Starting phenix.real_space_refine on Tue Apr 7 14:33:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ypr_73306/04_2026/9ypr_73306.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ypr_73306/04_2026/9ypr_73306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ypr_73306/04_2026/9ypr_73306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ypr_73306/04_2026/9ypr_73306.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ypr_73306/04_2026/9ypr_73306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ypr_73306/04_2026/9ypr_73306.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 115 5.16 5 C 17742 2.51 5 N 4604 2.21 5 O 5465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27926 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7243 Classifications: {'peptide': 928} Link IDs: {'PTRANS': 49, 'TRANS': 878} Chain breaks: 19 Chain: "B" Number of atoms: 7639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7639 Classifications: {'peptide': 978} Link IDs: {'PTRANS': 48, 'TRANS': 929} Chain breaks: 17 Chain: "C" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6300 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 39, 'TRANS': 768} Chain breaks: 10 Chain: "D" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1688 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain breaks: 2 Chain: "E" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1556 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Chain: "F" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1517 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "G" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1549 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 13, 'TRANS': 185} Chain breaks: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.96, per 1000 atoms: 0.21 Number of scatterers: 27926 At special positions: 0 Unit cell: (130.868, 134.224, 268.448, 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 115 16.00 O 5465 8.00 N 4604 7.00 C 17742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 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 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 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " 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 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=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 211 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 99 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 211 " 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 BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A1134 " " NAG A1306 " - " ASN A 717 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B1098 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C1098 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 717 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.2 seconds 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6632 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 65 sheets defined 21.5% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.974A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.871A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.396A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.121A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.561A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.747A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.539A pdb=" N PHE B 157 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.451A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 403 through 411 removed outlier: 4.720A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.555A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.527A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.201A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.226A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.678A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.512A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.862A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.653A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.833A pdb=" N VAL C 159 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.794A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.105A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.952A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.656A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.152A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.920A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'F' and resid 122 through 128 Processing helix chain 'F' and resid 182 through 189 removed outlier: 3.504A pdb=" N SER F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.748A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.103A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.287A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.860A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.886A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.690A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.938A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.436A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.388A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.808A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AC2, first strand: chain 'B' and resid 191 through 197 removed outlier: 5.472A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.507A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.661A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.679A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.679A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.948A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.950A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.764A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 116 through 117 removed outlier: 3.518A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 116 through 117 removed outlier: 3.518A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 313 through 317 removed outlier: 6.665A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.846A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.813A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.585A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.672A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AF1, first strand: chain 'D' and resid 59 through 63 removed outlier: 5.548A pdb=" N TYR D 55 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ALA D 34 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 117 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLU D 103 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET D 115 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N GLN D 105 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR D 113 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 135 through 139 removed outlier: 3.951A pdb=" N GLY D 154 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 192 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 166 through 169 Processing sheet with id=AF4, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.864A pdb=" N ILE E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR E 51 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'E' and resid 17 through 23 Processing sheet with id=AF7, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.536A pdb=" N PHE E 119 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TYR E 173 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.536A pdb=" N PHE E 119 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TYR E 173 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 154 through 155 removed outlier: 3.724A pdb=" N LYS E 205 " --> pdb=" O CYS E 194 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.953A pdb=" N ILE F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR F 51 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP F 37 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AG3, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AG4, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.846A pdb=" N VAL F 134 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR F 173 " --> pdb=" O ASP F 139 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.846A pdb=" N VAL F 134 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR F 173 " --> pdb=" O ASP F 139 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AG7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'G' and resid 60 through 63 removed outlier: 3.929A pdb=" N VAL G 117 " --> pdb=" O ARG G 101 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU G 103 " --> pdb=" O MET G 115 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET G 115 " --> pdb=" O GLU G 103 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 46 through 48 Processing sheet with id=AH1, first strand: chain 'G' and resid 135 through 139 removed outlier: 3.907A pdb=" N GLY G 154 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR G 191 " --> pdb=" O ASP G 159 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 166 through 168 1120 hydrogen bonds defined for protein. 2958 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: 8.08 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8519 1.34 - 1.46: 5703 1.46 - 1.58: 14158 1.58 - 1.70: 0 1.70 - 1.82: 143 Bond restraints: 28523 Sorted by residual: bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.24e+01 bond pdb=" N VAL C1094 " pdb=" CA VAL C1094 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.17e+01 bond pdb=" N VAL A 608 " pdb=" CA VAL A 608 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.09e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE C1114 " pdb=" CA ILE C1114 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.97e+00 ... (remaining 28518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 38126 2.35 - 4.70: 589 4.70 - 7.05: 51 7.05 - 9.41: 8 9.41 - 11.76: 5 Bond angle restraints: 38779 Sorted by residual: angle pdb=" N THR B1100 " pdb=" CA THR B1100 " pdb=" C THR B1100 " ideal model delta sigma weight residual 114.39 107.93 6.46 1.45e+00 4.76e-01 1.98e+01 angle pdb=" N ASN B1098 " pdb=" CA ASN B1098 " pdb=" C ASN B1098 " ideal model delta sigma weight residual 113.01 108.19 4.82 1.20e+00 6.94e-01 1.61e+01 angle pdb=" N GLY B1099 " pdb=" CA GLY B1099 " pdb=" C GLY B1099 " ideal model delta sigma weight residual 113.79 109.17 4.62 1.17e+00 7.31e-01 1.56e+01 angle pdb=" CB MET B1050 " pdb=" CG MET B1050 " pdb=" SD MET B1050 " ideal model delta sigma weight residual 112.70 100.94 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA ASN C 61 " pdb=" C ASN C 61 " pdb=" O ASN C 61 " ideal model delta sigma weight residual 122.37 117.92 4.45 1.15e+00 7.56e-01 1.50e+01 ... (remaining 38774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15313 17.58 - 35.15: 1590 35.15 - 52.73: 356 52.73 - 70.31: 124 70.31 - 87.89: 36 Dihedral angle restraints: 17419 sinusoidal: 7139 harmonic: 10280 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.89 87.89 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS G 155 " pdb=" SG CYS G 155 " pdb=" SG CYS G 211 " pdb=" CB CYS G 211 " ideal model delta sinusoidal sigma weight residual 93.00 -179.41 -87.59 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 0.95 -86.95 1 1.00e+01 1.00e-02 9.09e+01 ... (remaining 17416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4376 0.114 - 0.227: 128 0.227 - 0.341: 5 0.341 - 0.455: 3 0.455 - 0.568: 1 Chirality restraints: 4513 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.13e+01 ... (remaining 4510 not shown) Planarity restraints: 4978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.197 2.00e-02 2.50e+03 1.69e-01 3.55e+02 pdb=" C7 NAG B1309 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.280 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.181 2.00e-02 2.50e+03 1.59e-01 3.15e+02 pdb=" C7 NAG I 2 " -0.026 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.016 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.273 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.175 2.00e-02 2.50e+03 1.46e-01 2.66e+02 pdb=" C7 NAG I 1 " 0.042 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.125 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.242 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.015 2.00e-02 2.50e+03 ... (remaining 4975 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 412 2.63 - 3.20: 26338 3.20 - 3.77: 43561 3.77 - 4.33: 58670 4.33 - 4.90: 95408 Nonbonded interactions: 224389 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OD1 ASN A 440 " model vdw 2.068 3.040 nonbonded pdb=" OD1 ASN A 487 " pdb=" OH TYR A 489 " model vdw 2.116 3.040 nonbonded pdb=" NH2 ARG G 45 " pdb=" OE2 GLU G 92 " model vdw 2.159 3.120 nonbonded pdb=" OD1 ASP D 93 " pdb=" OH TYR D 97 " model vdw 2.175 3.040 nonbonded pdb=" OE1 GLN G 105 " pdb=" OH TYR G 113 " model vdw 2.194 3.040 ... (remaining 224384 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 28 through 64 or resid 66 through 67 or resid 81 through 2 \ 31 or resid 234 through 331 or resid 334 through 340 or resid 348 through 399 or \ resid 401 through 414 or resid 418 through 478 or resid 481 through 497 or resi \ d 506 through 827 or resid 853 through 1306)) selection = (chain 'B' and (resid 28 through 93 or resid 102 through 107 or resid 116 throug \ h 121 or resid 126 through 129 or resid 168 through 174 or resid 176 through 197 \ or resid 199 through 201 or resid 203 through 209 or resid 216 through 231 or r \ esid 234 through 238 or resid 263 through 385 or resid 391 through 434 or resid \ 437 through 497 or resid 506 through 568 or resid 570 through 1306)) } ncs_group { reference = (chain 'D' and (resid 1 through 143 or resid 152 through 168 or resid 179 throug \ h 198 or resid 211 through 229)) selection = chain 'G' } ncs_group { reference = (chain 'E' and (resid 2 through 79 or resid 85 through 213)) selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.00 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.750 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28594 Z= 0.265 Angle : 0.719 24.004 38952 Z= 0.399 Chirality : 0.049 0.568 4513 Planarity : 0.006 0.169 4950 Dihedral : 15.513 87.405 10667 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 0.84 % Allowed : 21.02 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3425 helix: 2.14 (0.20), residues: 664 sheet: -0.69 (0.17), residues: 896 loop : -1.29 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 983 TYR 0.029 0.001 TYR D 110 PHE 0.018 0.001 PHE A 58 TRP 0.039 0.002 TRP E 149 HIS 0.013 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00448 (28523) covalent geometry : angle 0.68626 (38779) SS BOND : bond 0.00251 ( 40) SS BOND : angle 0.91937 ( 80) hydrogen bonds : bond 0.13241 ( 1071) hydrogen bonds : angle 6.67473 ( 2958) link_BETA1-4 : bond 0.04120 ( 3) link_BETA1-4 : angle 11.83123 ( 9) link_NAG-ASN : bond 0.00412 ( 28) link_NAG-ASN : angle 2.53339 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 1.074 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: A 170 TYR cc_start: 0.9179 (t80) cc_final: 0.8832 (t80) REVERT: A 365 TYR cc_start: 0.8616 (m-80) cc_final: 0.8401 (p90) REVERT: A 410 ILE cc_start: 0.9165 (mt) cc_final: 0.8865 (mp) REVERT: A 456 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9138 (m-10) REVERT: A 740 MET cc_start: 0.8328 (tpt) cc_final: 0.7931 (tpt) REVERT: A 773 GLU cc_start: 0.9140 (tt0) cc_final: 0.8400 (tm-30) REVERT: A 855 PHE cc_start: 0.8630 (m-80) cc_final: 0.8347 (m-10) REVERT: A 995 ARG cc_start: 0.8819 (mtt-85) cc_final: 0.8510 (ttp-170) REVERT: A 1043 CYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8692 (m) REVERT: A 1107 ARG cc_start: 0.9200 (mtt180) cc_final: 0.8864 (mtt180) REVERT: B 220 PHE cc_start: 0.7412 (t80) cc_final: 0.7030 (t80) REVERT: B 318 PHE cc_start: 0.8293 (t80) cc_final: 0.7805 (t80) REVERT: B 451 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.5956 (p90) REVERT: B 456 PHE cc_start: 0.7668 (m-80) cc_final: 0.7126 (m-80) REVERT: B 495 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: B 508 TYR cc_start: 0.8350 (m-10) cc_final: 0.8063 (m-10) REVERT: B 568 ASP cc_start: 0.8946 (t0) cc_final: 0.8259 (p0) REVERT: C 65 PHE cc_start: 0.8735 (m-80) cc_final: 0.8114 (m-10) REVERT: C 104 TRP cc_start: 0.8520 (m-90) cc_final: 0.8007 (m-90) REVERT: C 131 CYS cc_start: 0.4986 (OUTLIER) cc_final: 0.4213 (m) REVERT: C 137 ASN cc_start: 0.9452 (t0) cc_final: 0.9226 (p0) REVERT: C 1041 ASP cc_start: 0.9212 (t0) cc_final: 0.8891 (t0) REVERT: D 169 TRP cc_start: 0.2020 (OUTLIER) cc_final: 0.1799 (m100) REVERT: E 16 GLN cc_start: 0.6770 (tt0) cc_final: 0.6282 (mm-40) REVERT: G 109 ASP cc_start: 0.8725 (t70) cc_final: 0.8476 (t70) outliers start: 26 outliers final: 13 residues processed: 263 average time/residue: 0.1979 time to fit residues: 80.3906 Evaluate side-chains 187 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 169 TRP Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 193 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 690 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1101 HIS C 134 GLN C 542 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1101 HIS D 16 GLN G 108 HIS ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.093636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056555 restraints weight = 95795.198| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.63 r_work: 0.2847 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28594 Z= 0.212 Angle : 0.618 13.299 38952 Z= 0.312 Chirality : 0.044 0.292 4513 Planarity : 0.004 0.054 4950 Dihedral : 5.941 57.678 4445 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.43 % Allowed : 19.44 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3425 helix: 2.17 (0.20), residues: 663 sheet: -0.72 (0.17), residues: 889 loop : -1.12 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 509 TYR 0.021 0.002 TYR D 110 PHE 0.027 0.001 PHE C 58 TRP 0.026 0.002 TRP B 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00477 (28523) covalent geometry : angle 0.60238 (38779) SS BOND : bond 0.00299 ( 40) SS BOND : angle 0.85571 ( 80) hydrogen bonds : bond 0.04317 ( 1071) hydrogen bonds : angle 5.64238 ( 2958) link_BETA1-4 : bond 0.00872 ( 3) link_BETA1-4 : angle 5.52109 ( 9) link_NAG-ASN : bond 0.00410 ( 28) link_NAG-ASN : angle 2.40906 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 182 time to evaluate : 0.778 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 170 TYR cc_start: 0.9188 (t80) cc_final: 0.8823 (t80) REVERT: A 410 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8849 (mp) REVERT: A 456 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.9097 (m-10) REVERT: A 740 MET cc_start: 0.8515 (tpt) cc_final: 0.8082 (tpt) REVERT: A 773 GLU cc_start: 0.9077 (tt0) cc_final: 0.8388 (tm-30) REVERT: A 855 PHE cc_start: 0.8521 (m-80) cc_final: 0.8225 (m-10) REVERT: A 856 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.8898 (p0) REVERT: A 869 MET cc_start: 0.9201 (mtm) cc_final: 0.8845 (mtm) REVERT: A 1107 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8812 (mtt180) REVERT: B 141 LEU cc_start: 0.8588 (tp) cc_final: 0.8146 (tp) REVERT: B 318 PHE cc_start: 0.8331 (t80) cc_final: 0.7939 (t80) REVERT: B 451 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.6246 (p90) REVERT: B 456 PHE cc_start: 0.7752 (m-80) cc_final: 0.7224 (m-80) REVERT: B 495 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: B 508 TYR cc_start: 0.8410 (m-10) cc_final: 0.8205 (m-10) REVERT: B 568 ASP cc_start: 0.8734 (t0) cc_final: 0.8368 (p0) REVERT: B 725 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8091 (mt-10) REVERT: C 65 PHE cc_start: 0.8502 (m-80) cc_final: 0.7995 (m-10) REVERT: C 84 LEU cc_start: 0.8186 (mt) cc_final: 0.7640 (mp) REVERT: C 104 TRP cc_start: 0.8610 (m-90) cc_final: 0.8166 (m-90) REVERT: C 131 CYS cc_start: 0.5281 (OUTLIER) cc_final: 0.4674 (m) REVERT: C 132 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: C 226 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8904 (mp) REVERT: C 740 MET cc_start: 0.8945 (tpt) cc_final: 0.8469 (tpp) REVERT: C 878 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9262 (mp) REVERT: C 1041 ASP cc_start: 0.9045 (t0) cc_final: 0.8774 (t0) REVERT: D 115 MET cc_start: 0.7693 (tpp) cc_final: 0.7195 (tpp) REVERT: D 169 TRP cc_start: 0.1496 (OUTLIER) cc_final: 0.1006 (t-100) REVERT: D 224 LYS cc_start: 0.1617 (OUTLIER) cc_final: 0.0948 (ptmm) REVERT: G 101 ARG cc_start: 0.9505 (tmm-80) cc_final: 0.9175 (tmm-80) REVERT: G 212 ASN cc_start: 0.5324 (OUTLIER) cc_final: 0.5077 (t0) outliers start: 106 outliers final: 56 residues processed: 274 average time/residue: 0.1665 time to fit residues: 73.9639 Evaluate side-chains 223 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 155 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 169 TRP Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 223 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 101 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 292 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 319 optimal weight: 5.9990 chunk 60 optimal weight: 0.0170 chunk 15 optimal weight: 0.7980 chunk 315 optimal weight: 9.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 506 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 99 ASN C 314 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.095412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.057377 restraints weight = 97840.678| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.80 r_work: 0.2860 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28594 Z= 0.131 Angle : 0.562 13.240 38952 Z= 0.283 Chirality : 0.043 0.306 4513 Planarity : 0.004 0.057 4950 Dihedral : 5.505 58.919 4431 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.37 % Allowed : 19.60 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3425 helix: 2.30 (0.20), residues: 665 sheet: -0.64 (0.17), residues: 904 loop : -1.05 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 63 TYR 0.021 0.001 TYR D 110 PHE 0.016 0.001 PHE C 238 TRP 0.014 0.001 TRP G 36 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00292 (28523) covalent geometry : angle 0.54627 (38779) SS BOND : bond 0.00332 ( 40) SS BOND : angle 0.80013 ( 80) hydrogen bonds : bond 0.03824 ( 1071) hydrogen bonds : angle 5.30871 ( 2958) link_BETA1-4 : bond 0.00628 ( 3) link_BETA1-4 : angle 5.30990 ( 9) link_NAG-ASN : bond 0.00403 ( 28) link_NAG-ASN : angle 2.21045 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 175 time to evaluate : 0.950 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 170 TYR cc_start: 0.9229 (t80) cc_final: 0.8862 (t80) REVERT: A 410 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8794 (mp) REVERT: A 456 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.9090 (m-10) REVERT: A 740 MET cc_start: 0.8509 (tpt) cc_final: 0.8084 (tpt) REVERT: A 773 GLU cc_start: 0.9061 (tt0) cc_final: 0.8373 (tm-30) REVERT: A 855 PHE cc_start: 0.8539 (m-80) cc_final: 0.8263 (m-10) REVERT: A 856 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8912 (p0) REVERT: A 1029 MET cc_start: 0.9355 (tpp) cc_final: 0.9116 (ttm) REVERT: B 141 LEU cc_start: 0.8711 (tp) cc_final: 0.8179 (tp) REVERT: B 159 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9181 (m) REVERT: B 218 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: B 220 PHE cc_start: 0.7645 (t80) cc_final: 0.7348 (t80) REVERT: B 318 PHE cc_start: 0.8319 (t80) cc_final: 0.7960 (t80) REVERT: B 451 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6253 (p90) REVERT: B 456 PHE cc_start: 0.7738 (m-80) cc_final: 0.7240 (m-80) REVERT: B 495 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: B 508 TYR cc_start: 0.8350 (m-10) cc_final: 0.8099 (m-10) REVERT: B 568 ASP cc_start: 0.8613 (t0) cc_final: 0.8307 (p0) REVERT: B 763 LEU cc_start: 0.9608 (mm) cc_final: 0.9408 (mp) REVERT: C 65 PHE cc_start: 0.8574 (m-80) cc_final: 0.8060 (m-10) REVERT: C 104 TRP cc_start: 0.8623 (m-90) cc_final: 0.8157 (m-90) REVERT: C 131 CYS cc_start: 0.4934 (OUTLIER) cc_final: 0.4405 (m) REVERT: C 226 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8680 (mp) REVERT: C 740 MET cc_start: 0.8965 (tpt) cc_final: 0.8427 (tpp) REVERT: C 855 PHE cc_start: 0.8379 (m-10) cc_final: 0.8154 (m-10) REVERT: C 1041 ASP cc_start: 0.8971 (t0) cc_final: 0.8677 (t0) REVERT: D 115 MET cc_start: 0.7723 (tpp) cc_final: 0.7242 (tpp) REVERT: D 198 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6894 (p) REVERT: D 224 LYS cc_start: 0.1943 (OUTLIER) cc_final: 0.1339 (ptmm) REVERT: F 56 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7859 (tpp-160) REVERT: F 99 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.5322 (m-80) REVERT: G 39 ILE cc_start: 0.8930 (mm) cc_final: 0.8430 (tp) REVERT: G 101 ARG cc_start: 0.9498 (tmm-80) cc_final: 0.9236 (tmm-80) REVERT: G 212 ASN cc_start: 0.5254 (OUTLIER) cc_final: 0.5008 (t0) outliers start: 104 outliers final: 56 residues processed: 263 average time/residue: 0.1632 time to fit residues: 69.9493 Evaluate side-chains 226 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 156 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 223 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 103 optimal weight: 6.9990 chunk 13 optimal weight: 0.0970 chunk 285 optimal weight: 0.0060 chunk 33 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 312 optimal weight: 0.0570 chunk 120 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN A 969 ASN A1101 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS D 212 ASN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.095393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.058255 restraints weight = 95546.524| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.72 r_work: 0.2887 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28594 Z= 0.112 Angle : 0.547 12.612 38952 Z= 0.273 Chirality : 0.043 0.312 4513 Planarity : 0.004 0.047 4950 Dihedral : 5.369 59.945 4427 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.11 % Allowed : 20.21 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3425 helix: 2.35 (0.20), residues: 667 sheet: -0.58 (0.17), residues: 916 loop : -0.93 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 983 TYR 0.019 0.001 TYR D 110 PHE 0.016 0.001 PHE C 238 TRP 0.022 0.001 TRP D 169 HIS 0.004 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00250 (28523) covalent geometry : angle 0.53177 (38779) SS BOND : bond 0.00198 ( 40) SS BOND : angle 0.85659 ( 80) hydrogen bonds : bond 0.03566 ( 1071) hydrogen bonds : angle 5.08183 ( 2958) link_BETA1-4 : bond 0.00621 ( 3) link_BETA1-4 : angle 4.99389 ( 9) link_NAG-ASN : bond 0.00407 ( 28) link_NAG-ASN : angle 2.15064 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 179 time to evaluate : 1.069 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 128 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.8852 (mp) REVERT: A 170 TYR cc_start: 0.9242 (t80) cc_final: 0.8796 (t80) REVERT: A 456 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.9033 (m-10) REVERT: A 740 MET cc_start: 0.8432 (tpt) cc_final: 0.8043 (tpt) REVERT: A 773 GLU cc_start: 0.9055 (tt0) cc_final: 0.8307 (tm-30) REVERT: A 855 PHE cc_start: 0.8501 (m-80) cc_final: 0.8277 (m-10) REVERT: B 141 LEU cc_start: 0.8590 (tp) cc_final: 0.8051 (tp) REVERT: B 170 TYR cc_start: 0.8752 (t80) cc_final: 0.8495 (t80) REVERT: B 218 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8361 (mp10) REVERT: B 318 PHE cc_start: 0.8318 (t80) cc_final: 0.7966 (t80) REVERT: B 451 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6275 (p90) REVERT: B 456 PHE cc_start: 0.7770 (m-80) cc_final: 0.7259 (m-80) REVERT: B 495 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: B 508 TYR cc_start: 0.8309 (m-10) cc_final: 0.8093 (m-10) REVERT: B 568 ASP cc_start: 0.8604 (t0) cc_final: 0.8235 (p0) REVERT: B 725 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7837 (mt-10) REVERT: B 763 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9409 (mp) REVERT: C 65 PHE cc_start: 0.8529 (m-80) cc_final: 0.8141 (m-10) REVERT: C 104 TRP cc_start: 0.8614 (m-90) cc_final: 0.8144 (m-90) REVERT: C 131 CYS cc_start: 0.4753 (OUTLIER) cc_final: 0.4045 (m) REVERT: C 226 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8713 (mp) REVERT: C 740 MET cc_start: 0.8935 (tpt) cc_final: 0.8419 (tpp) REVERT: C 855 PHE cc_start: 0.8319 (m-10) cc_final: 0.8106 (m-10) REVERT: C 858 LEU cc_start: 0.9407 (mt) cc_final: 0.9206 (mp) REVERT: C 1041 ASP cc_start: 0.8961 (t0) cc_final: 0.8664 (t0) REVERT: D 108 HIS cc_start: 0.8428 (m-70) cc_final: 0.8067 (m-70) REVERT: D 115 MET cc_start: 0.7812 (tpp) cc_final: 0.7591 (tpp) REVERT: D 211 CYS cc_start: 0.7199 (t) cc_final: 0.6740 (t) REVERT: E 35 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8675 (mm) REVERT: F 56 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7898 (tpp-160) REVERT: G 39 ILE cc_start: 0.8999 (mm) cc_final: 0.8554 (tp) REVERT: G 101 ARG cc_start: 0.9455 (tmm-80) cc_final: 0.9114 (tmm-80) REVERT: G 212 ASN cc_start: 0.5254 (OUTLIER) cc_final: 0.5026 (t0) outliers start: 96 outliers final: 60 residues processed: 254 average time/residue: 0.1704 time to fit residues: 70.2435 Evaluate side-chains 240 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 169 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 223 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 11 optimal weight: 0.0000 chunk 127 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 307 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 275 optimal weight: 0.0980 chunk 241 optimal weight: 0.0770 chunk 206 optimal weight: 1.9990 chunk 296 optimal weight: 7.9990 overall best weight: 1.2346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN A 657 ASN A 969 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.095039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057910 restraints weight = 95516.478| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.71 r_work: 0.2878 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28594 Z= 0.131 Angle : 0.543 12.785 38952 Z= 0.272 Chirality : 0.043 0.309 4513 Planarity : 0.004 0.047 4950 Dihedral : 5.297 59.187 4427 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.53 % Allowed : 20.18 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3425 helix: 2.37 (0.20), residues: 665 sheet: -0.55 (0.17), residues: 926 loop : -0.91 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.026 0.001 TYR D 54 PHE 0.023 0.001 PHE B 220 TRP 0.018 0.001 TRP D 169 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00298 (28523) covalent geometry : angle 0.52767 (38779) SS BOND : bond 0.00202 ( 40) SS BOND : angle 0.94686 ( 80) hydrogen bonds : bond 0.03540 ( 1071) hydrogen bonds : angle 4.99797 ( 2958) link_BETA1-4 : bond 0.00609 ( 3) link_BETA1-4 : angle 5.00256 ( 9) link_NAG-ASN : bond 0.00355 ( 28) link_NAG-ASN : angle 2.11997 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 175 time to evaluate : 1.021 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 128 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8839 (mp) REVERT: A 170 TYR cc_start: 0.9239 (t80) cc_final: 0.8785 (t80) REVERT: A 456 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.9001 (m-10) REVERT: A 740 MET cc_start: 0.8481 (tpt) cc_final: 0.8087 (tpt) REVERT: A 773 GLU cc_start: 0.9060 (tt0) cc_final: 0.8362 (tm-30) REVERT: A 855 PHE cc_start: 0.8498 (m-80) cc_final: 0.8283 (m-10) REVERT: B 141 LEU cc_start: 0.8633 (tp) cc_final: 0.8104 (tp) REVERT: B 218 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8359 (mp10) REVERT: B 318 PHE cc_start: 0.8333 (t80) cc_final: 0.7987 (t80) REVERT: B 451 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6279 (p90) REVERT: B 456 PHE cc_start: 0.7707 (m-80) cc_final: 0.7184 (m-80) REVERT: B 495 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: B 508 TYR cc_start: 0.8324 (m-10) cc_final: 0.8070 (m-10) REVERT: B 568 ASP cc_start: 0.8606 (t0) cc_final: 0.8232 (p0) REVERT: B 586 ASP cc_start: 0.8727 (t0) cc_final: 0.8246 (t0) REVERT: B 763 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9428 (mp) REVERT: C 65 PHE cc_start: 0.8574 (m-80) cc_final: 0.8227 (m-10) REVERT: C 104 TRP cc_start: 0.8646 (m-90) cc_final: 0.8138 (m-90) REVERT: C 131 CYS cc_start: 0.4687 (OUTLIER) cc_final: 0.4028 (m) REVERT: C 226 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8740 (mp) REVERT: C 740 MET cc_start: 0.8933 (tpt) cc_final: 0.8419 (tpp) REVERT: C 855 PHE cc_start: 0.8350 (m-10) cc_final: 0.8119 (m-10) REVERT: C 1041 ASP cc_start: 0.8951 (t0) cc_final: 0.8656 (t0) REVERT: D 115 MET cc_start: 0.8073 (tpp) cc_final: 0.7607 (tpp) REVERT: D 224 LYS cc_start: 0.2249 (OUTLIER) cc_final: 0.1855 (ptmm) REVERT: E 35 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8652 (mm) REVERT: F 99 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.5292 (m-80) REVERT: G 39 ILE cc_start: 0.9042 (mm) cc_final: 0.8495 (tp) REVERT: G 101 ARG cc_start: 0.9477 (tmm-80) cc_final: 0.9181 (tmm-80) REVERT: G 212 ASN cc_start: 0.5352 (OUTLIER) cc_final: 0.5089 (t0) outliers start: 109 outliers final: 75 residues processed: 263 average time/residue: 0.1602 time to fit residues: 69.1071 Evaluate side-chains 253 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 166 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 223 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 58 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 127 optimal weight: 0.1980 chunk 286 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 227 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 214 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 506 GLN A 969 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.095711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058668 restraints weight = 95577.109| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.73 r_work: 0.2898 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 28594 Z= 0.103 Angle : 0.533 12.510 38952 Z= 0.266 Chirality : 0.043 0.311 4513 Planarity : 0.004 0.047 4950 Dihedral : 5.195 58.353 4427 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.14 % Allowed : 20.51 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3425 helix: 2.44 (0.20), residues: 665 sheet: -0.46 (0.17), residues: 932 loop : -0.87 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.030 0.001 TYR G 113 PHE 0.040 0.001 PHE B 168 TRP 0.016 0.001 TRP D 169 HIS 0.003 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00229 (28523) covalent geometry : angle 0.51856 (38779) SS BOND : bond 0.00306 ( 40) SS BOND : angle 0.84482 ( 80) hydrogen bonds : bond 0.03378 ( 1071) hydrogen bonds : angle 4.86743 ( 2958) link_BETA1-4 : bond 0.00631 ( 3) link_BETA1-4 : angle 4.88793 ( 9) link_NAG-ASN : bond 0.00382 ( 28) link_NAG-ASN : angle 2.02759 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 177 time to evaluate : 1.030 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 40 ASP cc_start: 0.8898 (t0) cc_final: 0.8544 (t0) REVERT: A 41 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8733 (mttm) REVERT: A 128 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.8853 (mp) REVERT: A 170 TYR cc_start: 0.9252 (t80) cc_final: 0.8852 (t80) REVERT: A 410 ILE cc_start: 0.9039 (mt) cc_final: 0.8749 (mp) REVERT: A 456 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.8961 (m-10) REVERT: A 740 MET cc_start: 0.8433 (tpt) cc_final: 0.8039 (tpt) REVERT: A 855 PHE cc_start: 0.8507 (m-80) cc_final: 0.8280 (m-10) REVERT: A 869 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8931 (mtm) REVERT: B 135 PHE cc_start: 0.8439 (m-10) cc_final: 0.8202 (m-80) REVERT: B 141 LEU cc_start: 0.8671 (tp) cc_final: 0.8090 (tp) REVERT: B 218 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8298 (mp10) REVERT: B 318 PHE cc_start: 0.8317 (t80) cc_final: 0.7971 (t80) REVERT: B 451 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6285 (p90) REVERT: B 456 PHE cc_start: 0.7711 (m-80) cc_final: 0.7195 (m-80) REVERT: B 495 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: B 508 TYR cc_start: 0.8263 (m-10) cc_final: 0.8028 (m-10) REVERT: B 568 ASP cc_start: 0.8598 (t0) cc_final: 0.8342 (p0) REVERT: B 699 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8780 (mp) REVERT: B 950 ASP cc_start: 0.9265 (m-30) cc_final: 0.8956 (m-30) REVERT: C 65 PHE cc_start: 0.8555 (m-80) cc_final: 0.8222 (m-10) REVERT: C 104 TRP cc_start: 0.8629 (m-90) cc_final: 0.8075 (m-90) REVERT: C 131 CYS cc_start: 0.4778 (OUTLIER) cc_final: 0.4106 (m) REVERT: C 226 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8737 (mp) REVERT: C 740 MET cc_start: 0.8913 (tpt) cc_final: 0.8392 (tpp) REVERT: C 855 PHE cc_start: 0.8340 (m-10) cc_final: 0.8110 (m-10) REVERT: C 1041 ASP cc_start: 0.8929 (t0) cc_final: 0.8621 (t0) REVERT: D 108 HIS cc_start: 0.8405 (m-70) cc_final: 0.8043 (m-70) REVERT: D 115 MET cc_start: 0.8086 (tpp) cc_final: 0.7671 (tpp) REVERT: D 224 LYS cc_start: 0.2369 (OUTLIER) cc_final: 0.1945 (ptmm) REVERT: E 35 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8619 (mm) REVERT: F 62 TYR cc_start: 0.8665 (p90) cc_final: 0.8152 (p90) REVERT: F 99 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.5456 (m-80) REVERT: G 39 ILE cc_start: 0.9052 (mm) cc_final: 0.8493 (tp) REVERT: G 58 LYS cc_start: 0.9572 (pptt) cc_final: 0.9365 (pptt) REVERT: G 101 ARG cc_start: 0.9550 (tmm-80) cc_final: 0.9186 (tmm-80) REVERT: G 123 MET cc_start: 0.8771 (tpt) cc_final: 0.8530 (tpt) REVERT: G 212 ASN cc_start: 0.5349 (OUTLIER) cc_final: 0.5102 (t0) outliers start: 97 outliers final: 63 residues processed: 256 average time/residue: 0.1590 time to fit residues: 67.8237 Evaluate side-chains 239 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 162 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 230 optimal weight: 3.9990 chunk 344 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 334 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN A 969 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.094484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.057443 restraints weight = 95797.526| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.60 r_work: 0.2866 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28594 Z= 0.165 Angle : 0.554 12.484 38952 Z= 0.277 Chirality : 0.043 0.306 4513 Planarity : 0.004 0.050 4950 Dihedral : 5.222 58.034 4427 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.27 % Allowed : 20.60 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3425 helix: 2.38 (0.20), residues: 665 sheet: -0.45 (0.17), residues: 923 loop : -0.89 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 983 TYR 0.022 0.001 TYR B 170 PHE 0.029 0.001 PHE B 168 TRP 0.015 0.001 TRP D 169 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00374 (28523) covalent geometry : angle 0.53967 (38779) SS BOND : bond 0.00207 ( 40) SS BOND : angle 0.86994 ( 80) hydrogen bonds : bond 0.03608 ( 1071) hydrogen bonds : angle 4.91326 ( 2958) link_BETA1-4 : bond 0.00557 ( 3) link_BETA1-4 : angle 4.83719 ( 9) link_NAG-ASN : bond 0.00340 ( 28) link_NAG-ASN : angle 2.11834 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 169 time to evaluate : 1.015 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 40 ASP cc_start: 0.8865 (t0) cc_final: 0.8415 (t0) REVERT: A 41 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8760 (mttm) REVERT: A 128 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8819 (mp) REVERT: A 170 TYR cc_start: 0.9258 (t80) cc_final: 0.8775 (t80) REVERT: A 410 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8716 (mp) REVERT: A 456 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8892 (m-10) REVERT: A 740 MET cc_start: 0.8513 (tpt) cc_final: 0.8087 (tpt) REVERT: A 855 PHE cc_start: 0.8513 (m-80) cc_final: 0.8295 (m-10) REVERT: B 135 PHE cc_start: 0.8457 (m-10) cc_final: 0.8229 (m-80) REVERT: B 141 LEU cc_start: 0.8589 (tp) cc_final: 0.8082 (tp) REVERT: B 218 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8359 (mp10) REVERT: B 318 PHE cc_start: 0.8362 (t80) cc_final: 0.8016 (t80) REVERT: B 451 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6264 (p90) REVERT: B 456 PHE cc_start: 0.7713 (m-80) cc_final: 0.7189 (m-80) REVERT: B 495 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: B 508 TYR cc_start: 0.8342 (m-10) cc_final: 0.8111 (m-10) REVERT: B 568 ASP cc_start: 0.8626 (t0) cc_final: 0.8314 (p0) REVERT: B 1029 MET cc_start: 0.9614 (tpp) cc_final: 0.9341 (ttm) REVERT: C 65 PHE cc_start: 0.8571 (m-80) cc_final: 0.8295 (m-10) REVERT: C 104 TRP cc_start: 0.8694 (m-90) cc_final: 0.8202 (m-90) REVERT: C 131 CYS cc_start: 0.4919 (OUTLIER) cc_final: 0.4203 (m) REVERT: C 226 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8799 (mp) REVERT: C 740 MET cc_start: 0.8975 (tpt) cc_final: 0.8439 (tpp) REVERT: C 855 PHE cc_start: 0.8454 (m-10) cc_final: 0.8204 (m-10) REVERT: C 1041 ASP cc_start: 0.8992 (t0) cc_final: 0.8698 (t0) REVERT: D 108 HIS cc_start: 0.8460 (m-70) cc_final: 0.8125 (m-70) REVERT: D 115 MET cc_start: 0.8184 (tpp) cc_final: 0.7803 (tpp) REVERT: D 224 LYS cc_start: 0.2486 (OUTLIER) cc_final: 0.2075 (ptmm) REVERT: E 20 ILE cc_start: 0.6075 (mm) cc_final: 0.5715 (mm) REVERT: E 35 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8631 (mm) REVERT: F 99 PHE cc_start: 0.6956 (OUTLIER) cc_final: 0.5430 (m-80) REVERT: G 39 ILE cc_start: 0.9097 (mm) cc_final: 0.8532 (tp) REVERT: G 101 ARG cc_start: 0.9552 (tmm-80) cc_final: 0.9196 (tmm-80) REVERT: G 212 ASN cc_start: 0.5244 (OUTLIER) cc_final: 0.5016 (t0) outliers start: 101 outliers final: 72 residues processed: 256 average time/residue: 0.1519 time to fit residues: 65.1243 Evaluate side-chains 247 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 162 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 349 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN A 675 GLN B 122 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 787 GLN D 186 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.091500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054186 restraints weight = 97994.209| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.57 r_work: 0.2776 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 28594 Z= 0.375 Angle : 0.717 13.002 38952 Z= 0.360 Chirality : 0.046 0.289 4513 Planarity : 0.004 0.057 4950 Dihedral : 5.860 58.602 4427 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.47 % Allowed : 20.73 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3425 helix: 1.86 (0.20), residues: 667 sheet: -0.72 (0.16), residues: 925 loop : -1.03 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 983 TYR 0.028 0.002 TYR B 91 PHE 0.025 0.002 PHE B 220 TRP 0.012 0.002 TRP B 64 HIS 0.007 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00847 (28523) covalent geometry : angle 0.70248 (38779) SS BOND : bond 0.00337 ( 40) SS BOND : angle 1.09963 ( 80) hydrogen bonds : bond 0.04678 ( 1071) hydrogen bonds : angle 5.44916 ( 2958) link_BETA1-4 : bond 0.00691 ( 3) link_BETA1-4 : angle 5.00377 ( 9) link_NAG-ASN : bond 0.00603 ( 28) link_NAG-ASN : angle 2.64319 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 153 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.9076 (t0) cc_final: 0.8582 (t0) REVERT: A 41 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8766 (mttm) REVERT: A 128 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.8745 (mp) REVERT: A 170 TYR cc_start: 0.9299 (t80) cc_final: 0.8547 (t80) REVERT: A 456 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8936 (m-10) REVERT: A 581 THR cc_start: 0.9619 (OUTLIER) cc_final: 0.9397 (p) REVERT: A 856 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.8885 (p0) REVERT: A 869 MET cc_start: 0.9258 (mtm) cc_final: 0.8982 (mtm) REVERT: B 135 PHE cc_start: 0.8588 (m-10) cc_final: 0.8374 (m-80) REVERT: B 218 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8541 (mp10) REVERT: B 220 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7674 (t80) REVERT: B 318 PHE cc_start: 0.8388 (t80) cc_final: 0.8083 (t80) REVERT: B 451 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.6192 (p90) REVERT: B 456 PHE cc_start: 0.7796 (m-80) cc_final: 0.7252 (m-80) REVERT: B 568 ASP cc_start: 0.8749 (t0) cc_final: 0.8345 (p0) REVERT: B 586 ASP cc_start: 0.8867 (t0) cc_final: 0.8364 (t0) REVERT: C 104 TRP cc_start: 0.8807 (m-90) cc_final: 0.8557 (m-90) REVERT: C 131 CYS cc_start: 0.5193 (OUTLIER) cc_final: 0.4445 (m) REVERT: C 226 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8759 (mp) REVERT: C 740 MET cc_start: 0.9059 (tpt) cc_final: 0.8493 (tpp) REVERT: C 855 PHE cc_start: 0.8564 (m-10) cc_final: 0.8286 (m-10) REVERT: C 878 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9177 (mp) REVERT: C 1041 ASP cc_start: 0.9048 (t0) cc_final: 0.8799 (t0) REVERT: D 115 MET cc_start: 0.8552 (tpp) cc_final: 0.8210 (tpp) REVERT: D 211 CYS cc_start: 0.7047 (t) cc_final: 0.6571 (t) REVERT: D 224 LYS cc_start: 0.2388 (OUTLIER) cc_final: 0.1739 (ptmm) REVERT: F 99 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.5402 (m-80) REVERT: G 39 ILE cc_start: 0.9142 (mm) cc_final: 0.8613 (tp) REVERT: G 123 MET cc_start: 0.8816 (tpt) cc_final: 0.8613 (tpt) REVERT: G 212 ASN cc_start: 0.5220 (OUTLIER) cc_final: 0.5013 (t0) outliers start: 107 outliers final: 77 residues processed: 248 average time/residue: 0.1514 time to fit residues: 62.8350 Evaluate side-chains 227 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 136 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 135 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 35 optimal weight: 7.9990 chunk 308 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 277 optimal weight: 20.0000 chunk 328 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 291 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 506 GLN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.093369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056103 restraints weight = 95785.790| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.65 r_work: 0.2828 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28594 Z= 0.171 Angle : 0.595 12.740 38952 Z= 0.298 Chirality : 0.044 0.371 4513 Planarity : 0.004 0.050 4950 Dihedral : 5.503 57.874 4423 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.62 % Allowed : 21.48 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3425 helix: 2.17 (0.20), residues: 665 sheet: -0.60 (0.17), residues: 932 loop : -0.96 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 983 TYR 0.021 0.001 TYR B 170 PHE 0.021 0.001 PHE B 168 TRP 0.056 0.001 TRP E 186 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00391 (28523) covalent geometry : angle 0.57877 (38779) SS BOND : bond 0.00218 ( 40) SS BOND : angle 0.92018 ( 80) hydrogen bonds : bond 0.03907 ( 1071) hydrogen bonds : angle 5.13452 ( 2958) link_BETA1-4 : bond 0.00570 ( 3) link_BETA1-4 : angle 4.83833 ( 9) link_NAG-ASN : bond 0.00401 ( 28) link_NAG-ASN : angle 2.49411 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 158 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.9001 (t0) cc_final: 0.8515 (t0) REVERT: A 41 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8733 (mttm) REVERT: A 128 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.8920 (mp) REVERT: A 170 TYR cc_start: 0.9264 (t80) cc_final: 0.8694 (t80) REVERT: A 456 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8901 (m-10) REVERT: A 581 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9384 (p) REVERT: A 740 MET cc_start: 0.8557 (tpt) cc_final: 0.8140 (tpt) REVERT: A 855 PHE cc_start: 0.8216 (m-10) cc_final: 0.7930 (m-10) REVERT: A 856 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8879 (p0) REVERT: A 869 MET cc_start: 0.9223 (mtm) cc_final: 0.8920 (mtm) REVERT: B 135 PHE cc_start: 0.8547 (m-10) cc_final: 0.8328 (m-80) REVERT: B 218 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8434 (mp10) REVERT: B 318 PHE cc_start: 0.8365 (t80) cc_final: 0.8048 (t80) REVERT: B 451 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6274 (p90) REVERT: B 456 PHE cc_start: 0.7741 (m-80) cc_final: 0.7211 (m-80) REVERT: B 508 TYR cc_start: 0.8478 (m-10) cc_final: 0.8212 (m-10) REVERT: B 568 ASP cc_start: 0.8733 (t0) cc_final: 0.8409 (p0) REVERT: C 104 TRP cc_start: 0.8780 (m-90) cc_final: 0.8265 (m-90) REVERT: C 131 CYS cc_start: 0.5113 (OUTLIER) cc_final: 0.4349 (m) REVERT: C 226 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8751 (mp) REVERT: C 740 MET cc_start: 0.8997 (tpt) cc_final: 0.8656 (tpp) REVERT: C 855 PHE cc_start: 0.8541 (m-10) cc_final: 0.8293 (m-10) REVERT: C 1041 ASP cc_start: 0.8970 (t0) cc_final: 0.8684 (t0) REVERT: D 115 MET cc_start: 0.8414 (tpp) cc_final: 0.8068 (tpp) REVERT: D 211 CYS cc_start: 0.7090 (t) cc_final: 0.6671 (t) REVERT: D 224 LYS cc_start: 0.2595 (OUTLIER) cc_final: 0.1906 (ptmm) REVERT: E 186 TRP cc_start: 0.4802 (OUTLIER) cc_final: 0.3696 (p-90) REVERT: F 99 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.5343 (m-80) REVERT: G 39 ILE cc_start: 0.9152 (mm) cc_final: 0.8608 (tp) REVERT: G 101 ARG cc_start: 0.9557 (tmm-80) cc_final: 0.9189 (tmm-80) REVERT: G 212 ASN cc_start: 0.5505 (OUTLIER) cc_final: 0.5154 (t0) outliers start: 81 outliers final: 65 residues processed: 232 average time/residue: 0.1615 time to fit residues: 62.5273 Evaluate side-chains 231 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 153 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 135 CYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 241 optimal weight: 0.0000 chunk 160 optimal weight: 4.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN B 437 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.094200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057162 restraints weight = 95263.699| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.65 r_work: 0.2859 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 28594 Z= 0.129 Angle : 0.577 13.338 38952 Z= 0.287 Chirality : 0.043 0.356 4513 Planarity : 0.004 0.063 4950 Dihedral : 5.250 57.034 4423 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.43 % Allowed : 21.93 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 3425 helix: 2.38 (0.20), residues: 659 sheet: -0.50 (0.17), residues: 936 loop : -0.90 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 983 TYR 0.020 0.001 TYR B 170 PHE 0.021 0.001 PHE C 238 TRP 0.055 0.001 TRP E 186 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00296 (28523) covalent geometry : angle 0.56202 (38779) SS BOND : bond 0.00200 ( 40) SS BOND : angle 0.84285 ( 80) hydrogen bonds : bond 0.03559 ( 1071) hydrogen bonds : angle 4.91564 ( 2958) link_BETA1-4 : bond 0.00662 ( 3) link_BETA1-4 : angle 4.68034 ( 9) link_NAG-ASN : bond 0.00383 ( 28) link_NAG-ASN : angle 2.30765 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 161 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8950 (t0) cc_final: 0.8444 (t0) REVERT: A 41 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8755 (mttm) REVERT: A 128 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8911 (mp) REVERT: A 170 TYR cc_start: 0.9276 (t80) cc_final: 0.8711 (t80) REVERT: A 410 ILE cc_start: 0.8997 (mt) cc_final: 0.8702 (mp) REVERT: A 456 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.8849 (m-10) REVERT: A 581 THR cc_start: 0.9576 (OUTLIER) cc_final: 0.9367 (p) REVERT: A 740 MET cc_start: 0.8489 (tpt) cc_final: 0.8008 (tpt) REVERT: A 855 PHE cc_start: 0.8206 (m-10) cc_final: 0.7892 (m-10) REVERT: A 856 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8952 (p0) REVERT: A 869 MET cc_start: 0.9199 (mtm) cc_final: 0.8906 (mtm) REVERT: B 135 PHE cc_start: 0.8536 (m-10) cc_final: 0.8323 (m-80) REVERT: B 218 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.9035 (mm-40) REVERT: B 220 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7562 (t80) REVERT: B 318 PHE cc_start: 0.8367 (t80) cc_final: 0.8052 (t80) REVERT: B 451 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6283 (p90) REVERT: B 456 PHE cc_start: 0.7728 (m-80) cc_final: 0.7203 (m-80) REVERT: B 508 TYR cc_start: 0.8345 (m-10) cc_final: 0.8070 (m-10) REVERT: B 950 ASP cc_start: 0.9282 (m-30) cc_final: 0.8987 (m-30) REVERT: B 983 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8230 (tmm160) REVERT: B 1029 MET cc_start: 0.9580 (tpp) cc_final: 0.9335 (ttm) REVERT: C 104 TRP cc_start: 0.8641 (m-90) cc_final: 0.8122 (m-90) REVERT: C 226 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8766 (mp) REVERT: C 242 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8373 (mm) REVERT: C 740 MET cc_start: 0.8941 (tpt) cc_final: 0.8597 (tpp) REVERT: C 855 PHE cc_start: 0.8582 (m-10) cc_final: 0.8317 (m-10) REVERT: C 1041 ASP cc_start: 0.8960 (t0) cc_final: 0.8659 (t0) REVERT: C 1115 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9099 (mm) REVERT: D 115 MET cc_start: 0.8342 (tpp) cc_final: 0.7979 (tpp) REVERT: D 211 CYS cc_start: 0.7060 (t) cc_final: 0.6583 (t) REVERT: D 216 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8363 (ptmm) REVERT: D 224 LYS cc_start: 0.2637 (OUTLIER) cc_final: 0.1984 (ptmm) REVERT: E 186 TRP cc_start: 0.4557 (OUTLIER) cc_final: 0.3493 (p-90) REVERT: F 99 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.5345 (m-80) REVERT: G 39 ILE cc_start: 0.9195 (mm) cc_final: 0.8628 (tp) REVERT: G 101 ARG cc_start: 0.9545 (tmm-80) cc_final: 0.9170 (tmm-80) outliers start: 75 outliers final: 56 residues processed: 229 average time/residue: 0.1640 time to fit residues: 62.5417 Evaluate side-chains 225 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 154 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 135 CYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 232 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 163 optimal weight: 0.0060 chunk 219 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 126 optimal weight: 0.0020 chunk 170 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 506 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.095166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058216 restraints weight = 95356.487| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.69 r_work: 0.2891 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28594 Z= 0.103 Angle : 0.557 12.019 38952 Z= 0.278 Chirality : 0.043 0.323 4513 Planarity : 0.004 0.049 4950 Dihedral : 5.025 56.117 4423 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 2.14 % Allowed : 22.42 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3425 helix: 2.47 (0.20), residues: 654 sheet: -0.35 (0.17), residues: 936 loop : -0.87 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 983 TYR 0.021 0.001 TYR B 170 PHE 0.020 0.001 PHE B 168 TRP 0.052 0.001 TRP E 186 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00231 (28523) covalent geometry : angle 0.54387 (38779) SS BOND : bond 0.00192 ( 40) SS BOND : angle 0.79619 ( 80) hydrogen bonds : bond 0.03327 ( 1071) hydrogen bonds : angle 4.75084 ( 2958) link_BETA1-4 : bond 0.00622 ( 3) link_BETA1-4 : angle 4.60798 ( 9) link_NAG-ASN : bond 0.00399 ( 28) link_NAG-ASN : angle 2.13725 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7387.18 seconds wall clock time: 127 minutes 5.44 seconds (7625.44 seconds total)