Starting phenix.real_space_refine on Thu Mar 5 22:59:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wg9_32481/03_2026/7wg9_32481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg9_32481/03_2026/7wg9_32481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wg9_32481/03_2026/7wg9_32481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg9_32481/03_2026/7wg9_32481.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wg9_32481/03_2026/7wg9_32481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg9_32481/03_2026/7wg9_32481.map" } resolution = 3.5 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16388 2.51 5 N 4228 2.21 5 O 5036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25769 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: "G" 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: "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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.90, per 1000 atoms: 0.23 Number of scatterers: 25769 At special positions: 0 Unit cell: (141.24, 146.59, 200.09, 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 117 16.00 O 5036 8.00 N 4228 7.00 C 16388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.04 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.02 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.02 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 280 " " NAG A1304 " - " ASN A 329 " " NAG A1305 " - " ASN A 341 " " NAG A1306 " - " ASN A 601 " " NAG A1307 " - " ASN A 614 " " NAG A1308 " - " ASN A 655 " " NAG A1309 " - " ASN A 707 " " NAG A1310 " - " ASN A1072 " " NAG A1311 " - " ASN A 163 " " NAG A1312 " - " ASN A 232 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 280 " " NAG B1304 " - " ASN B 329 " " NAG B1305 " - " ASN B 341 " " NAG B1306 " - " ASN B 614 " " NAG B1307 " - " ASN B 655 " " NAG B1308 " - " ASN B 707 " " NAG B1309 " - " ASN B1072 " " NAG B1310 " - " ASN B 163 " " NAG B1311 " - " ASN B 601 " " NAG B1312 " - " ASN B 232 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 280 " " NAG C1304 " - " ASN C 329 " " NAG C1305 " - " ASN C 341 " " NAG C1306 " - " ASN C 614 " " NAG C1307 " - " ASN C 655 " " NAG C1308 " - " ASN C1072 " " NAG C1309 " - " ASN C 163 " " NAG C1310 " - " ASN C 232 " " NAG C1311 " - " ASN C 601 " " NAG D 1 " - " ASN A 715 " " NAG E 1 " - " ASN A 799 " " NAG F 1 " - " ASN A1096 " " NAG G 1 " - " ASN A1132 " " NAG H 1 " - " ASN B 715 " " NAG I 1 " - " ASN B 799 " " NAG J 1 " - " ASN B1096 " " NAG K 1 " - " ASN B1132 " " NAG L 1 " - " ASN C 707 " " NAG M 1 " - " ASN C 715 " " NAG N 1 " - " ASN C 799 " " NAG O 1 " - " ASN C1096 " " NAG P 1 " - " ASN C1132 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 940.6 milliseconds 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 44 sheets defined 25.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.661A pdb=" N HIS A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.558A pdb=" N VAL A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.689A pdb=" N VAL A 618 " --> pdb=" O CYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 removed outlier: 3.891A pdb=" N TYR A 739 " --> pdb=" O ASP A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.748A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 848 through 853 removed outlier: 3.553A pdb=" N LYS A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 889 removed outlier: 4.146A pdb=" N ALA A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.879A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.866A pdb=" N VAL A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 Processing helix chain 'A' and resid 983 through 1032 removed outlier: 3.743A pdb=" N GLU A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1139 through 1146 removed outlier: 4.261A pdb=" N LEU A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.559A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.061A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 4.234A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 409 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 618 removed outlier: 3.606A pdb=" N VAL B 618 " --> pdb=" O CYS B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.564A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 848 through 855 removed outlier: 4.292A pdb=" N LYS B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 854 " --> pdb=" O ALA B 850 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 882 Processing helix chain 'B' and resid 895 through 908 Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.635A pdb=" N VAL B 913 " --> pdb=" O THR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 940 through 942 No H-bonds generated for 'chain 'B' and resid 940 through 942' Processing helix chain 'B' and resid 943 through 963 removed outlier: 4.339A pdb=" N VAL B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 982 Processing helix chain 'B' and resid 983 through 1030 removed outlier: 5.144A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1146 removed outlier: 4.655A pdb=" N GLU B1142 " --> pdb=" O PRO B1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.918A pdb=" N VAL C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 removed outlier: 3.738A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.503A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 5.133A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 741 removed outlier: 3.550A pdb=" N TYR C 739 " --> pdb=" O ASP C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 4.145A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 848 through 852 Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.506A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 908 removed outlier: 3.623A pdb=" N ILE C 907 " --> pdb=" O ARG C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.809A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.882A pdb=" N THR C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 942 No H-bonds generated for 'chain 'C' and resid 940 through 942' Processing helix chain 'C' and resid 943 through 963 removed outlier: 4.312A pdb=" N VAL C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.549A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 986 Processing helix chain 'C' and resid 987 through 1030 Processing helix chain 'C' and resid 1139 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.516A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 96 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN A 186 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 195 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE A 199 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP A 226 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE A 201 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.663A pdb=" N PHE A 43 " --> pdb=" O PHE B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.582A pdb=" N GLY A 107 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N VAL A 126 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N GLU A 167 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N ILE A 128 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR A 165 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL A 130 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASN A 163 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU A 132 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 161 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 312 Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 326 removed outlier: 3.508A pdb=" N ARG A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 removed outlier: 3.603A pdb=" N CYS A 430 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.694A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 654 removed outlier: 4.619A pdb=" N THR A 694 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.907A pdb=" N ALA A 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.828A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN A 715 " --> pdb=" O ALA A1068 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A1054 " --> pdb=" O GLY A1057 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.828A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN A 715 " --> pdb=" O ALA A1068 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 734 Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 4.391A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.661A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU B 96 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 225 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.610A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 317 removed outlier: 4.680A pdb=" N VAL B 593 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN B 315 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY B 591 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 611 " --> pdb=" O GLY B 592 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.726A pdb=" N ASN B 392 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 removed outlier: 7.327A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC6, first strand: chain 'B' and resid 471 through 472 removed outlier: 3.584A pdb=" N TYR B 471 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 487 " --> pdb=" O TYR B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 540 Processing sheet with id=AC8, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.022A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 709 through 713 Processing sheet with id=AD1, first strand: chain 'B' and resid 716 through 726 removed outlier: 3.559A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 732 through 734 Processing sheet with id=AD3, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.875A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.897A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 263 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 227 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 201 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 225 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.896A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.805A pdb=" N VAL C 130 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU C 132 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N GLN C 134 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N ASN C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 316 removed outlier: 4.651A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 648 " --> pdb=" O PHE C 641 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.527A pdb=" N ILE C 324 " --> pdb=" O ASN C 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 352 through 356 removed outlier: 3.900A pdb=" N ALA C 433 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR C 374 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE2, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE3, first strand: chain 'C' and resid 549 through 552 Processing sheet with id=AE4, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.084A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 668 " --> pdb=" O ILE C 664 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 709 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 726 removed outlier: 3.648A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE8, first strand: chain 'C' and resid 1092 through 1095 958 hydrogen bonds defined for protein. 2625 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: 6.00 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8186 1.34 - 1.47: 6584 1.47 - 1.59: 11424 1.59 - 1.71: 1 1.71 - 1.83: 147 Bond restraints: 26342 Sorted by residual: bond pdb=" CA LEU B 177 " pdb=" C LEU B 177 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.34e-02 5.57e+03 4.48e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" CB PRO C 525 " pdb=" CG PRO C 525 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.14e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 26337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 35097 1.97 - 3.93: 665 3.93 - 5.90: 53 5.90 - 7.86: 12 7.86 - 9.83: 3 Bond angle restraints: 35830 Sorted by residual: angle pdb=" CA TRP C 152 " pdb=" CB TRP C 152 " pdb=" CG TRP C 152 " ideal model delta sigma weight residual 113.60 120.35 -6.75 1.90e+00 2.77e-01 1.26e+01 angle pdb=" C ALA A 568 " pdb=" N ASP A 569 " pdb=" CA ASP A 569 " ideal model delta sigma weight residual 122.46 127.32 -4.86 1.41e+00 5.03e-01 1.19e+01 angle pdb=" C LYS B 97 " pdb=" N SER B 98 " pdb=" CA SER B 98 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.21e+00 angle pdb=" C ALA C 568 " pdb=" N ASP C 569 " pdb=" CA ASP C 569 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.52e+00 angle pdb=" CA CYS A 536 " pdb=" CB CYS A 536 " pdb=" SG CYS A 536 " ideal model delta sigma weight residual 114.40 121.10 -6.70 2.30e+00 1.89e-01 8.48e+00 ... (remaining 35825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.66: 15087 19.66 - 39.31: 1119 39.31 - 58.97: 226 58.97 - 78.62: 57 78.62 - 98.28: 17 Dihedral angle restraints: 16506 sinusoidal: 7233 harmonic: 9273 Sorted by residual: dihedral pdb=" CB CYS B 289 " pdb=" SG CYS B 289 " pdb=" SG CYS B 299 " pdb=" CB CYS B 299 " ideal model delta sinusoidal sigma weight residual -86.00 -4.64 -81.36 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS B 478 " pdb=" SG CYS B 478 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual 93.00 173.47 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 149.89 -56.89 1 1.00e+01 1.00e-02 4.36e+01 ... (remaining 16503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4135 0.112 - 0.225: 84 0.225 - 0.337: 3 0.337 - 0.449: 0 0.449 - 0.562: 1 Chirality restraints: 4223 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 707 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C1096 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C1132 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 4220 not shown) Planarity restraints: 4615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 227 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO C 228 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 206 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO B 207 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 227 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO B 228 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.030 5.00e-02 4.00e+02 ... (remaining 4612 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 632 2.69 - 3.25: 25204 3.25 - 3.80: 39060 3.80 - 4.35: 49159 4.35 - 4.90: 83638 Nonbonded interactions: 197693 Sorted by model distance: nonbonded pdb=" OG SER B 436 " pdb=" OD2 ASP B 440 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR A 391 " pdb=" O GLU A 514 " model vdw 2.161 3.040 nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.181 3.040 nonbonded pdb=" NH1 ARG C1017 " pdb=" OD1 ASN C1021 " model vdw 2.211 3.120 nonbonded pdb=" O ASP B 440 " pdb=" ND2 ASN B 446 " model vdw 2.212 3.120 ... (remaining 197688 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 14 through 1311) selection = (chain 'B' and resid 14 through 1311) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.020 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 26446 Z= 0.170 Angle : 0.647 19.948 36097 Z= 0.319 Chirality : 0.046 0.562 4223 Planarity : 0.004 0.073 4567 Dihedral : 14.257 98.277 10416 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3153 helix: 1.64 (0.21), residues: 662 sheet: -0.22 (0.20), residues: 625 loop : -1.62 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 326 TYR 0.019 0.001 TYR B 168 PHE 0.015 0.001 PHE A 390 TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00342 (26342) covalent geometry : angle 0.61479 (35830) SS BOND : bond 0.00296 ( 42) SS BOND : angle 1.00615 ( 84) hydrogen bonds : bond 0.14627 ( 947) hydrogen bonds : angle 6.79740 ( 2625) Misc. bond : bond 0.00132 ( 1) link_BETA1-4 : bond 0.00814 ( 13) link_BETA1-4 : angle 3.16607 ( 39) link_NAG-ASN : bond 0.00466 ( 48) link_NAG-ASN : angle 2.73988 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 0.816 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 118 LEU cc_start: 0.8813 (tp) cc_final: 0.8570 (tp) REVERT: A 168 TYR cc_start: 0.8385 (t80) cc_final: 0.8171 (t80) REVERT: A 554 ASN cc_start: 0.7887 (p0) cc_final: 0.7584 (p0) REVERT: A 582 ILE cc_start: 0.8426 (mm) cc_final: 0.8217 (mm) REVERT: A 882 SER cc_start: 0.9008 (m) cc_final: 0.8797 (p) REVERT: A 974 VAL cc_start: 0.8850 (t) cc_final: 0.8510 (t) REVERT: B 79 PHE cc_start: 0.6721 (t80) cc_final: 0.6376 (t80) REVERT: B 135 PHE cc_start: 0.8092 (m-80) cc_final: 0.7611 (m-80) REVERT: B 264 TYR cc_start: 0.6882 (m-80) cc_final: 0.6631 (m-80) REVERT: B 368 ASN cc_start: 0.8440 (m-40) cc_final: 0.7394 (p0) REVERT: B 386 ASN cc_start: 0.8020 (m-40) cc_final: 0.7584 (p0) REVERT: B 416 ILE cc_start: 0.8794 (pt) cc_final: 0.8513 (pt) REVERT: B 435 ASN cc_start: 0.7739 (t0) cc_final: 0.6771 (m-40) REVERT: B 491 GLN cc_start: 0.7412 (tm-30) cc_final: 0.7067 (tm-30) REVERT: B 527 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7680 (mtmt) REVERT: B 705 TYR cc_start: 0.7322 (t80) cc_final: 0.6742 (t80) REVERT: B 778 GLU cc_start: 0.7715 (tt0) cc_final: 0.7461 (pt0) REVERT: B 867 MET cc_start: 0.8509 (mtt) cc_final: 0.8257 (mtt) REVERT: B 915 TYR cc_start: 0.8543 (m-80) cc_final: 0.8211 (m-10) REVERT: B 1111 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8164 (mt0) REVERT: C 240 LEU cc_start: 0.7360 (pt) cc_final: 0.7052 (pp) REVERT: C 352 ASN cc_start: 0.7361 (t0) cc_final: 0.6433 (p0) REVERT: C 898 MET cc_start: 0.7490 (mtt) cc_final: 0.7241 (mtt) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.1643 time to fit residues: 128.7440 Evaluate side-chains 222 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN A 911 GLN A 933 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 205 HIS C 899 GLN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.174818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117327 restraints weight = 41236.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.117000 restraints weight = 23750.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116546 restraints weight = 17245.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117596 restraints weight = 17744.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117810 restraints weight = 14532.976| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26446 Z= 0.170 Angle : 0.681 18.827 36097 Z= 0.330 Chirality : 0.047 0.445 4223 Planarity : 0.004 0.059 4567 Dihedral : 8.235 77.869 4698 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.98 % Allowed : 8.56 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.71 (0.14), residues: 3153 helix: 2.04 (0.20), residues: 674 sheet: -0.24 (0.20), residues: 619 loop : -1.60 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 235 TYR 0.019 0.001 TYR C 506 PHE 0.020 0.002 PHE C 166 TRP 0.022 0.002 TRP B 434 HIS 0.009 0.001 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00402 (26342) covalent geometry : angle 0.64581 (35830) SS BOND : bond 0.00610 ( 42) SS BOND : angle 2.22396 ( 84) hydrogen bonds : bond 0.05571 ( 947) hydrogen bonds : angle 5.38282 ( 2625) Misc. bond : bond 0.00119 ( 1) link_BETA1-4 : bond 0.00606 ( 13) link_BETA1-4 : angle 2.64059 ( 39) link_NAG-ASN : bond 0.00446 ( 48) link_NAG-ASN : angle 2.75511 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6782 (mpp) cc_final: 0.5820 (pmm) REVERT: A 168 TYR cc_start: 0.8424 (t80) cc_final: 0.8061 (t80) REVERT: A 327 PHE cc_start: 0.7523 (m-10) cc_final: 0.7213 (m-10) REVERT: A 554 ASN cc_start: 0.8060 (p0) cc_final: 0.7771 (p0) REVERT: A 673 GLN cc_start: 0.6819 (tp40) cc_final: 0.6607 (pt0) REVERT: A 853 PHE cc_start: 0.7847 (m-10) cc_final: 0.7510 (m-80) REVERT: A 882 SER cc_start: 0.9172 (m) cc_final: 0.8924 (p) REVERT: A 952 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: A 975 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7548 (mp) REVERT: A 1029 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: B 135 PHE cc_start: 0.7943 (m-80) cc_final: 0.7206 (m-80) REVERT: B 189 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: B 264 TYR cc_start: 0.6608 (m-80) cc_final: 0.6320 (m-80) REVERT: B 527 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7680 (mtmt) REVERT: B 705 TYR cc_start: 0.7769 (t80) cc_final: 0.7230 (t80) REVERT: B 915 TYR cc_start: 0.8687 (m-80) cc_final: 0.8155 (m-10) REVERT: B 974 VAL cc_start: 0.8548 (t) cc_final: 0.8295 (t) REVERT: B 1111 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8167 (mt0) REVERT: C 168 TYR cc_start: 0.6926 (t80) cc_final: 0.6658 (t80) REVERT: C 240 LEU cc_start: 0.7891 (pt) cc_final: 0.7649 (pp) REVERT: C 352 ASN cc_start: 0.7345 (t0) cc_final: 0.6311 (p0) REVERT: C 376 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8558 (ttpp) REVERT: C 557 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7243 (t80) REVERT: C 898 MET cc_start: 0.7793 (mtt) cc_final: 0.7563 (mtt) REVERT: C 902 TYR cc_start: 0.7036 (m-10) cc_final: 0.6825 (m-10) outliers start: 55 outliers final: 34 residues processed: 294 average time/residue: 0.1620 time to fit residues: 78.1182 Evaluate side-chains 243 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 557 PHE Chi-restraints excluded: chain C residue 919 LYS Chi-restraints excluded: chain C residue 962 LYS Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1008 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 134 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 210 optimal weight: 0.7980 chunk 265 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 297 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN A 933 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 ASN C 924 GLN C1086 HIS ** C1099 HIS ** 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 = 0.4190 r_free = 0.4190 target = 0.170608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108697 restraints weight = 41132.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110462 restraints weight = 24464.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111116 restraints weight = 15480.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112050 restraints weight = 15770.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112108 restraints weight = 14067.541| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 26446 Z= 0.214 Angle : 0.685 18.951 36097 Z= 0.336 Chirality : 0.047 0.443 4223 Planarity : 0.005 0.068 4567 Dihedral : 7.633 67.795 4698 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.80 % Allowed : 11.72 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.84 (0.14), residues: 3153 helix: 1.83 (0.20), residues: 669 sheet: -0.19 (0.21), residues: 578 loop : -1.65 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 903 TYR 0.019 0.001 TYR B1065 PHE 0.026 0.002 PHE C 560 TRP 0.015 0.002 TRP C 434 HIS 0.009 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00523 (26342) covalent geometry : angle 0.65260 (35830) SS BOND : bond 0.00549 ( 42) SS BOND : angle 1.70501 ( 84) hydrogen bonds : bond 0.06075 ( 947) hydrogen bonds : angle 5.35271 ( 2625) Misc. bond : bond 0.00103 ( 1) link_BETA1-4 : bond 0.00804 ( 13) link_BETA1-4 : angle 2.69078 ( 39) link_NAG-ASN : bond 0.00448 ( 48) link_NAG-ASN : angle 2.83332 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 220 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8881 (mm) cc_final: 0.8552 (mt) REVERT: A 168 TYR cc_start: 0.8517 (t80) cc_final: 0.7950 (t80) REVERT: A 327 PHE cc_start: 0.7660 (m-10) cc_final: 0.7451 (m-10) REVERT: A 882 SER cc_start: 0.9238 (m) cc_final: 0.9008 (p) REVERT: A 952 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: A 1029 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: B 135 PHE cc_start: 0.8061 (m-80) cc_final: 0.7357 (m-80) REVERT: B 200 LYS cc_start: 0.7233 (mttp) cc_final: 0.6881 (mtmt) REVERT: B 264 TYR cc_start: 0.6423 (m-80) cc_final: 0.6183 (m-80) REVERT: B 415 LYS cc_start: 0.9079 (mttt) cc_final: 0.8825 (mmmt) REVERT: B 527 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7679 (mtmm) REVERT: B 853 PHE cc_start: 0.7261 (m-10) cc_final: 0.6927 (m-10) REVERT: B 867 MET cc_start: 0.8810 (mtt) cc_final: 0.8529 (mtm) REVERT: B 876 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 955 GLN cc_start: 0.8347 (tp40) cc_final: 0.8016 (tt0) REVERT: B 977 ASP cc_start: 0.7851 (t0) cc_final: 0.7578 (t0) REVERT: B 1029 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: B 1111 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8184 (mt0) REVERT: C 168 TYR cc_start: 0.7058 (t80) cc_final: 0.6755 (t80) REVERT: C 240 LEU cc_start: 0.7676 (pt) cc_final: 0.7464 (pp) REVERT: C 325 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7998 (t) REVERT: C 390 PHE cc_start: 0.8866 (m-80) cc_final: 0.8650 (m-80) REVERT: C 547 THR cc_start: 0.8490 (p) cc_final: 0.8253 (p) REVERT: C 576 ASP cc_start: 0.8126 (t0) cc_final: 0.7710 (t0) REVERT: C 880 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8757 (mp) REVERT: C 902 TYR cc_start: 0.7318 (m-10) cc_final: 0.7088 (m-10) REVERT: C 1048 MET cc_start: 0.8312 (ptt) cc_final: 0.8022 (ptt) outliers start: 78 outliers final: 44 residues processed: 277 average time/residue: 0.1518 time to fit residues: 69.3256 Evaluate side-chains 243 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 773 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 996 THR Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 560 PHE Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1029 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 2.9990 chunk 168 optimal weight: 0.0170 chunk 56 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 239 optimal weight: 0.0670 chunk 93 optimal weight: 0.5980 overall best weight: 1.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN C 49 HIS C 66 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 GLN C1008 GLN ** C1099 HIS ** 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 = 0.4194 r_free = 0.4194 target = 0.171033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107503 restraints weight = 40980.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112343 restraints weight = 21636.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112821 restraints weight = 14284.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113736 restraints weight = 12692.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113924 restraints weight = 11674.556| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26446 Z= 0.162 Angle : 0.636 18.895 36097 Z= 0.308 Chirality : 0.046 0.441 4223 Planarity : 0.004 0.068 4567 Dihedral : 7.263 60.904 4698 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.88 % Allowed : 13.59 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.72 (0.14), residues: 3153 helix: 2.02 (0.20), residues: 659 sheet: -0.04 (0.21), residues: 594 loop : -1.64 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1017 TYR 0.017 0.001 TYR B1065 PHE 0.022 0.002 PHE C 560 TRP 0.013 0.001 TRP C 434 HIS 0.010 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00391 (26342) covalent geometry : angle 0.60296 (35830) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.54688 ( 84) hydrogen bonds : bond 0.05433 ( 947) hydrogen bonds : angle 5.16770 ( 2625) Misc. bond : bond 0.00075 ( 1) link_BETA1-4 : bond 0.00674 ( 13) link_BETA1-4 : angle 2.73262 ( 39) link_NAG-ASN : bond 0.00433 ( 48) link_NAG-ASN : angle 2.74175 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 213 time to evaluate : 0.979 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 128 ILE cc_start: 0.8824 (mm) cc_final: 0.8520 (mt) REVERT: A 153 MET cc_start: 0.6381 (mpp) cc_final: 0.5788 (pmm) REVERT: A 168 TYR cc_start: 0.8556 (t80) cc_final: 0.8100 (t80) REVERT: A 882 SER cc_start: 0.9211 (m) cc_final: 0.8975 (p) REVERT: A 952 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: A 1029 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: B 135 PHE cc_start: 0.8133 (m-80) cc_final: 0.7460 (m-80) REVERT: B 200 LYS cc_start: 0.7139 (mttp) cc_final: 0.6782 (mtmt) REVERT: B 423 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7344 (mp) REVERT: B 527 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7740 (mttp) REVERT: B 955 GLN cc_start: 0.8356 (tp40) cc_final: 0.7994 (tt0) REVERT: B 977 ASP cc_start: 0.8021 (t0) cc_final: 0.7729 (t0) REVERT: B 1029 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: B 1111 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8162 (mt0) REVERT: C 168 TYR cc_start: 0.6960 (t80) cc_final: 0.6650 (t80) REVERT: C 240 LEU cc_start: 0.7876 (pt) cc_final: 0.7645 (pp) REVERT: C 327 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.5454 (t80) REVERT: C 547 THR cc_start: 0.8478 (p) cc_final: 0.8241 (p) REVERT: C 576 ASP cc_start: 0.8165 (t0) cc_final: 0.7724 (t0) REVERT: C 880 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8744 (mp) REVERT: C 1048 MET cc_start: 0.8337 (ptt) cc_final: 0.8122 (ptt) outliers start: 80 outliers final: 40 residues processed: 272 average time/residue: 0.1518 time to fit residues: 68.5527 Evaluate side-chains 242 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 773 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN Chi-restraints excluded: chain C residue 1008 GLN Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1029 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 234 optimal weight: 30.0000 chunk 67 optimal weight: 0.8980 chunk 217 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 118 optimal weight: 0.0670 chunk 218 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS B 149 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN C 49 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.172558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115123 restraints weight = 40953.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114801 restraints weight = 22557.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114277 restraints weight = 16757.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115037 restraints weight = 17756.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115526 restraints weight = 14940.306| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26446 Z= 0.117 Angle : 0.605 18.740 36097 Z= 0.291 Chirality : 0.045 0.440 4223 Planarity : 0.004 0.068 4567 Dihedral : 6.912 57.736 4698 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.37 % Allowed : 14.81 % Favored : 82.81 % 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: -0.53 (0.15), residues: 3153 helix: 2.28 (0.20), residues: 664 sheet: 0.02 (0.21), residues: 590 loop : -1.54 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 188 TYR 0.015 0.001 TYR B1065 PHE 0.022 0.001 PHE C 560 TRP 0.013 0.001 TRP C 434 HIS 0.012 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00267 (26342) covalent geometry : angle 0.57415 (35830) SS BOND : bond 0.00305 ( 42) SS BOND : angle 1.25182 ( 84) hydrogen bonds : bond 0.04731 ( 947) hydrogen bonds : angle 4.98535 ( 2625) Misc. bond : bond 0.00055 ( 1) link_BETA1-4 : bond 0.00784 ( 13) link_BETA1-4 : angle 2.70258 ( 39) link_NAG-ASN : bond 0.00440 ( 48) link_NAG-ASN : angle 2.63543 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.788 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 128 ILE cc_start: 0.8890 (mm) cc_final: 0.8552 (mt) REVERT: A 153 MET cc_start: 0.6375 (mpp) cc_final: 0.6140 (pmm) REVERT: A 168 TYR cc_start: 0.8615 (t80) cc_final: 0.8175 (t80) REVERT: A 853 PHE cc_start: 0.7768 (m-80) cc_final: 0.7365 (m-80) REVERT: A 882 SER cc_start: 0.9199 (m) cc_final: 0.8950 (p) REVERT: A 952 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: A 1029 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: B 135 PHE cc_start: 0.8059 (m-80) cc_final: 0.7462 (m-80) REVERT: B 200 LYS cc_start: 0.7138 (mttp) cc_final: 0.6798 (mtmt) REVERT: B 527 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7744 (mttp) REVERT: B 579 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8352 (p) REVERT: B 867 MET cc_start: 0.8770 (mtt) cc_final: 0.8535 (mtm) REVERT: B 955 GLN cc_start: 0.8312 (tp40) cc_final: 0.8026 (tt0) REVERT: B 986 GLU cc_start: 0.7562 (tp30) cc_final: 0.7229 (tp30) REVERT: B 1029 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: B 1111 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8125 (mt0) REVERT: C 168 TYR cc_start: 0.7154 (t80) cc_final: 0.6841 (t80) REVERT: C 240 LEU cc_start: 0.7957 (pt) cc_final: 0.7748 (pp) REVERT: C 327 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.5556 (t80) REVERT: C 352 ASN cc_start: 0.7111 (t0) cc_final: 0.6904 (t0) REVERT: C 547 THR cc_start: 0.8484 (p) cc_final: 0.8251 (p) REVERT: C 576 ASP cc_start: 0.8206 (t0) cc_final: 0.7749 (t0) REVERT: C 880 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8758 (mp) REVERT: C 1048 MET cc_start: 0.8073 (ptt) cc_final: 0.7864 (ptt) outliers start: 66 outliers final: 37 residues processed: 256 average time/residue: 0.1538 time to fit residues: 64.5102 Evaluate side-chains 239 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1028 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 16 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 34 optimal weight: 30.0000 chunk 136 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 924 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C1008 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.171062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113696 restraints weight = 40991.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112749 restraints weight = 23333.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112478 restraints weight = 18314.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113047 restraints weight = 17050.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113280 restraints weight = 15584.374| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26446 Z= 0.157 Angle : 0.625 18.557 36097 Z= 0.301 Chirality : 0.045 0.449 4223 Planarity : 0.004 0.071 4567 Dihedral : 6.754 57.924 4698 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.55 % Allowed : 15.03 % Favored : 82.42 % 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: 3153 helix: 2.19 (0.20), residues: 664 sheet: -0.02 (0.21), residues: 608 loop : -1.55 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 188 TYR 0.016 0.001 TYR B1065 PHE 0.022 0.001 PHE C 560 TRP 0.012 0.001 TRP C 434 HIS 0.009 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00382 (26342) covalent geometry : angle 0.59452 (35830) SS BOND : bond 0.00332 ( 42) SS BOND : angle 1.35894 ( 84) hydrogen bonds : bond 0.05168 ( 947) hydrogen bonds : angle 5.02449 ( 2625) Misc. bond : bond 0.00058 ( 1) link_BETA1-4 : bond 0.00764 ( 13) link_BETA1-4 : angle 2.69781 ( 39) link_NAG-ASN : bond 0.00415 ( 48) link_NAG-ASN : angle 2.64068 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 203 time to evaluate : 0.919 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: A 128 ILE cc_start: 0.8906 (mm) cc_final: 0.8594 (mt) REVERT: A 168 TYR cc_start: 0.8672 (t80) cc_final: 0.8187 (t80) REVERT: A 853 PHE cc_start: 0.7770 (m-80) cc_final: 0.7363 (m-80) REVERT: A 882 SER cc_start: 0.9213 (m) cc_final: 0.8991 (p) REVERT: A 952 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: A 1029 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: B 135 PHE cc_start: 0.8045 (m-80) cc_final: 0.7420 (m-80) REVERT: B 200 LYS cc_start: 0.7107 (mttp) cc_final: 0.6770 (mtmt) REVERT: B 527 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7706 (mttp) REVERT: B 579 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.7446 (p) REVERT: B 785 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: B 955 GLN cc_start: 0.8338 (tp40) cc_final: 0.8019 (tt0) REVERT: B 982 LEU cc_start: 0.8560 (mp) cc_final: 0.8330 (mt) REVERT: B 986 GLU cc_start: 0.7560 (tp30) cc_final: 0.7304 (tp30) REVERT: B 1029 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: B 1111 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8125 (mt0) REVERT: C 168 TYR cc_start: 0.7297 (t80) cc_final: 0.6988 (t80) REVERT: C 240 LEU cc_start: 0.8047 (pt) cc_final: 0.7828 (pp) REVERT: C 327 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.5669 (t80) REVERT: C 352 ASN cc_start: 0.7091 (t0) cc_final: 0.6858 (t0) REVERT: C 547 THR cc_start: 0.8598 (p) cc_final: 0.8371 (p) REVERT: C 576 ASP cc_start: 0.8265 (t0) cc_final: 0.7779 (t0) REVERT: C 880 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8747 (mp) REVERT: C 1048 MET cc_start: 0.8267 (ptt) cc_final: 0.7989 (ptt) outliers start: 71 outliers final: 49 residues processed: 256 average time/residue: 0.1444 time to fit residues: 61.8972 Evaluate side-chains 256 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 236 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 313 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 15 optimal weight: 0.0000 chunk 257 optimal weight: 0.0020 chunk 143 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** C1099 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 = 0.4220 r_free = 0.4220 target = 0.173331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116047 restraints weight = 40796.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115447 restraints weight = 22925.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115546 restraints weight = 16691.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116142 restraints weight = 16451.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116407 restraints weight = 14880.592| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26446 Z= 0.106 Angle : 0.594 18.527 36097 Z= 0.283 Chirality : 0.044 0.449 4223 Planarity : 0.004 0.072 4567 Dihedral : 6.483 57.779 4698 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.09 % Allowed : 16.25 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3153 helix: 2.46 (0.20), residues: 666 sheet: 0.09 (0.21), residues: 589 loop : -1.44 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 188 TYR 0.015 0.001 TYR B1065 PHE 0.020 0.001 PHE C 560 TRP 0.013 0.001 TRP C 64 HIS 0.008 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00236 (26342) covalent geometry : angle 0.56430 (35830) SS BOND : bond 0.00262 ( 42) SS BOND : angle 1.07542 ( 84) hydrogen bonds : bond 0.04376 ( 947) hydrogen bonds : angle 4.83269 ( 2625) Misc. bond : bond 0.00036 ( 1) link_BETA1-4 : bond 0.00798 ( 13) link_BETA1-4 : angle 2.70083 ( 39) link_NAG-ASN : bond 0.00446 ( 48) link_NAG-ASN : angle 2.55180 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 0.904 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 128 ILE cc_start: 0.8894 (mm) cc_final: 0.8592 (mt) REVERT: A 153 MET cc_start: 0.6434 (pmm) cc_final: 0.5468 (pmm) REVERT: A 168 TYR cc_start: 0.8731 (t80) cc_final: 0.8302 (t80) REVERT: A 853 PHE cc_start: 0.7749 (m-80) cc_final: 0.7333 (m-80) REVERT: A 882 SER cc_start: 0.9175 (m) cc_final: 0.8937 (p) REVERT: A 952 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: A 1029 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: B 135 PHE cc_start: 0.7921 (m-80) cc_final: 0.7308 (m-80) REVERT: B 200 LYS cc_start: 0.7084 (mttp) cc_final: 0.6765 (mtmt) REVERT: B 527 LYS cc_start: 0.7886 (mmtm) cc_final: 0.7643 (mttp) REVERT: B 955 GLN cc_start: 0.8264 (tp40) cc_final: 0.7869 (tt0) REVERT: B 982 LEU cc_start: 0.8397 (mp) cc_final: 0.8142 (mt) REVERT: B 986 GLU cc_start: 0.7524 (tp30) cc_final: 0.7257 (tp30) REVERT: B 1029 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: B 1111 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8102 (mt0) REVERT: C 168 TYR cc_start: 0.7323 (t80) cc_final: 0.7013 (t80) REVERT: C 240 LEU cc_start: 0.8033 (pt) cc_final: 0.7810 (pp) REVERT: C 327 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.5845 (t80) REVERT: C 352 ASN cc_start: 0.7230 (t0) cc_final: 0.6969 (t0) REVERT: C 547 THR cc_start: 0.8587 (p) cc_final: 0.8362 (p) REVERT: C 576 ASP cc_start: 0.8305 (t0) cc_final: 0.7935 (t0) REVERT: C 880 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8722 (mp) REVERT: C 1048 MET cc_start: 0.8029 (ptt) cc_final: 0.7786 (ptt) outliers start: 58 outliers final: 39 residues processed: 254 average time/residue: 0.1472 time to fit residues: 62.7380 Evaluate side-chains 242 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 71 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 201 optimal weight: 0.4980 chunk 277 optimal weight: 0.0970 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 41 optimal weight: 40.0000 chunk 314 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 924 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 HIS ** 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 = 0.4199 r_free = 0.4199 target = 0.171349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.114102 restraints weight = 40919.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113335 restraints weight = 22682.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112914 restraints weight = 17288.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113714 restraints weight = 17794.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114015 restraints weight = 14966.612| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26446 Z= 0.145 Angle : 0.621 18.308 36097 Z= 0.297 Chirality : 0.045 0.458 4223 Planarity : 0.004 0.069 4567 Dihedral : 6.444 57.977 4698 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.09 % Allowed : 16.79 % Favored : 81.12 % 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: -0.40 (0.15), residues: 3153 helix: 2.36 (0.20), residues: 666 sheet: 0.14 (0.21), residues: 601 loop : -1.47 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1012 TYR 0.016 0.001 TYR B1065 PHE 0.025 0.001 PHE A 372 TRP 0.013 0.001 TRP C 434 HIS 0.007 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00349 (26342) covalent geometry : angle 0.59180 (35830) SS BOND : bond 0.00328 ( 42) SS BOND : angle 1.23572 ( 84) hydrogen bonds : bond 0.04918 ( 947) hydrogen bonds : angle 4.89530 ( 2625) Misc. bond : bond 0.00051 ( 1) link_BETA1-4 : bond 0.00763 ( 13) link_BETA1-4 : angle 2.68240 ( 39) link_NAG-ASN : bond 0.00408 ( 48) link_NAG-ASN : angle 2.55846 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8909 (mm) cc_final: 0.8606 (mt) REVERT: A 153 MET cc_start: 0.6508 (pmm) cc_final: 0.6152 (pmm) REVERT: A 154 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.4962 (tm-30) REVERT: A 168 TYR cc_start: 0.8748 (t80) cc_final: 0.8265 (t80) REVERT: A 175 MET cc_start: 0.5724 (ttt) cc_final: 0.4697 (tpt) REVERT: A 853 PHE cc_start: 0.7663 (m-80) cc_final: 0.7272 (m-80) REVERT: A 882 SER cc_start: 0.9206 (m) cc_final: 0.8970 (p) REVERT: A 952 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7543 (mt0) REVERT: A 1029 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: B 135 PHE cc_start: 0.7944 (m-80) cc_final: 0.7360 (m-80) REVERT: B 527 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7646 (mttp) REVERT: B 579 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 982 LEU cc_start: 0.8479 (mp) cc_final: 0.8230 (mt) REVERT: B 986 GLU cc_start: 0.7585 (tp30) cc_final: 0.7301 (tp30) REVERT: B 1029 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: B 1111 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8117 (mt0) REVERT: C 168 TYR cc_start: 0.7418 (t80) cc_final: 0.7121 (t80) REVERT: C 240 LEU cc_start: 0.8069 (pt) cc_final: 0.7846 (pp) REVERT: C 327 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.5983 (t80) REVERT: C 352 ASN cc_start: 0.7277 (t0) cc_final: 0.7024 (t0) REVERT: C 547 THR cc_start: 0.8649 (p) cc_final: 0.8428 (p) REVERT: C 576 ASP cc_start: 0.8305 (t0) cc_final: 0.7928 (t0) REVERT: C 880 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8702 (mp) REVERT: C 1048 MET cc_start: 0.8209 (ptt) cc_final: 0.7967 (ptt) outliers start: 58 outliers final: 44 residues processed: 248 average time/residue: 0.1531 time to fit residues: 63.5176 Evaluate side-chains 250 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 143 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 190 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 171 GLN A 933 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.174806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113908 restraints weight = 40998.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.116391 restraints weight = 28097.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116878 restraints weight = 17934.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117217 restraints weight = 16578.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117499 restraints weight = 15877.966| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26446 Z= 0.164 Angle : 0.634 18.331 36097 Z= 0.307 Chirality : 0.046 0.466 4223 Planarity : 0.004 0.066 4567 Dihedral : 6.460 57.995 4698 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.19 % Allowed : 17.04 % Favored : 80.76 % 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: -0.49 (0.15), residues: 3153 helix: 2.26 (0.20), residues: 666 sheet: 0.07 (0.21), residues: 616 loop : -1.52 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.016 0.001 TYR B1065 PHE 0.033 0.002 PHE A 372 TRP 0.013 0.001 TRP C 434 HIS 0.007 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00396 (26342) covalent geometry : angle 0.60559 (35830) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.29786 ( 84) hydrogen bonds : bond 0.05168 ( 947) hydrogen bonds : angle 4.95643 ( 2625) Misc. bond : bond 0.00049 ( 1) link_BETA1-4 : bond 0.00747 ( 13) link_BETA1-4 : angle 2.69902 ( 39) link_NAG-ASN : bond 0.00412 ( 48) link_NAG-ASN : angle 2.57139 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 0.903 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: A 128 ILE cc_start: 0.8950 (mm) cc_final: 0.8662 (mt) REVERT: A 134 GLN cc_start: 0.7877 (tp-100) cc_final: 0.7309 (tm-30) REVERT: A 168 TYR cc_start: 0.8829 (t80) cc_final: 0.8368 (t80) REVERT: A 882 SER cc_start: 0.9229 (m) cc_final: 0.9013 (p) REVERT: A 1029 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: B 135 PHE cc_start: 0.7907 (m-80) cc_final: 0.7310 (m-80) REVERT: B 175 MET cc_start: 0.3433 (pmm) cc_final: 0.2250 (pmm) REVERT: B 527 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7798 (mtmm) REVERT: B 579 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8107 (p) REVERT: B 982 LEU cc_start: 0.8574 (mp) cc_final: 0.8331 (mt) REVERT: B 986 GLU cc_start: 0.7634 (tp30) cc_final: 0.7334 (tp30) REVERT: B 1029 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: B 1111 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8148 (mt0) REVERT: C 49 HIS cc_start: 0.8001 (t-170) cc_final: 0.7674 (t70) REVERT: C 168 TYR cc_start: 0.7413 (t80) cc_final: 0.7126 (t80) REVERT: C 240 LEU cc_start: 0.8030 (pt) cc_final: 0.7801 (pp) REVERT: C 327 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.5954 (t80) REVERT: C 352 ASN cc_start: 0.7208 (t0) cc_final: 0.6947 (t0) REVERT: C 562 GLN cc_start: 0.7132 (mp10) cc_final: 0.6700 (mp10) REVERT: C 576 ASP cc_start: 0.8356 (t0) cc_final: 0.7991 (t0) REVERT: C 880 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8760 (mp) REVERT: C 1048 MET cc_start: 0.8254 (ptt) cc_final: 0.8018 (ptt) outliers start: 61 outliers final: 50 residues processed: 250 average time/residue: 0.1437 time to fit residues: 60.2925 Evaluate side-chains 254 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 244 optimal weight: 10.0000 chunk 314 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 44 optimal weight: 40.0000 chunk 203 optimal weight: 0.8980 chunk 282 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 140 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C1099 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 = 0.4216 r_free = 0.4216 target = 0.173610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112591 restraints weight = 40808.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115525 restraints weight = 24376.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116144 restraints weight = 16001.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116446 restraints weight = 14268.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116647 restraints weight = 14138.498| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26446 Z= 0.112 Angle : 0.605 17.979 36097 Z= 0.289 Chirality : 0.045 0.453 4223 Planarity : 0.004 0.077 4567 Dihedral : 6.271 57.841 4698 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.98 % Allowed : 17.12 % Favored : 80.91 % 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: -0.34 (0.15), residues: 3153 helix: 2.47 (0.20), residues: 667 sheet: 0.10 (0.21), residues: 617 loop : -1.44 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.015 0.001 TYR B1065 PHE 0.035 0.001 PHE A 372 TRP 0.012 0.001 TRP C 64 HIS 0.007 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00257 (26342) covalent geometry : angle 0.57737 (35830) SS BOND : bond 0.00304 ( 42) SS BOND : angle 1.07477 ( 84) hydrogen bonds : bond 0.04436 ( 947) hydrogen bonds : angle 4.79663 ( 2625) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.00769 ( 13) link_BETA1-4 : angle 2.70477 ( 39) link_NAG-ASN : bond 0.00429 ( 48) link_NAG-ASN : angle 2.46979 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.842 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: A 134 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7160 (tm-30) REVERT: A 168 TYR cc_start: 0.8832 (t80) cc_final: 0.8405 (t80) REVERT: A 853 PHE cc_start: 0.7639 (m-10) cc_final: 0.7252 (m-80) REVERT: A 882 SER cc_start: 0.9191 (m) cc_final: 0.8964 (p) REVERT: A 1029 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: B 135 PHE cc_start: 0.7916 (m-80) cc_final: 0.7289 (m-80) REVERT: B 439 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8660 (pt) REVERT: B 527 LYS cc_start: 0.7889 (mmtm) cc_final: 0.7657 (mtmm) REVERT: B 579 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8143 (p) REVERT: B 853 PHE cc_start: 0.7232 (m-10) cc_final: 0.7022 (m-10) REVERT: B 986 GLU cc_start: 0.7532 (tp30) cc_final: 0.7199 (tp30) REVERT: B 1029 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 1111 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8119 (mt0) REVERT: C 49 HIS cc_start: 0.7905 (t-170) cc_final: 0.7618 (t70) REVERT: C 168 TYR cc_start: 0.7364 (t80) cc_final: 0.7071 (t80) REVERT: C 240 LEU cc_start: 0.8042 (pt) cc_final: 0.7811 (pp) REVERT: C 327 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6163 (t80) REVERT: C 352 ASN cc_start: 0.7399 (t0) cc_final: 0.7138 (t0) REVERT: C 376 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8628 (ttpp) REVERT: C 562 GLN cc_start: 0.7187 (mp10) cc_final: 0.6764 (mp10) REVERT: C 563 PHE cc_start: 0.6754 (m-10) cc_final: 0.6502 (m-80) REVERT: C 576 ASP cc_start: 0.8290 (t0) cc_final: 0.7924 (t0) REVERT: C 880 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8728 (mp) REVERT: C 1048 MET cc_start: 0.8254 (ptt) cc_final: 0.7985 (ptt) outliers start: 55 outliers final: 42 residues processed: 255 average time/residue: 0.1433 time to fit residues: 61.1662 Evaluate side-chains 247 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 280 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 227 optimal weight: 0.0050 chunk 31 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 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 = 0.4196 r_free = 0.4196 target = 0.171840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111073 restraints weight = 40672.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113111 restraints weight = 28420.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113249 restraints weight = 17291.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113605 restraints weight = 16563.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113818 restraints weight = 15736.350| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26446 Z= 0.150 Angle : 0.626 17.932 36097 Z= 0.302 Chirality : 0.045 0.463 4223 Planarity : 0.004 0.074 4567 Dihedral : 6.318 57.985 4698 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.05 % Allowed : 17.37 % Favored : 80.58 % 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: -0.43 (0.15), residues: 3153 helix: 2.32 (0.20), residues: 667 sheet: 0.07 (0.20), residues: 624 loop : -1.47 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1105 TYR 0.015 0.001 TYR B1065 PHE 0.042 0.001 PHE A 372 TRP 0.013 0.001 TRP A 434 HIS 0.007 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00363 (26342) covalent geometry : angle 0.59885 (35830) SS BOND : bond 0.00318 ( 42) SS BOND : angle 1.22814 ( 84) hydrogen bonds : bond 0.04976 ( 947) hydrogen bonds : angle 4.87691 ( 2625) Misc. bond : bond 0.00042 ( 1) link_BETA1-4 : bond 0.00746 ( 13) link_BETA1-4 : angle 2.67028 ( 39) link_NAG-ASN : bond 0.00407 ( 48) link_NAG-ASN : angle 2.51209 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4168.83 seconds wall clock time: 72 minutes 56.62 seconds (4376.62 seconds total)