start: 0.7681 (t70) cc_final: 0.7407 (t0) REVERT: A 851 CYS cc_start: 0.8319 (m) cc_final: 0.7632 (p) REVERT: A 868 GLU cc_start: 0.7373 (mp0) cc_final: 0.6950 (mp0) REVERT: A 921 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8065 (mmtt) REVERT: A 1017 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 1047 TYR cc_start: 0.8270 (m-10) cc_final: 0.7987 (m-80) REVERT: A 1086 LYS cc_start: 0.8295 (ptpt) cc_final: 0.7971 (mtmt) REVERT: A 1125 ASN cc_start: 0.8090 (p0) cc_final: 0.7864 (p0) REVERT: B 41 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8493 (mmtm) REVERT: B 53 ASP cc_start: 0.7092 (t0) cc_final: 0.6676 (t0) REVERT: B 237 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.7507 (mtp-110) REVERT: B 290 ASP cc_start: 0.7712 (t0) cc_final: 0.7487 (t70) REVERT: B 534 VAL cc_start: 0.8853 (p) cc_final: 0.8640 (m) REVERT: B 541 PHE cc_start: 0.7131 (p90) cc_final: 0.6888 (p90) REVERT: B 574 ASP cc_start: 0.8095 (p0) cc_final: 0.7812 (p0) REVERT: B 767 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8310 (mt) REVERT: B 779 GLN cc_start: 0.7877 (tp40) cc_final: 0.7615 (tp40) REVERT: B 804 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7803 (mm-40) REVERT: B 950 ASP cc_start: 0.7485 (t0) cc_final: 0.7058 (t0) REVERT: B 957 GLN cc_start: 0.7762 (tt0) cc_final: 0.7427 (tt0) REVERT: B 981 PHE cc_start: 0.8007 (m-10) cc_final: 0.7699 (m-80) REVERT: B 988 GLU cc_start: 0.7829 (tp30) cc_final: 0.7530 (tp30) REVERT: B 1072 GLU cc_start: 0.8148 (pm20) cc_final: 0.7716 (pm20) REVERT: B 1101 HIS cc_start: 0.8149 (m170) cc_final: 0.7854 (m-70) REVERT: C 52 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7744 (tp40) REVERT: C 84 LEU cc_start: 0.8248 (mt) cc_final: 0.8022 (mp) REVERT: C 97 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7884 (ttmm) REVERT: C 132 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5931 (mt-10) REVERT: C 168 PHE cc_start: 0.7589 (t80) cc_final: 0.7299 (t80) REVERT: C 189 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7569 (mt-10) REVERT: C 236 THR cc_start: 0.8463 (p) cc_final: 0.8186 (t) REVERT: C 267 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8115 (t) REVERT: C 281 GLU cc_start: 0.7350 (pm20) cc_final: 0.6882 (pm20) REVERT: C 303 LEU cc_start: 0.8748 (mp) cc_final: 0.8469 (mt) REVERT: C 314 GLN cc_start: 0.8137 (mt0) cc_final: 0.7724 (mt0) REVERT: C 327 VAL cc_start: 0.8100 (m) cc_final: 0.7892 (p) REVERT: C 394 ASN cc_start: 0.7956 (p0) cc_final: 0.7549 (p0) REVERT: C 406 GLU cc_start: 0.8130 (mp0) cc_final: 0.7694 (mp0) REVERT: C 430 THR cc_start: 0.7600 (p) cc_final: 0.7354 (p) REVERT: C 509 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7277 (mtt180) REVERT: C 556 ASN cc_start: 0.8495 (p0) cc_final: 0.8088 (p0) REVERT: C 558 LYS cc_start: 0.8442 (mppt) cc_final: 0.7898 (mppt) REVERT: C 788 ILE cc_start: 0.8568 (mm) cc_final: 0.8332 (mt) REVERT: C 819 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7154 (mt-10) REVERT: C 824 ASN cc_start: 0.8040 (m-40) cc_final: 0.7728 (m-40) REVERT: C 854 LYS cc_start: 0.8121 (tmtt) cc_final: 0.7672 (tmtt) REVERT: C 933 LYS cc_start: 0.7801 (mtpp) cc_final: 0.7275 (mtmm) REVERT: C 947 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8203 (mttp) REVERT: C 969 LYS cc_start: 0.8779 (mttp) cc_final: 0.8427 (mttp) REVERT: C 984 LEU cc_start: 0.6666 (mp) cc_final: 0.6379 (mp) REVERT: C 1050 MET cc_start: 0.7903 (ptm) cc_final: 0.7699 (ptm) REVERT: C 1100 THR cc_start: 0.8104 (p) cc_final: 0.7874 (p) REVERT: C 1144 GLU cc_start: 0.7500 (mp0) cc_final: 0.7196 (mp0) REVERT: E 77 MET cc_start: 0.6176 (tmm) cc_final: 0.5966 (tmm) REVERT: F 172 MET cc_start: 0.8053 (mtp) cc_final: 0.7584 (mtm) REVERT: F 174 TRP cc_start: 0.7984 (m100) cc_final: 0.7470 (m100) REVERT: F 219 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6759 (mt) REVERT: F 229 THR cc_start: 0.7252 (t) cc_final: 0.6787 (m) REVERT: F 248 TRP cc_start: 0.7130 (m100) cc_final: 0.6579 (m100) REVERT: F 254 VAL cc_start: 0.7205 (OUTLIER) cc_final: 0.6985 (p) outliers start: 88 outliers final: 48 residues processed: 698 average time/residue: 0.4101 time to fit residues: 451.8711 Evaluate side-chains 642 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 588 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 296 optimal weight: 0.0670 chunk 283 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 338 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 613 GLN A1135 ASN B 394 ASN B 824 ASN B 913 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1119 ASN C 690 GLN C 762 GLN C1048 HIS E 3 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.154133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122789 restraints weight = 42196.127| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.59 r_work: 0.3383 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 28525 Z= 0.255 Angle : 0.704 16.904 38936 Z= 0.346 Chirality : 0.051 0.416 4492 Planarity : 0.005 0.059 4950 Dihedral : 6.937 84.393 4623 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.42 % Rotamer: Outliers : 3.45 % Allowed : 13.87 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.21 (0.14), residues: 3445 helix: 1.03 (0.21), residues: 689 sheet: -1.47 (0.18), residues: 743 loop : -2.50 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 353 HIS 0.007 0.001 HIS A1064 PHE 0.022 0.002 PHE A 429 TYR 0.024 0.002 TYR C 265 ARG 0.006 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 40) link_NAG-ASN : angle 3.18092 ( 120) hydrogen bonds : bond 0.04752 ( 831) hydrogen bonds : angle 5.43798 ( 2298) SS BOND : bond 0.00635 ( 44) SS BOND : angle 2.10214 ( 88) covalent geometry : bond 0.00591 (28441) covalent geometry : angle 0.67563 (38728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 618 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 79 PHE cc_start: 0.5384 (OUTLIER) cc_final: 0.5174 (t80) REVERT: A 399 SER cc_start: 0.8929 (m) cc_final: 0.8295 (p) REVERT: A 409 GLN cc_start: 0.7602 (mt0) cc_final: 0.7393 (mt0) REVERT: A 465 GLU cc_start: 0.7881 (tp30) cc_final: 0.7477 (tp30) REVERT: A 473 TYR cc_start: 0.7883 (t80) cc_final: 0.7614 (t80) REVERT: A 487 ASN cc_start: 0.7907 (m-40) cc_final: 0.6959 (t0) REVERT: A 501 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: A 542 ASN cc_start: 0.7737 (t0) cc_final: 0.7338 (t0) REVERT: A 556 ASN cc_start: 0.8380 (p0) cc_final: 0.8155 (p0) REVERT: A 776 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8366 (ttpp) REVERT: A 779 GLN cc_start: 0.8376 (tp40) cc_final: 0.7974 (tp40) REVERT: A 780 GLU cc_start: 0.8224 (tp30) cc_final: 0.7711 (tp30) REVERT: A 820 ASP cc_start: 0.7943 (t70) cc_final: 0.7671 (t0) REVERT: A 851 CYS cc_start: 0.8508 (m) cc_final: 0.7872 (p) REVERT: A 868 GLU cc_start: 0.7753 (mp0) cc_final: 0.7335 (mp0) REVERT: A 921 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8167 (mmtt) REVERT: A 1017 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 1086 LYS cc_start: 0.8434 (ptpt) cc_final: 0.8100 (mtmt) REVERT: A 1133 VAL cc_start: 0.8512 (p) cc_final: 0.8265 (m) REVERT: B 41 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8536 (mmtm) REVERT: B 53 ASP cc_start: 0.7521 (t0) cc_final: 0.7169 (t0) REVERT: B 188 ARG cc_start: 0.8807 (mtm-85) cc_final: 0.8452 (mtt180) REVERT: B 237 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7874 (mtp-110) REVERT: B 271 GLN cc_start: 0.8348 (mt0) cc_final: 0.8121 (mt0) REVERT: B 273 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7790 (mtp180) REVERT: B 329 PHE cc_start: 0.8577 (m-80) cc_final: 0.8354 (m-80) REVERT: B 355 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7462 (ttm-80) REVERT: B 394 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8010 (m-40) REVERT: B 414 GLN cc_start: 0.7114 (tt0) cc_final: 0.6889 (tt0) REVERT: B 537 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8111 (ttpp) REVERT: B 547 LYS cc_start: 0.8230 (mttp) cc_final: 0.7965 (mtpp) REVERT: B 571 ASP cc_start: 0.7664 (t0) cc_final: 0.7300 (t70) REVERT: B 671 CYS cc_start: 0.7731 (m) cc_final: 0.7346 (m) REVERT: B 674 TYR cc_start: 0.8769 (t80) cc_final: 0.8535 (t80) REVERT: B 779 GLN cc_start: 0.8173 (tp40) cc_final: 0.7949 (tp40) REVERT: B 931 ILE cc_start: 0.8392 (mm) cc_final: 0.8060 (tp) REVERT: B 957 GLN cc_start: 0.8248 (tt0) cc_final: 0.7881 (tt0) REVERT: B 981 PHE cc_start: 0.8253 (m-10) cc_final: 0.8014 (m-80) REVERT: B 988 GLU cc_start: 0.8247 (tp30) cc_final: 0.7921 (tp30) REVERT: B 1072 GLU cc_start: 0.8366 (pm20) cc_final: 0.8077 (pm20) REVERT: B 1101 HIS cc_start: 0.8311 (m170) cc_final: 0.7922 (m-70) REVERT: B 1136 THR cc_start: 0.8187 (t) cc_final: 0.7983 (p) REVERT: C 52 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8020 (tp40) REVERT: C 81 ASN cc_start: 0.8060 (p0) cc_final: 0.7857 (p0) REVERT: C 84 LEU cc_start: 0.8496 (mt) cc_final: 0.8272 (mp) REVERT: C 118 LEU cc_start: 0.8051 (tp) cc_final: 0.7831 (tt) REVERT: C 177 MET cc_start: 0.5836 (mmp) cc_final: 0.5448 (mmp) REVERT: C 185 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7759 (mttt) REVERT: C 189 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8057 (mt-10) REVERT: C 236 THR cc_start: 0.8610 (p) cc_final: 0.8332 (t) REVERT: C 267 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8313 (t) REVERT: C 281 GLU cc_start: 0.7761 (pm20) cc_final: 0.7323 (pm20) REVERT: C 294 ASP cc_start: 0.7333 (p0) cc_final: 0.7005 (p0) REVERT: C 303 LEU cc_start: 0.8801 (mp) cc_final: 0.8520 (mt) REVERT: C 340 GLU cc_start: 0.7482 (pm20) cc_final: 0.7177 (pm20) REVERT: C 341 VAL cc_start: 0.8687 (p) cc_final: 0.8486 (t) REVERT: C 394 ASN cc_start: 0.8067 (p0) cc_final: 0.7852 (p0) REVERT: C 406 GLU cc_start: 0.8165 (mp0) cc_final: 0.7771 (mp0) REVERT: C 509 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7559 (mtt180) REVERT: C 556 ASN cc_start: 0.8540 (p0) cc_final: 0.8131 (p0) REVERT: C 558 LYS cc_start: 0.8539 (mppt) cc_final: 0.7992 (mppt) REVERT: C 605 SER cc_start: 0.8674 (p) cc_final: 0.8415 (t) REVERT: C 711 SER cc_start: 0.8871 (p) cc_final: 0.8633 (t) REVERT: C 776 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8208 (ttmm) REVERT: C 788 ILE cc_start: 0.8681 (mm) cc_final: 0.8348 (mt) REVERT: C 819 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 824 ASN cc_start: 0.8160 (m-40) cc_final: 0.7857 (m-40) REVERT: C 854 LYS cc_start: 0.8096 (tmtt) cc_final: 0.7613 (tmtt) REVERT: C 933 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7662 (mtpp) REVERT: C 947 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8352 (mttp) REVERT: C 969 LYS cc_start: 0.8941 (mttp) cc_final: 0.8692 (mttp) REVERT: C 984 LEU cc_start: 0.7025 (mp) cc_final: 0.6794 (mp) REVERT: C 1002 GLN cc_start: 0.8068 (tp40) cc_final: 0.7768 (tp40) REVERT: C 1086 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8487 (mtmm) REVERT: E 77 MET cc_start: 0.6206 (tmm) cc_final: 0.5966 (tmm) REVERT: F 172 MET cc_start: 0.8406 (mtp) cc_final: 0.7971 (mtm) REVERT: F 174 TRP cc_start: 0.8267 (m100) cc_final: 0.7992 (m100) REVERT: F 229 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7031 (m) REVERT: F 254 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7351 (p) outliers start: 104 outliers final: 67 residues processed: 685 average time/residue: 0.4186 time to fit residues: 457.1605 Evaluate side-chains 661 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 588 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 299 optimal weight: 0.7980 chunk 265 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 287 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A1005 GLN B 394 ASN B 564 GLN B 603 ASN B 824 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 690 GLN C1135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123872 restraints weight = 41842.748| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.58 r_work: 0.3394 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28525 Z= 0.155 Angle : 0.650 26.808 38936 Z= 0.321 Chirality : 0.048 0.479 4492 Planarity : 0.004 0.054 4950 Dihedral : 6.599 74.752 4618 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.15 % Allowed : 15.23 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.01 (0.14), residues: 3445 helix: 1.27 (0.21), residues: 683 sheet: -1.33 (0.18), residues: 731 loop : -2.39 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 353 HIS 0.005 0.001 HIS B 519 PHE 0.020 0.001 PHE A 392 TYR 0.020 0.001 TYR C 265 ARG 0.007 0.000 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 40) link_NAG-ASN : angle 2.88269 ( 120) hydrogen bonds : bond 0.04192 ( 831) hydrogen bonds : angle 5.26546 ( 2298) SS BOND : bond 0.00672 ( 44) SS BOND : angle 2.38918 ( 88) covalent geometry : bond 0.00356 (28441) covalent geometry : angle 0.62142 (38728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 598 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 399 SER cc_start: 0.8954 (m) cc_final: 0.8313 (p) REVERT: A 423 TYR cc_start: 0.7655 (t80) cc_final: 0.7426 (t80) REVERT: A 457 ARG cc_start: 0.8358 (ttt-90) cc_final: 0.7540 (ttp-110) REVERT: A 461 LEU cc_start: 0.8170 (tt) cc_final: 0.7840 (tp) REVERT: A 465 GLU cc_start: 0.7799 (tp30) cc_final: 0.7361 (tp30) REVERT: A 473 TYR cc_start: 0.7800 (t80) cc_final: 0.7547 (t80) REVERT: A 487 ASN cc_start: 0.7882 (m-40) cc_final: 0.6914 (t0) REVERT: A 501 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: A 542 ASN cc_start: 0.7722 (t0) cc_final: 0.7308 (t0) REVERT: A 556 ASN cc_start: 0.8358 (p0) cc_final: 0.8150 (p0) REVERT: A 776 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8301 (ttpp) REVERT: A 779 GLN cc_start: 0.8358 (tp40) cc_final: 0.7954 (tp40) REVERT: A 780 GLU cc_start: 0.8250 (tp30) cc_final: 0.7744 (tp30) REVERT: A 804 GLN cc_start: 0.8409 (mt0) cc_final: 0.8208 (mt0) REVERT: A 820 ASP cc_start: 0.7884 (t70) cc_final: 0.7600 (t0) REVERT: A 851 CYS cc_start: 0.8454 (m) cc_final: 0.7808 (p) REVERT: A 868 GLU cc_start: 0.7741 (mp0) cc_final: 0.7323 (mp0) REVERT: A 921 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8109 (mmtt) REVERT: A 985 ASP cc_start: 0.4836 (OUTLIER) cc_final: 0.4634 (p0) REVERT: A 1017 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 1086 LYS cc_start: 0.8407 (ptpt) cc_final: 0.8058 (mtmt) REVERT: A 1133 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8043 (m) REVERT: B 53 ASP cc_start: 0.7501 (t0) cc_final: 0.7122 (t0) REVERT: B 188 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8436 (mtt180) REVERT: B 204 LYS cc_start: 0.8813 (ttpp) cc_final: 0.8599 (ttpp) REVERT: B 237 ARG cc_start: 0.8181 (mtp-110) cc_final: 0.7870 (mtp-110) REVERT: B 271 GLN cc_start: 0.8335 (mt0) cc_final: 0.8094 (mt0) REVERT: B 380 TYR cc_start: 0.7899 (m-80) cc_final: 0.7684 (m-10) REVERT: B 537 LYS cc_start: 0.8262 (mtpp) cc_final: 0.8030 (ttpp) REVERT: B 544 ASN cc_start: 0.8051 (t0) cc_final: 0.7806 (t0) REVERT: B 547 LYS cc_start: 0.8247 (mttp) cc_final: 0.7980 (mtpp) REVERT: B 571 ASP cc_start: 0.7643 (t0) cc_final: 0.7294 (t70) REVERT: B 674 TYR cc_start: 0.8724 (t80) cc_final: 0.8509 (t80) REVERT: B 779 GLN cc_start: 0.8116 (tp40) cc_final: 0.7660 (tp40) REVERT: B 804 GLN cc_start: 0.8460 (mm-40) cc_final: 0.7901 (mm-40) REVERT: B 931 ILE cc_start: 0.8327 (mm) cc_final: 0.7997 (tp) REVERT: B 957 GLN cc_start: 0.8243 (tt0) cc_final: 0.7846 (tt0) REVERT: B 964 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8543 (tmmt) REVERT: B 981 PHE cc_start: 0.8264 (m-10) cc_final: 0.8057 (m-80) REVERT: B 988 GLU cc_start: 0.8242 (tp30) cc_final: 0.7885 (tp30) REVERT: B 1072 GLU cc_start: 0.8384 (pm20) cc_final: 0.7979 (pm20) REVERT: B 1101 HIS cc_start: 0.8325 (m170) cc_final: 0.7956 (m-70) REVERT: C 52 GLN cc_start: 0.8293 (tm-30) cc_final: 0.8016 (tp40) REVERT: C 84 LEU cc_start: 0.8433 (mt) cc_final: 0.8221 (mp) REVERT: C 97 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8138 (tppp) REVERT: C 177 MET cc_start: 0.5840 (mmp) cc_final: 0.5485 (mmp) REVERT: C 188 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8610 (mtt90) REVERT: C 236 THR cc_start: 0.8574 (p) cc_final: 0.8293 (t) REVERT: C 267 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8232 (t) REVERT: C 281 GLU cc_start: 0.7716 (pm20) cc_final: 0.7254 (pm20) REVERT: C 286 THR cc_start: 0.8369 (p) cc_final: 0.8039 (m) REVERT: C 303 LEU cc_start: 0.8770 (mp) cc_final: 0.8484 (mt) REVERT: C 349 SER cc_start: 0.8366 (t) cc_final: 0.7840 (m) REVERT: C 362 VAL cc_start: 0.8757 (t) cc_final: 0.8464 (p) REVERT: C 406 GLU cc_start: 0.8071 (mp0) cc_final: 0.7871 (mp0) REVERT: C 509 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7499 (mtt180) REVERT: C 542 ASN cc_start: 0.7713 (t0) cc_final: 0.7322 (t0) REVERT: C 556 ASN cc_start: 0.8505 (p0) cc_final: 0.8093 (p0) REVERT: C 558 LYS cc_start: 0.8516 (mppt) cc_final: 0.7936 (mppt) REVERT: C 605 SER cc_start: 0.8666 (p) cc_final: 0.8412 (t) REVERT: C 776 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8158 (ttmm) REVERT: C 788 ILE cc_start: 0.8659 (mm) cc_final: 0.8381 (mt) REVERT: C 933 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7592 (mtpp) REVERT: C 947 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8314 (mttp) REVERT: C 1094 VAL cc_start: 0.8622 (p) cc_final: 0.8220 (m) REVERT: C 1144 GLU cc_start: 0.7771 (mp0) cc_final: 0.7446 (mp0) REVERT: E 77 MET cc_start: 0.6162 (tmm) cc_final: 0.5936 (tmm) REVERT: F 172 MET cc_start: 0.8386 (mtp) cc_final: 0.7927 (mtm) REVERT: F 174 TRP cc_start: 0.8260 (m100) cc_final: 0.7795 (m100) REVERT: F 219 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7033 (mt) REVERT: F 229 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.6992 (m) REVERT: F 254 VAL cc_start: 0.7534 (OUTLIER) cc_final: 0.7318 (p) outliers start: 95 outliers final: 66 residues processed: 656 average time/residue: 0.4150 time to fit residues: 433.6684 Evaluate side-chains 656 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 581 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 242 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 292 optimal weight: 5.9990 chunk 268 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.0040 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1135 ASN B 394 ASN B 564 GLN B 690 GLN B 824 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 321 GLN C 690 GLN C 949 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.155198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123998 restraints weight = 42057.926| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.61 r_work: 0.3407 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 28525 Z= 0.147 Angle : 0.664 27.010 38936 Z= 0.324 Chirality : 0.051 1.121 4492 Planarity : 0.004 0.053 4950 Dihedral : 6.398 75.944 4618 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.15 % Allowed : 16.10 % Favored : 80.75 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.85 (0.14), residues: 3445 helix: 1.38 (0.21), residues: 683 sheet: -1.19 (0.19), residues: 708 loop : -2.29 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 353 HIS 0.004 0.001 HIS B 519 PHE 0.023 0.001 PHE A 392 TYR 0.020 0.001 TYR C 265 ARG 0.012 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 40) link_NAG-ASN : angle 3.48658 ( 120) hydrogen bonds : bond 0.04006 ( 831) hydrogen bonds : angle 5.15459 ( 2298) SS BOND : bond 0.00700 ( 44) SS BOND : angle 2.66358 ( 88) covalent geometry : bond 0.00339 (28441) covalent geometry : angle 0.62417 (38728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 594 time to evaluate : 3.042 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: A 52 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 353 TRP cc_start: 0.8442 (p-90) cc_final: 0.7491 (p-90) REVERT: A 399 SER cc_start: 0.8939 (m) cc_final: 0.8325 (p) REVERT: A 457 ARG cc_start: 0.8330 (ttt-90) cc_final: 0.7621 (ttp-110) REVERT: A 461 LEU cc_start: 0.8161 (tt) cc_final: 0.7810 (tp) REVERT: A 465 GLU cc_start: 0.7724 (tp30) cc_final: 0.7520 (tp30) REVERT: A 473 TYR cc_start: 0.7846 (t80) cc_final: 0.7635 (t80) REVERT: A 487 ASN cc_start: 0.7869 (m-40) cc_final: 0.6930 (t0) REVERT: A 501 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: A 542 ASN cc_start: 0.7686 (t0) cc_final: 0.7288 (t0) REVERT: A 592 PHE cc_start: 0.7923 (p90) cc_final: 0.7691 (p90) REVERT: A 776 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8343 (ttpp) REVERT: A 779 GLN cc_start: 0.8396 (tp40) cc_final: 0.7991 (tp40) REVERT: A 780 GLU cc_start: 0.8252 (tp30) cc_final: 0.7786 (tp30) REVERT: A 804 GLN cc_start: 0.8430 (mt0) cc_final: 0.8161 (mt0) REVERT: A 820 ASP cc_start: 0.7925 (t70) cc_final: 0.7634 (t0) REVERT: A 851 CYS cc_start: 0.8390 (m) cc_final: 0.7828 (p) REVERT: A 868 GLU cc_start: 0.7770 (mp0) cc_final: 0.7367 (mp0) REVERT: A 1017 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 1086 LYS cc_start: 0.8437 (ptpt) cc_final: 0.8098 (mtmt) REVERT: A 1133 VAL cc_start: 0.8325 (p) cc_final: 0.8102 (m) REVERT: B 53 ASP cc_start: 0.7519 (t0) cc_final: 0.7144 (t0) REVERT: B 65 PHE cc_start: 0.7589 (m-80) cc_final: 0.6720 (m-80) REVERT: B 188 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8490 (mtt180) REVERT: B 237 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7967 (mtp-110) REVERT: B 239 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7622 (tm-30) REVERT: B 271 GLN cc_start: 0.8330 (mt0) cc_final: 0.8106 (mt0) REVERT: B 355 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7697 (ttm-80) REVERT: B 380 TYR cc_start: 0.7911 (m-80) cc_final: 0.7674 (m-10) REVERT: B 533 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8810 (tp) REVERT: B 537 LYS cc_start: 0.8233 (mtpp) cc_final: 0.8033 (ttpp) REVERT: B 544 ASN cc_start: 0.8018 (t0) cc_final: 0.7747 (t0) REVERT: B 547 LYS cc_start: 0.8263 (mttp) cc_final: 0.8056 (mtpp) REVERT: B 571 ASP cc_start: 0.7596 (t0) cc_final: 0.7246 (t70) REVERT: B 599 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8385 (p) REVERT: B 779 GLN cc_start: 0.8130 (tp40) cc_final: 0.7682 (tp40) REVERT: B 804 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7914 (mm-40) REVERT: B 957 GLN cc_start: 0.8237 (tt0) cc_final: 0.7859 (tt0) REVERT: B 981 PHE cc_start: 0.8251 (m-10) cc_final: 0.8035 (m-80) REVERT: B 988 GLU cc_start: 0.8273 (tp30) cc_final: 0.7924 (tp30) REVERT: B 1101 HIS cc_start: 0.8315 (m170) cc_final: 0.7948 (m-70) REVERT: B 1134 ASN cc_start: 0.6722 (OUTLIER) cc_final: 0.6215 (m-40) REVERT: C 52 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8023 (tp40) REVERT: C 84 LEU cc_start: 0.8425 (mt) cc_final: 0.8209 (mp) REVERT: C 177 MET cc_start: 0.6184 (mmp) cc_final: 0.5923 (mmp) REVERT: C 185 LYS cc_start: 0.7984 (mttt) cc_final: 0.7750 (mttt) REVERT: C 236 THR cc_start: 0.8558 (p) cc_final: 0.8280 (t) REVERT: C 267 VAL cc_start: 0.8446 (p) cc_final: 0.8210 (t) REVERT: C 281 GLU cc_start: 0.7743 (pm20) cc_final: 0.7283 (pm20) REVERT: C 303 LEU cc_start: 0.8788 (mp) cc_final: 0.8517 (mt) REVERT: C 349 SER cc_start: 0.8373 (t) cc_final: 0.7835 (m) REVERT: C 362 VAL cc_start: 0.8791 (t) cc_final: 0.8476 (p) REVERT: C 406 GLU cc_start: 0.8079 (mp0) cc_final: 0.7859 (mp0) REVERT: C 509 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7581 (mtt180) REVERT: C 542 ASN cc_start: 0.7707 (t0) cc_final: 0.7354 (t0) REVERT: C 546 LEU cc_start: 0.8230 (mm) cc_final: 0.7966 (mp) REVERT: C 556 ASN cc_start: 0.8560 (p0) cc_final: 0.8144 (p0) REVERT: C 558 LYS cc_start: 0.8522 (mppt) cc_final: 0.7934 (mppt) REVERT: C 605 SER cc_start: 0.8671 (p) cc_final: 0.8413 (t) REVERT: C 788 ILE cc_start: 0.8677 (mm) cc_final: 0.8401 (mt) REVERT: C 933 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7610 (mtpp) REVERT: C 970 PHE cc_start: 0.8523 (m-80) cc_final: 0.8285 (m-10) REVERT: C 1118 ASP cc_start: 0.8041 (p0) cc_final: 0.7779 (p0) REVERT: C 1144 GLU cc_start: 0.7764 (mp0) cc_final: 0.7519 (mp0) REVERT: E 34 MET cc_start: 0.3719 (mmm) cc_final: 0.3505 (mmm) REVERT: F 172 MET cc_start: 0.8384 (mtp) cc_final: 0.7938 (mtm) REVERT: F 174 TRP cc_start: 0.8265 (m100) cc_final: 0.7824 (m100) REVERT: F 219 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7104 (mt) REVERT: F 229 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7005 (m) REVERT: F 254 VAL cc_start: 0.7561 (OUTLIER) cc_final: 0.7340 (p) outliers start: 95 outliers final: 72 residues processed: 657 average time/residue: 0.3924 time to fit residues: 404.8725 Evaluate side-chains 670 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 591 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 188 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 329 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 341 optimal weight: 0.6980 chunk 316 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 239 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 580 GLN B 824 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 239 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122289 restraints weight = 41962.156| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.61 r_work: 0.3377 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28525 Z= 0.205 Angle : 0.691 27.904 38936 Z= 0.341 Chirality : 0.050 0.499 4492 Planarity : 0.004 0.057 4950 Dihedral : 6.232 65.853 4616 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.58 % Allowed : 16.53 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.83 (0.14), residues: 3445 helix: 1.28 (0.21), residues: 683 sheet: -1.21 (0.18), residues: 733 loop : -2.22 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 353 HIS 0.006 0.001 HIS C1064 PHE 0.029 0.002 PHE C 32 TYR 0.022 0.002 TYR C 265 ARG 0.009 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 40) link_NAG-ASN : angle 3.07129 ( 120) hydrogen bonds : bond 0.04436 ( 831) hydrogen bonds : angle 5.19808 ( 2298) SS BOND : bond 0.00668 ( 44) SS BOND : angle 2.68419 ( 88) covalent geometry : bond 0.00475 (28441) covalent geometry : angle 0.65892 (38728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 603 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 377 PHE cc_start: 0.8093 (t80) cc_final: 0.7855 (t80) REVERT: A 399 SER cc_start: 0.8907 (m) cc_final: 0.8289 (p) REVERT: A 409 GLN cc_start: 0.7555 (mt0) cc_final: 0.7346 (tt0) REVERT: A 418 ILE cc_start: 0.7828 (mm) cc_final: 0.7478 (mm) REVERT: A 465 GLU cc_start: 0.7892 (tp30) cc_final: 0.7576 (tp30) REVERT: A 487 ASN cc_start: 0.7901 (m-40) cc_final: 0.6984 (t0) REVERT: A 501 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: A 542 ASN cc_start: 0.7722 (t0) cc_final: 0.7326 (t0) REVERT: A 615 VAL cc_start: 0.8484 (m) cc_final: 0.8245 (t) REVERT: A 776 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8328 (ttpp) REVERT: A 779 GLN cc_start: 0.8445 (tp40) cc_final: 0.8058 (tp40) REVERT: A 780 GLU cc_start: 0.8279 (tp30) cc_final: 0.7818 (tp30) REVERT: A 820 ASP cc_start: 0.7930 (t70) cc_final: 0.7639 (t0) REVERT: A 851 CYS cc_start: 0.8389 (m) cc_final: 0.7870 (p) REVERT: A 854 LYS cc_start: 0.8682 (tttp) cc_final: 0.8180 (ttmm) REVERT: A 856 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7846 (mttm) REVERT: A 868 GLU cc_start: 0.7774 (mp0) cc_final: 0.7349 (mp0) REVERT: A 969 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8140 (mmtm) REVERT: A 1017 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 1086 LYS cc_start: 0.8425 (ptpt) cc_final: 0.8080 (mtmt) REVERT: A 1133 VAL cc_start: 0.8273 (p) cc_final: 0.7984 (m) REVERT: A 1135 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8090 (m110) REVERT: B 53 ASP cc_start: 0.7541 (t0) cc_final: 0.7188 (t0) REVERT: B 188 ARG cc_start: 0.8769 (mtm-85) cc_final: 0.8493 (mtt180) REVERT: B 237 ARG cc_start: 0.8244 (mtp-110) cc_final: 0.7925 (mtm-85) REVERT: B 271 GLN cc_start: 0.8352 (mt0) cc_final: 0.8106 (mt0) REVERT: B 281 GLU cc_start: 0.8082 (pm20) cc_final: 0.7876 (pm20) REVERT: B 349 SER cc_start: 0.7956 (m) cc_final: 0.7677 (m) REVERT: B 355 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7605 (ttm-80) REVERT: B 377 PHE cc_start: 0.7735 (t80) cc_final: 0.7415 (t80) REVERT: B 533 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8799 (tp) REVERT: B 571 ASP cc_start: 0.7718 (t0) cc_final: 0.7367 (t70) REVERT: B 599 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8422 (p) REVERT: B 671 CYS cc_start: 0.7716 (m) cc_final: 0.7476 (m) REVERT: B 746 SER cc_start: 0.7854 (m) cc_final: 0.7636 (t) REVERT: B 779 GLN cc_start: 0.8191 (tp40) cc_final: 0.7630 (tp40) REVERT: B 804 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7928 (mm-40) REVERT: B 957 GLN cc_start: 0.8272 (tt0) cc_final: 0.7880 (tt0) REVERT: B 988 GLU cc_start: 0.8310 (tp30) cc_final: 0.7995 (tp30) REVERT: B 1072 GLU cc_start: 0.8333 (pm20) cc_final: 0.8075 (pm20) REVERT: B 1101 HIS cc_start: 0.8324 (m170) cc_final: 0.7956 (m-70) REVERT: B 1134 ASN cc_start: 0.6964 (OUTLIER) cc_final: 0.6404 (m-40) REVERT: C 52 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8028 (tp40) REVERT: C 84 LEU cc_start: 0.8454 (mt) cc_final: 0.8236 (mp) REVERT: C 188 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8739 (mtt90) REVERT: C 236 THR cc_start: 0.8596 (p) cc_final: 0.8321 (t) REVERT: C 267 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8248 (t) REVERT: C 281 GLU cc_start: 0.7757 (pm20) cc_final: 0.7305 (pm20) REVERT: C 303 LEU cc_start: 0.8817 (mp) cc_final: 0.8557 (mt) REVERT: C 349 SER cc_start: 0.8444 (t) cc_final: 0.7904 (m) REVERT: C 362 VAL cc_start: 0.8811 (t) cc_final: 0.8498 (p) REVERT: C 509 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7576 (mtt180) REVERT: C 542 ASN cc_start: 0.7690 (t0) cc_final: 0.7319 (t0) REVERT: C 546 LEU cc_start: 0.8306 (mm) cc_final: 0.8066 (mp) REVERT: C 556 ASN cc_start: 0.8552 (p0) cc_final: 0.8127 (p0) REVERT: C 558 LYS cc_start: 0.8550 (mppt) cc_final: 0.7934 (mppt) REVERT: C 788 ILE cc_start: 0.8671 (mm) cc_final: 0.8364 (mt) REVERT: C 933 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7630 (mtpp) REVERT: C 1118 ASP cc_start: 0.8052 (p0) cc_final: 0.7798 (p0) REVERT: C 1128 VAL cc_start: 0.8636 (m) cc_final: 0.8381 (p) REVERT: C 1144 GLU cc_start: 0.7795 (mp0) cc_final: 0.7573 (mp0) REVERT: E 34 MET cc_start: 0.3753 (mmm) cc_final: 0.3513 (mmm) REVERT: F 172 MET cc_start: 0.8378 (mtp) cc_final: 0.7931 (mtm) REVERT: F 174 TRP cc_start: 0.8261 (m100) cc_final: 0.7851 (m100) REVERT: F 219 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7150 (mt) REVERT: F 227 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: F 229 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7078 (m) REVERT: F 254 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7352 (p) outliers start: 108 outliers final: 84 residues processed: 670 average time/residue: 0.3901 time to fit residues: 411.7730 Evaluate side-chains 684 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 588 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 206 optimal weight: 1.9990 chunk 55 optimal weight: 0.0060 chunk 327 optimal weight: 0.9980 chunk 333 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 148 optimal weight: 0.0070 chunk 135 optimal weight: 4.9990 chunk 133 optimal weight: 0.1980 chunk 195 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 239 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A1135 ASN B 394 ASN B 564 GLN B 824 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 321 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN E 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.155191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124076 restraints weight = 42066.527| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.60 r_work: 0.3410 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 28525 Z= 0.121 Angle : 0.644 25.834 38936 Z= 0.315 Chirality : 0.047 0.411 4492 Planarity : 0.004 0.059 4950 Dihedral : 6.087 68.422 4616 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.25 % Allowed : 17.16 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.63 (0.14), residues: 3445 helix: 1.48 (0.21), residues: 684 sheet: -1.05 (0.18), residues: 721 loop : -2.12 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 353 HIS 0.004 0.001 HIS C1088 PHE 0.027 0.001 PHE A 392 TYR 0.021 0.001 TYR B 380 ARG 0.007 0.000 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 40) link_NAG-ASN : angle 2.75981 ( 120) hydrogen bonds : bond 0.03831 ( 831) hydrogen bonds : angle 5.06808 ( 2298) SS BOND : bond 0.00587 ( 44) SS BOND : angle 2.51885 ( 88) covalent geometry : bond 0.00278 (28441) covalent geometry : angle 0.61577 (38728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 584 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 60 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8007 (t) REVERT: A 353 TRP cc_start: 0.8382 (p-90) cc_final: 0.7406 (p-90) REVERT: A 377 PHE cc_start: 0.7791 (t80) cc_final: 0.7553 (t80) REVERT: A 399 SER cc_start: 0.8790 (m) cc_final: 0.8319 (p) REVERT: A 409 GLN cc_start: 0.7262 (mt0) cc_final: 0.7058 (tt0) REVERT: A 430 THR cc_start: 0.8436 (m) cc_final: 0.8131 (p) REVERT: A 465 GLU cc_start: 0.7621 (tp30) cc_final: 0.7359 (tp30) REVERT: A 487 ASN cc_start: 0.7898 (m-40) cc_final: 0.7016 (t0) REVERT: A 501 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: A 708 SER cc_start: 0.8297 (t) cc_final: 0.7920 (p) REVERT: A 776 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8166 (ttpp) REVERT: A 779 GLN cc_start: 0.8214 (tp40) cc_final: 0.7787 (tp40) REVERT: A 780 GLU cc_start: 0.7942 (tp30) cc_final: 0.7502 (tp30) REVERT: A 820 ASP cc_start: 0.7730 (t70) cc_final: 0.7431 (t0) REVERT: A 851 CYS cc_start: 0.8062 (m) cc_final: 0.7630 (p) REVERT: A 854 LYS cc_start: 0.8537 (tttp) cc_final: 0.8037 (ttmm) REVERT: A 856 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7641 (mttm) REVERT: A 868 GLU cc_start: 0.7457 (mp0) cc_final: 0.7048 (mp0) REVERT: A 1017 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 1086 LYS cc_start: 0.8350 (ptpt) cc_final: 0.8021 (mtmt) REVERT: B 53 ASP cc_start: 0.7109 (t0) cc_final: 0.6788 (t0) REVERT: B 188 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.8317 (mtt180) REVERT: B 237 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7722 (mtm-85) REVERT: B 239 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7324 (tm-30) REVERT: B 271 GLN cc_start: 0.8098 (mt0) cc_final: 0.7890 (mt0) REVERT: B 355 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7260 (ttm-80) REVERT: B 377 PHE cc_start: 0.7374 (t80) cc_final: 0.7161 (t80) REVERT: B 533 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8737 (tp) REVERT: B 544 ASN cc_start: 0.7838 (t0) cc_final: 0.7578 (t0) REVERT: B 571 ASP cc_start: 0.7629 (t0) cc_final: 0.7306 (t70) REVERT: B 599 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8298 (p) REVERT: B 671 CYS cc_start: 0.6874 (m) cc_final: 0.6560 (m) REVERT: B 779 GLN cc_start: 0.7939 (tp40) cc_final: 0.7484 (tp40) REVERT: B 804 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7727 (mm-40) REVERT: B 957 GLN cc_start: 0.7929 (tt0) cc_final: 0.7540 (tt0) REVERT: B 988 GLU cc_start: 0.7943 (tp30) cc_final: 0.7609 (tp30) REVERT: B 1072 GLU cc_start: 0.8087 (pm20) cc_final: 0.7875 (pm20) REVERT: B 1101 HIS cc_start: 0.8193 (m170) cc_final: 0.7859 (m-70) REVERT: B 1113 GLN cc_start: 0.8416 (mt0) cc_final: 0.8210 (mt0) REVERT: B 1134 ASN cc_start: 0.6379 (OUTLIER) cc_final: 0.5961 (m-40) REVERT: C 52 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7789 (tp40) REVERT: C 84 LEU cc_start: 0.8179 (mt) cc_final: 0.7965 (mp) REVERT: C 115 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7555 (tp-100) REVERT: C 236 THR cc_start: 0.8396 (p) cc_final: 0.8120 (t) REVERT: C 281 GLU cc_start: 0.7343 (pm20) cc_final: 0.6869 (pm20) REVERT: C 303 LEU cc_start: 0.8778 (mp) cc_final: 0.8510 (mt) REVERT: C 349 SER cc_start: 0.8327 (t) cc_final: 0.7731 (m) REVERT: C 362 VAL cc_start: 0.8748 (t) cc_final: 0.8448 (p) REVERT: C 406 GLU cc_start: 0.8055 (mp0) cc_final: 0.7600 (mp0) REVERT: C 453 TYR cc_start: 0.8066 (p90) cc_final: 0.7675 (p90) REVERT: C 509 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7265 (mtt180) REVERT: C 542 ASN cc_start: 0.7379 (t0) cc_final: 0.7025 (t0) REVERT: C 546 LEU cc_start: 0.8114 (mm) cc_final: 0.7870 (mp) REVERT: C 556 ASN cc_start: 0.8493 (p0) cc_final: 0.8066 (p0) REVERT: C 558 LYS cc_start: 0.8444 (mppt) cc_final: 0.7814 (mppt) REVERT: C 599 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8571 (p) REVERT: C 788 ILE cc_start: 0.8640 (mm) cc_final: 0.8357 (mt) REVERT: C 820 ASP cc_start: 0.7389 (m-30) cc_final: 0.7004 (m-30) REVERT: C 933 LYS cc_start: 0.7827 (mtpp) cc_final: 0.7530 (mtpp) REVERT: C 1073 LYS cc_start: 0.8395 (ptmm) cc_final: 0.8120 (ptmm) REVERT: C 1118 ASP cc_start: 0.7774 (p0) cc_final: 0.7483 (p0) REVERT: C 1144 GLU cc_start: 0.7530 (mp0) cc_final: 0.7325 (mp0) REVERT: D 77 MET cc_start: 0.4860 (ttt) cc_final: 0.4567 (ttt) REVERT: E 34 MET cc_start: 0.3685 (mmm) cc_final: 0.3453 (mmm) REVERT: F 172 MET cc_start: 0.8122 (mtp) cc_final: 0.7673 (mtm) REVERT: F 174 TRP cc_start: 0.7988 (m100) cc_final: 0.7547 (m100) REVERT: F 229 THR cc_start: 0.7384 (OUTLIER) cc_final: 0.6880 (m) REVERT: F 254 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.7165 (p) outliers start: 98 outliers final: 71 residues processed: 645 average time/residue: 0.4045 time to fit residues: 411.2288 Evaluate side-chains 657 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 576 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 110 optimal weight: 0.1980 chunk 181 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 339 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 212 optimal weight: 0.4980 chunk 189 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 690 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.154854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123901 restraints weight = 42052.785| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.58 r_work: 0.3394 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28525 Z= 0.148 Angle : 0.666 27.015 38936 Z= 0.326 Chirality : 0.048 0.415 4492 Planarity : 0.004 0.057 4950 Dihedral : 6.005 64.682 4616 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.02 % Allowed : 17.52 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.58 (0.14), residues: 3445 helix: 1.41 (0.21), residues: 691 sheet: -0.98 (0.18), residues: 726 loop : -2.06 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 353 HIS 0.004 0.001 HIS B 519 PHE 0.029 0.001 PHE A 392 TYR 0.031 0.001 TYR B 380 ARG 0.008 0.000 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 40) link_NAG-ASN : angle 2.86341 ( 120) hydrogen bonds : bond 0.03991 ( 831) hydrogen bonds : angle 5.02856 ( 2298) SS BOND : bond 0.00604 ( 44) SS BOND : angle 2.66144 ( 88) covalent geometry : bond 0.00342 (28441) covalent geometry : angle 0.63627 (38728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 590 time to evaluate : 2.859 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: A 52 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 60 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8237 (t) REVERT: A 239 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 353 TRP cc_start: 0.8468 (p-90) cc_final: 0.7482 (p-90) REVERT: A 377 PHE cc_start: 0.7987 (t80) cc_final: 0.7771 (t80) REVERT: A 385 THR cc_start: 0.9170 (t) cc_final: 0.8939 (p) REVERT: A 399 SER cc_start: 0.8927 (m) cc_final: 0.8482 (p) REVERT: A 409 GLN cc_start: 0.7526 (mt0) cc_final: 0.7287 (tt0) REVERT: A 430 THR cc_start: 0.8598 (m) cc_final: 0.8236 (p) REVERT: A 465 GLU cc_start: 0.7912 (tp30) cc_final: 0.7642 (tp30) REVERT: A 487 ASN cc_start: 0.7962 (m-40) cc_final: 0.7018 (t0) REVERT: A 501 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: A 592 PHE cc_start: 0.7778 (p90) cc_final: 0.7477 (p90) REVERT: A 708 SER cc_start: 0.8366 (t) cc_final: 0.8134 (p) REVERT: A 711 SER cc_start: 0.8833 (p) cc_final: 0.8627 (t) REVERT: A 764 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7842 (mtmt) REVERT: A 776 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8289 (ttpp) REVERT: A 779 GLN cc_start: 0.8383 (tp40) cc_final: 0.7985 (tp40) REVERT: A 780 GLU cc_start: 0.8241 (tp30) cc_final: 0.7803 (tp30) REVERT: A 804 GLN cc_start: 0.8578 (mt0) cc_final: 0.8283 (mm-40) REVERT: A 820 ASP cc_start: 0.7879 (t70) cc_final: 0.7580 (t0) REVERT: A 851 CYS cc_start: 0.8338 (m) cc_final: 0.7850 (p) REVERT: A 854 LYS cc_start: 0.8672 (tttp) cc_final: 0.8121 (ttmm) REVERT: A 856 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7785 (mttm) REVERT: A 868 GLU cc_start: 0.7793 (mp0) cc_final: 0.7367 (mp0) REVERT: A 1017 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 1086 LYS cc_start: 0.8400 (ptpt) cc_final: 0.8058 (mtmt) REVERT: B 53 ASP cc_start: 0.7484 (t0) cc_final: 0.7161 (t0) REVERT: B 65 PHE cc_start: 0.7467 (m-80) cc_final: 0.6683 (m-80) REVERT: B 188 ARG cc_start: 0.8758 (mtm-85) cc_final: 0.8521 (mtt180) REVERT: B 237 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7925 (mtm-85) REVERT: B 239 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7487 (tm-30) REVERT: B 271 GLN cc_start: 0.8302 (mt0) cc_final: 0.8087 (mt0) REVERT: B 355 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7653 (ttm-80) REVERT: B 377 PHE cc_start: 0.7549 (t80) cc_final: 0.7270 (t80) REVERT: B 533 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8798 (tp) REVERT: B 537 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8127 (ttpp) REVERT: B 571 ASP cc_start: 0.7712 (t0) cc_final: 0.7386 (t70) REVERT: B 599 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8374 (p) REVERT: B 671 CYS cc_start: 0.7678 (m) cc_final: 0.7422 (m) REVERT: B 779 GLN cc_start: 0.8135 (tp40) cc_final: 0.7582 (tp40) REVERT: B 797 PHE cc_start: 0.8211 (m-80) cc_final: 0.7865 (m-80) REVERT: B 886 TRP cc_start: 0.8494 (p90) cc_final: 0.8257 (p90) REVERT: B 957 GLN cc_start: 0.8242 (tt0) cc_final: 0.7852 (tt0) REVERT: B 988 GLU cc_start: 0.8271 (tp30) cc_final: 0.7947 (tp30) REVERT: B 1031 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: B 1101 HIS cc_start: 0.8324 (m170) cc_final: 0.7961 (m-70) REVERT: B 1113 GLN cc_start: 0.8677 (mt0) cc_final: 0.8462 (mt0) REVERT: B 1134 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.6281 (m-40) REVERT: C 52 GLN cc_start: 0.8299 (tm-30) cc_final: 0.8012 (tp40) REVERT: C 84 LEU cc_start: 0.8392 (mt) cc_final: 0.8158 (mp) REVERT: C 115 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7688 (tp-100) REVERT: C 236 THR cc_start: 0.8527 (p) cc_final: 0.8273 (t) REVERT: C 281 GLU cc_start: 0.7614 (pm20) cc_final: 0.7117 (pm20) REVERT: C 349 SER cc_start: 0.8453 (t) cc_final: 0.7892 (m) REVERT: C 362 VAL cc_start: 0.8774 (t) cc_final: 0.8472 (p) REVERT: C 406 GLU cc_start: 0.8160 (mp0) cc_final: 0.7472 (mp0) REVERT: C 453 TYR cc_start: 0.8217 (p90) cc_final: 0.7832 (p90) REVERT: C 509 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7546 (mtt180) REVERT: C 542 ASN cc_start: 0.7620 (t0) cc_final: 0.7234 (t0) REVERT: C 546 LEU cc_start: 0.8203 (mm) cc_final: 0.7987 (mp) REVERT: C 556 ASN cc_start: 0.8496 (p0) cc_final: 0.7948 (p0) REVERT: C 558 LYS cc_start: 0.8549 (mppt) cc_final: 0.7881 (mppt) REVERT: C 592 PHE cc_start: 0.8482 (p90) cc_final: 0.8077 (p90) REVERT: C 599 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8582 (p) REVERT: C 788 ILE cc_start: 0.8690 (mm) cc_final: 0.8388 (mt) REVERT: C 820 ASP cc_start: 0.7593 (m-30) cc_final: 0.7229 (m-30) REVERT: C 933 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7598 (mtpp) REVERT: C 970 PHE cc_start: 0.8329 (m-10) cc_final: 0.8024 (m-10) REVERT: C 1041 ASP cc_start: 0.7564 (t0) cc_final: 0.7311 (t0) REVERT: C 1073 LYS cc_start: 0.8532 (ptmm) cc_final: 0.8313 (ptmm) REVERT: C 1118 ASP cc_start: 0.8047 (p0) cc_final: 0.7786 (p0) REVERT: C 1128 VAL cc_start: 0.8619 (m) cc_final: 0.8350 (p) REVERT: C 1144 GLU cc_start: 0.7751 (mp0) cc_final: 0.7501 (mp0) REVERT: D 77 MET cc_start: 0.4995 (ttt) cc_final: 0.4688 (ttt) REVERT: E 34 MET cc_start: 0.3759 (mmm) cc_final: 0.3515 (mmm) REVERT: F 172 MET cc_start: 0.8403 (mtp) cc_final: 0.7952 (mtm) REVERT: F 174 TRP cc_start: 0.8001 (m100) cc_final: 0.7532 (m100) REVERT: F 229 THR cc_start: 0.7542 (OUTLIER) cc_final: 0.7052 (m) REVERT: F 254 VAL cc_start: 0.7534 (OUTLIER) cc_final: 0.7311 (p) outliers start: 91 outliers final: 73 residues processed: 647 average time/residue: 0.4021 time to fit residues: 408.2244 Evaluate side-chains 662 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 578 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 318 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1135 ASN B 544 ASN B 824 ASN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 321 GLN C 690 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.152448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121366 restraints weight = 41843.301| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.60 r_work: 0.3357 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28525 Z= 0.228 Angle : 0.723 27.363 38936 Z= 0.357 Chirality : 0.050 0.422 4492 Planarity : 0.005 0.060 4950 Dihedral : 6.160 57.186 4616 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.19 % Allowed : 17.46 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.66 (0.14), residues: 3445 helix: 1.29 (0.21), residues: 690 sheet: -1.04 (0.18), residues: 742 loop : -2.08 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 248 HIS 0.005 0.001 HIS C1064 PHE 0.032 0.002 PHE A 65 TYR 0.029 0.002 TYR B 380 ARG 0.011 0.001 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 40) link_NAG-ASN : angle 2.80397 ( 120) hydrogen bonds : bond 0.04670 ( 831) hydrogen bonds : angle 5.19358 ( 2298) SS BOND : bond 0.00676 ( 44) SS BOND : angle 2.85819 ( 88) covalent geometry : bond 0.00532 (28441) covalent geometry : angle 0.69419 (38728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 603 time to evaluate : 2.942 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: A 52 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 220 PHE cc_start: 0.8520 (t80) cc_final: 0.8164 (t80) REVERT: A 377 PHE cc_start: 0.8025 (t80) cc_final: 0.7822 (t80) REVERT: A 399 SER cc_start: 0.8941 (m) cc_final: 0.8334 (p) REVERT: A 418 ILE cc_start: 0.7944 (mm) cc_final: 0.7731 (mm) REVERT: A 430 THR cc_start: 0.8564 (m) cc_final: 0.8299 (p) REVERT: A 465 GLU cc_start: 0.8061 (tp30) cc_final: 0.7725 (tp30) REVERT: A 487 ASN cc_start: 0.7901 (m-40) cc_final: 0.6914 (t0) REVERT: A 501 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: A 708 SER cc_start: 0.8396 (t) cc_final: 0.8186 (p) REVERT: A 711 SER cc_start: 0.8831 (p) cc_final: 0.8627 (t) REVERT: A 776 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8326 (ttpp) REVERT: A 779 GLN cc_start: 0.8411 (tp40) cc_final: 0.8047 (tp40) REVERT: A 780 GLU cc_start: 0.8299 (tp30) cc_final: 0.7857 (tp30) REVERT: A 804 GLN cc_start: 0.8486 (mt0) cc_final: 0.8149 (mm-40) REVERT: A 820 ASP cc_start: 0.7877 (t70) cc_final: 0.7595 (t0) REVERT: A 851 CYS cc_start: 0.8373 (m) cc_final: 0.7906 (p) REVERT: A 854 LYS cc_start: 0.8683 (tttp) cc_final: 0.8170 (ttmm) REVERT: A 856 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7872 (mttm) REVERT: A 868 GLU cc_start: 0.7808 (mp0) cc_final: 0.7367 (mp0) REVERT: A 969 LYS cc_start: 0.8319 (mmtm) cc_final: 0.8033 (mmtm) REVERT: A 1017 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7822 (tm-30) REVERT: A 1086 LYS cc_start: 0.8390 (ptpt) cc_final: 0.8082 (mtmt) REVERT: B 188 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8511 (mtt180) REVERT: B 237 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.7952 (mtm-85) REVERT: B 239 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 269 TYR cc_start: 0.7649 (m-10) cc_final: 0.7392 (m-10) REVERT: B 271 GLN cc_start: 0.8322 (mt0) cc_final: 0.8060 (mt0) REVERT: B 281 GLU cc_start: 0.8067 (pm20) cc_final: 0.7797 (pm20) REVERT: B 355 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7531 (ttm-80) REVERT: B 377 PHE cc_start: 0.7624 (t80) cc_final: 0.7396 (t80) REVERT: B 533 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8801 (tp) REVERT: B 537 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8342 (ttpp) REVERT: B 571 ASP cc_start: 0.7750 (t0) cc_final: 0.7380 (t70) REVERT: B 599 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 671 CYS cc_start: 0.7713 (m) cc_final: 0.7442 (m) REVERT: B 779 GLN cc_start: 0.8218 (tp40) cc_final: 0.7655 (tp40) REVERT: B 797 PHE cc_start: 0.8207 (m-80) cc_final: 0.7844 (m-80) REVERT: B 804 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7948 (mm-40) REVERT: B 886 TRP cc_start: 0.8531 (p90) cc_final: 0.8172 (p90) REVERT: B 931 ILE cc_start: 0.8419 (mm) cc_final: 0.8089 (tp) REVERT: B 957 GLN cc_start: 0.8233 (tt0) cc_final: 0.7843 (tt0) REVERT: B 988 GLU cc_start: 0.8277 (tp30) cc_final: 0.7955 (tp30) REVERT: B 1101 HIS cc_start: 0.8333 (m170) cc_final: 0.7968 (m-70) REVERT: B 1134 ASN cc_start: 0.6999 (OUTLIER) cc_final: 0.6597 (m-40) REVERT: C 52 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8015 (tp40) REVERT: C 84 LEU cc_start: 0.8483 (mt) cc_final: 0.8257 (mp) REVERT: C 99 ASN cc_start: 0.8287 (t0) cc_final: 0.8021 (t0) REVERT: C 115 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7688 (tp-100) REVERT: C 236 THR cc_start: 0.8577 (p) cc_final: 0.8316 (t) REVERT: C 281 GLU cc_start: 0.7648 (pm20) cc_final: 0.7182 (pm20) REVERT: C 294 ASP cc_start: 0.7319 (p0) cc_final: 0.7020 (p0) REVERT: C 349 SER cc_start: 0.8377 (t) cc_final: 0.7753 (m) REVERT: C 362 VAL cc_start: 0.8807 (t) cc_final: 0.8522 (p) REVERT: C 386 LYS cc_start: 0.8308 (pttm) cc_final: 0.8033 (pttm) REVERT: C 406 GLU cc_start: 0.8187 (mp0) cc_final: 0.7561 (mp0) REVERT: C 509 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7543 (mtt180) REVERT: C 542 ASN cc_start: 0.7838 (t0) cc_final: 0.7584 (t0) REVERT: C 546 LEU cc_start: 0.8395 (mm) cc_final: 0.8185 (mp) REVERT: C 556 ASN cc_start: 0.8554 (p0) cc_final: 0.7988 (p0) REVERT: C 558 LYS cc_start: 0.8591 (mppt) cc_final: 0.7937 (mppt) REVERT: C 592 PHE cc_start: 0.8536 (p90) cc_final: 0.8085 (p90) REVERT: C 599 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8602 (p) REVERT: C 776 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8118 (ttmm) REVERT: C 788 ILE cc_start: 0.8660 (mm) cc_final: 0.8362 (mt) REVERT: C 933 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7573 (mtpp) REVERT: C 1073 LYS cc_start: 0.8516 (ptmm) cc_final: 0.8263 (ptmm) REVERT: C 1118 ASP cc_start: 0.8083 (p0) cc_final: 0.7780 (p0) REVERT: C 1144 GLU cc_start: 0.7816 (mp0) cc_final: 0.7582 (mp0) REVERT: D 77 MET cc_start: 0.5063 (ttt) cc_final: 0.4745 (ttt) REVERT: E 34 MET cc_start: 0.4013 (mmm) cc_final: 0.3771 (mmm) REVERT: F 172 MET cc_start: 0.8413 (mtp) cc_final: 0.7975 (mtm) REVERT: F 174 TRP cc_start: 0.8067 (m100) cc_final: 0.7644 (m100) REVERT: F 229 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7096 (m) REVERT: F 254 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7421 (p) outliers start: 96 outliers final: 78 residues processed: 662 average time/residue: 0.4131 time to fit residues: 430.1099 Evaluate side-chains 679 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 592 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 31 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 330 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 228 optimal weight: 0.4980 chunk 274 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A1005 GLN A1135 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN F 141 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.122056 restraints weight = 42013.283| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.58 r_work: 0.3376 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28525 Z= 0.178 Angle : 0.709 26.822 38936 Z= 0.349 Chirality : 0.049 0.413 4492 Planarity : 0.005 0.072 4950 Dihedral : 6.135 56.581 4616 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.32 % Allowed : 17.79 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.63 (0.14), residues: 3445 helix: 1.37 (0.21), residues: 685 sheet: -1.11 (0.18), residues: 750 loop : -2.05 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 353 HIS 0.004 0.001 HIS C1064 PHE 0.033 0.002 PHE A 392 TYR 0.036 0.002 TYR A 423 ARG 0.010 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 40) link_NAG-ASN : angle 2.79433 ( 120) hydrogen bonds : bond 0.04432 ( 831) hydrogen bonds : angle 5.17745 ( 2298) SS BOND : bond 0.00631 ( 44) SS BOND : angle 2.80114 ( 88) covalent geometry : bond 0.00414 (28441) covalent geometry : angle 0.68082 (38728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18062.33 seconds wall clock time: 311 minutes 37.41 seconds (18697.41 seconds total)