Starting phenix.real_space_refine on Sun Jul 5 06:07:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wg9_32481/07_2026/7wg9_32481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg9_32481/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wg9_32481/07_2026/7wg9_32481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg9_32481/07_2026/7wg9_32481.map" model { file = "/net/cci-nas-00/data/ceres_data/7wg9_32481/07_2026/7wg9_32481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg9_32481/07_2026/7wg9_32481.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wg9_32481/07_2026/7wg9_32481.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wg9_32481/07_2026/7wg9_32481.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 5.85, 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: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 6.45 Time building geometry restraints manager: 3.38 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 - 17.69: 13737 17.69 - 35.38: 1187 35.38 - 53.07: 218 53.07 - 70.76: 59 70.76 - 88.45: 24 Dihedral angle restraints: 15225 sinusoidal: 5952 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 15222 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 25.960 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 13.911 88.449 9135 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/Z covalent geometry : bond 0.00342 / 0.17 (26342) covalent geometry : angle 0.61479 / 0.31 (35830) SS BOND : bond 0.00296 / 0.19 ( 42) SS BOND : angle 1.00615 / 0.73 ( 84) hydrogen bonds : bond 0.14627 / 9.04 ( 947) hydrogen bonds : angle 6.79740 / 4.68 ( 2625) Misc. bond : bond 0.00132 / 0.07 ( 1) link_BETA1-4 : bond 0.00814 / 0.53 ( 13) link_BETA1-4 : angle 3.16607 / 2.13 ( 39) link_NAG-ASN : bond 0.00466 / 0.36 ( 48) link_NAG-ASN : angle 2.73988 / 2.01 ( 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 : 0.873 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: 0.1715 time to fit residues: 134.4217 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 : 0.804 ------------------------------------------------------------------------------- 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... ** 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117746 restraints weight = 41233.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.117353 restraints weight = 23450.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117175 restraints weight = 17203.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117755 restraints weight = 17009.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118058 restraints weight = 15311.806| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26446 Z= 0.169 Angle : 0.678 18.665 36097 Z= 0.330 Chirality : 0.047 0.430 4223 Planarity : 0.004 0.058 4567 Dihedral : 4.483 31.494 3417 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.98 % Allowed : 8.81 % Favored : 89.21 % 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: -0.75 (0.14), residues: 3153 helix: 2.00 (0.20), residues: 674 sheet: -0.29 (0.20), residues: 627 loop : -1.61 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 235 TYR 0.018 0.001 TYR B1065 PHE 0.018 0.002 PHE C 166 TRP 0.024 0.002 TRP B 434 HIS 0.008 0.001 HIS B 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (26342) covalent geometry : angle 0.64559 / 0.32 (35830) SS BOND : bond 0.00556 / 0.35 ( 42) SS BOND : angle 2.10992 / 1.50 ( 84) hydrogen bonds : bond 0.05494 / 3.59 ( 947) hydrogen bonds : angle 5.37690 / 3.73 ( 2625) Misc. bond : bond 0.00094 / 0.05 ( 1) link_BETA1-4 : bond 0.00623 / 0.42 ( 13) link_BETA1-4 : angle 2.52333 / 1.57 ( 39) link_NAG-ASN : bond 0.00438 / 0.31 ( 48) link_NAG-ASN : angle 2.71109 / 1.99 ( 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 312 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 0.965 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 153 MET cc_start: 0.6831 (mpp) cc_final: 0.6296 (pmm) REVERT: A 168 TYR cc_start: 0.8422 (t80) cc_final: 0.8041 (t80) REVERT: A 327 PHE cc_start: 0.7610 (m-10) cc_final: 0.7307 (m-10) REVERT: A 554 ASN cc_start: 0.8090 (p0) cc_final: 0.7831 (p0) REVERT: A 673 GLN cc_start: 0.6842 (tp40) cc_final: 0.6620 (pt0) REVERT: A 853 PHE cc_start: 0.7839 (m-10) cc_final: 0.7479 (m-80) REVERT: A 882 SER cc_start: 0.9184 (m) cc_final: 0.8936 (p) REVERT: A 1029 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: B 81 ASN cc_start: 0.7580 (p0) cc_final: 0.7363 (p0) REVERT: B 135 PHE cc_start: 0.8013 (m-80) cc_final: 0.7282 (m-80) REVERT: B 264 TYR cc_start: 0.6548 (m-80) cc_final: 0.6257 (m-80) REVERT: B 407 GLN cc_start: 0.7591 (mt0) cc_final: 0.7350 (mp10) REVERT: B 416 ILE cc_start: 0.8726 (pt) cc_final: 0.8483 (pt) REVERT: B 527 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7697 (mtmt) REVERT: B 705 TYR cc_start: 0.7801 (t80) cc_final: 0.7263 (t80) REVERT: B 915 TYR cc_start: 0.8686 (m-80) cc_final: 0.8138 (m-10) REVERT: B 974 VAL cc_start: 0.8545 (t) cc_final: 0.8292 (t) REVERT: B 1111 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8175 (mt0) REVERT: C 168 TYR cc_start: 0.6867 (t80) cc_final: 0.6599 (t80) REVERT: C 240 LEU cc_start: 0.7876 (pt) cc_final: 0.7628 (pp) REVERT: C 352 ASN cc_start: 0.7337 (t0) cc_final: 0.6290 (p0) REVERT: C 376 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8555 (ttpp) REVERT: C 557 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7349 (t80) REVERT: C 563 PHE cc_start: 0.6704 (m-10) cc_final: 0.6469 (m-10) REVERT: C 898 MET cc_start: 0.7818 (mtt) cc_final: 0.7574 (mtt) REVERT: C 902 TYR cc_start: 0.7082 (m-10) cc_final: 0.6879 (m-10) outliers start: 55 outliers final: 31 residues processed: 294 average time/residue: 0.1533 time to fit residues: 74.0886 Evaluate side-chains 236 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 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 709 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 952 GLN 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 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 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 974 VAL 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: 1.9990 chunk 195 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 265 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 297 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 561 GLN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 ASN C 438 ASN C 911 GLN C 924 GLN C1086 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108688 restraints weight = 41185.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109361 restraints weight = 24989.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109704 restraints weight = 17440.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110480 restraints weight = 16352.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110668 restraints weight = 14576.385| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 26446 Z= 0.244 Angle : 0.708 18.738 36097 Z= 0.349 Chirality : 0.048 0.425 4223 Planarity : 0.005 0.069 4567 Dihedral : 4.713 31.581 3417 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.80 % Allowed : 11.79 % Favored : 85.40 % 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: -0.95 (0.14), residues: 3153 helix: 1.75 (0.20), residues: 660 sheet: -0.22 (0.20), residues: 598 loop : -1.75 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 406 TYR 0.020 0.002 TYR B1065 PHE 0.027 0.002 PHE A 904 TRP 0.015 0.002 TRP A 884 HIS 0.010 0.001 HIS A1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.24 (26342) covalent geometry : angle 0.67778 / 0.34 (35830) SS BOND : bond 0.00515 / 0.29 ( 42) SS BOND : angle 1.71528 / 1.19 ( 84) hydrogen bonds : bond 0.06414 / 4.24 ( 947) hydrogen bonds : angle 5.43564 / 3.76 ( 2625) Misc. bond : bond 0.00133 / 0.07 ( 1) link_BETA1-4 : bond 0.00690 / 0.48 ( 13) link_BETA1-4 : angle 2.51511 / 1.52 ( 39) link_NAG-ASN : bond 0.00443 / 0.32 ( 48) link_NAG-ASN : angle 2.81764 / 2.10 ( 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 294 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 216 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8912 (mm) cc_final: 0.8590 (mt) REVERT: A 168 TYR cc_start: 0.8522 (t80) cc_final: 0.8022 (t80) REVERT: A 952 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: A 1029 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: B 135 PHE cc_start: 0.8094 (m-80) cc_final: 0.7401 (m-80) REVERT: B 200 LYS cc_start: 0.7309 (mttp) cc_final: 0.6937 (mtmt) REVERT: B 527 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7802 (mttp) REVERT: B 561 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.6227 (mm-40) REVERT: B 853 PHE cc_start: 0.7290 (m-10) cc_final: 0.6962 (m-10) REVERT: B 867 MET cc_start: 0.8838 (mtt) cc_final: 0.8574 (mtm) REVERT: B 876 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8175 (tt) REVERT: B 977 ASP cc_start: 0.7926 (t0) cc_final: 0.7659 (t0) REVERT: B 1029 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: B 1111 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8187 (mt0) REVERT: C 49 HIS cc_start: 0.8038 (t-170) cc_final: 0.7779 (t70) REVERT: C 168 TYR cc_start: 0.7134 (t80) cc_final: 0.6865 (t80) REVERT: C 240 LEU cc_start: 0.7743 (pt) cc_final: 0.7528 (pp) REVERT: C 325 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8063 (t) REVERT: C 390 PHE cc_start: 0.8879 (m-80) cc_final: 0.8665 (m-80) REVERT: C 547 THR cc_start: 0.8529 (p) cc_final: 0.8284 (p) REVERT: C 576 ASP cc_start: 0.8189 (t0) cc_final: 0.7798 (t0) REVERT: C 880 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8847 (mp) REVERT: C 902 TYR cc_start: 0.7340 (m-10) cc_final: 0.7117 (m-10) REVERT: C 1048 MET cc_start: 0.8361 (ptt) cc_final: 0.8081 (ptt) outliers start: 78 outliers final: 45 residues processed: 274 average time/residue: 0.1500 time to fit residues: 67.4860 Evaluate side-chains 238 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain B residue 227 LEU 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 561 GLN 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 709 SER 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 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 919 LYS Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1028 SER 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: 0.9980 chunk 56 optimal weight: 0.5980 chunk 268 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN C 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.172270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115225 restraints weight = 40918.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114275 restraints weight = 22931.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114408 restraints weight = 17629.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115040 restraints weight = 16696.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115264 restraints weight = 15063.123| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26446 Z= 0.127 Angle : 0.612 18.511 36097 Z= 0.296 Chirality : 0.045 0.421 4223 Planarity : 0.004 0.074 4567 Dihedral : 4.468 29.948 3417 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.55 % Allowed : 13.88 % Favored : 83.57 % 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: -0.65 (0.14), residues: 3153 helix: 2.22 (0.20), residues: 653 sheet: -0.06 (0.21), residues: 598 loop : -1.61 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 565 TYR 0.016 0.001 TYR B1065 PHE 0.021 0.001 PHE C 560 TRP 0.013 0.001 TRP C 434 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (26342) covalent geometry : angle 0.58210 / 0.29 (35830) SS BOND : bond 0.00347 / 0.22 ( 42) SS BOND : angle 1.46017 / 0.99 ( 84) hydrogen bonds : bond 0.05086 / 3.36 ( 947) hydrogen bonds : angle 5.09462 / 3.53 ( 2625) Misc. bond : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : bond 0.00712 / 0.49 ( 13) link_BETA1-4 : angle 2.45391 / 1.49 ( 39) link_NAG-ASN : bond 0.00450 / 0.34 ( 48) link_NAG-ASN : angle 2.59614 / 1.92 ( 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 286 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 215 time to evaluate : 0.848 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: 0.8912 (mm) cc_final: 0.8573 (mt) REVERT: A 153 MET cc_start: 0.6190 (mpp) cc_final: 0.5954 (pmm) REVERT: A 168 TYR cc_start: 0.8597 (t80) cc_final: 0.8138 (t80) REVERT: A 952 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: A 1029 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: B 135 PHE cc_start: 0.8055 (m-80) cc_final: 0.7403 (m-80) REVERT: B 200 LYS cc_start: 0.7235 (mttp) cc_final: 0.6882 (mtmt) REVERT: B 527 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7726 (mttp) REVERT: B 867 MET cc_start: 0.8772 (mtt) cc_final: 0.8514 (mtm) REVERT: B 955 GLN cc_start: 0.8303 (tp40) cc_final: 0.7996 (tt0) REVERT: B 977 ASP cc_start: 0.7973 (t0) cc_final: 0.7725 (t0) REVERT: B 1029 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: B 1111 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8155 (mt0) REVERT: C 49 HIS cc_start: 0.8021 (t-170) cc_final: 0.7757 (t70) REVERT: C 168 TYR cc_start: 0.7069 (t80) cc_final: 0.6768 (t80) REVERT: C 240 LEU cc_start: 0.7868 (pt) cc_final: 0.7645 (pp) REVERT: C 327 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.5505 (t80) REVERT: C 547 THR cc_start: 0.8455 (p) cc_final: 0.8216 (p) REVERT: C 576 ASP cc_start: 0.8147 (t0) cc_final: 0.7705 (t0) REVERT: C 880 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8742 (mp) REVERT: C 1048 MET cc_start: 0.8119 (ptt) cc_final: 0.7881 (ptt) outliers start: 71 outliers final: 35 residues processed: 267 average time/residue: 0.1458 time to fit residues: 64.4061 Evaluate side-chains 235 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 862 LEU 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 227 LEU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 664 ILE 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 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 205 HIS 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 652 GLU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN 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: 1.9990 chunk 217 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 924 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN B 785 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.170456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108999 restraints weight = 40917.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111253 restraints weight = 23962.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111400 restraints weight = 16240.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112770 restraints weight = 15298.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112846 restraints weight = 13541.443| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26446 Z= 0.170 Angle : 0.636 18.039 36097 Z= 0.310 Chirality : 0.046 0.426 4223 Planarity : 0.004 0.067 4567 Dihedral : 4.477 29.633 3417 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.52 % Allowed : 14.92 % Favored : 82.56 % 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: -0.69 (0.14), residues: 3153 helix: 2.10 (0.20), residues: 660 sheet: -0.07 (0.20), residues: 608 loop : -1.63 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 565 TYR 0.017 0.001 TYR B1065 PHE 0.018 0.002 PHE C 560 TRP 0.014 0.001 TRP C 434 HIS 0.006 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (26342) covalent geometry : angle 0.60837 / 0.30 (35830) SS BOND : bond 0.00355 / 0.23 ( 42) SS BOND : angle 1.35039 / 0.93 ( 84) hydrogen bonds : bond 0.05478 / 3.63 ( 947) hydrogen bonds : angle 5.11134 / 3.55 ( 2625) Misc. bond : bond 0.00069 / 0.04 ( 1) link_BETA1-4 : bond 0.00653 / 0.45 ( 13) link_BETA1-4 : angle 2.40833 / 1.46 ( 39) link_NAG-ASN : bond 0.00417 / 0.31 ( 48) link_NAG-ASN : angle 2.57257 / 1.89 ( 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 275 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 205 time to evaluate : 0.830 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 128 ILE cc_start: 0.8882 (mm) cc_final: 0.8580 (mt) REVERT: A 153 MET cc_start: 0.6351 (mpp) cc_final: 0.6120 (pmm) REVERT: A 168 TYR cc_start: 0.8658 (t80) cc_final: 0.8163 (t80) REVERT: A 853 PHE cc_start: 0.7680 (m-80) cc_final: 0.7330 (m-80) REVERT: A 952 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: A 1029 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: B 135 PHE cc_start: 0.8076 (m-80) cc_final: 0.7434 (m-80) REVERT: B 200 LYS cc_start: 0.7129 (mttp) cc_final: 0.6763 (mtmt) REVERT: B 523 CYS cc_start: 0.6535 (OUTLIER) cc_final: 0.5966 (m) REVERT: B 527 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7770 (mttp) REVERT: B 561 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6232 (mm-40) REVERT: B 579 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8320 (p) REVERT: B 955 GLN cc_start: 0.8306 (tp40) cc_final: 0.7980 (tt0) REVERT: B 986 GLU cc_start: 0.7615 (tp30) cc_final: 0.7259 (tp30) REVERT: B 1029 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: B 1111 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8102 (mt0) REVERT: C 49 HIS cc_start: 0.8053 (t-170) cc_final: 0.7744 (t-170) REVERT: C 168 TYR cc_start: 0.7296 (t80) cc_final: 0.7016 (t80) REVERT: C 240 LEU cc_start: 0.8012 (pt) cc_final: 0.7791 (pp) REVERT: C 327 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.5580 (t80) REVERT: C 352 ASN cc_start: 0.7123 (t0) cc_final: 0.6903 (t0) REVERT: C 576 ASP cc_start: 0.8275 (t0) cc_final: 0.7823 (t0) REVERT: C 880 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8712 (mp) REVERT: C 1048 MET cc_start: 0.8314 (ptt) cc_final: 0.8032 (ptt) outliers start: 70 outliers final: 40 residues processed: 256 average time/residue: 0.1522 time to fit residues: 63.9567 Evaluate side-chains 242 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 803 ILE Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 957 LEU 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 153 MET Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 561 GLN 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 697 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 16 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 289 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 136 optimal weight: 4.9990 chunk 183 optimal weight: 0.0050 chunk 9 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 HIS B 149 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.171470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108867 restraints weight = 40974.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112366 restraints weight = 22825.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114148 restraints weight = 14673.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114547 restraints weight = 12857.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115068 restraints weight = 12575.466| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26446 Z= 0.131 Angle : 0.604 17.950 36097 Z= 0.292 Chirality : 0.045 0.431 4223 Planarity : 0.004 0.058 4567 Dihedral : 4.362 28.871 3417 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.59 % Allowed : 15.43 % Favored : 81.98 % 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: 2.26 (0.20), residues: 660 sheet: 0.01 (0.21), residues: 593 loop : -1.57 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 188 TYR 0.016 0.001 TYR B1065 PHE 0.022 0.001 PHE A 92 TRP 0.012 0.001 TRP C 434 HIS 0.006 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (26342) covalent geometry : angle 0.57716 / 0.29 (35830) SS BOND : bond 0.00316 / 0.21 ( 42) SS BOND : angle 1.26566 / 0.86 ( 84) hydrogen bonds : bond 0.04945 / 3.28 ( 947) hydrogen bonds : angle 4.96301 / 3.44 ( 2625) Misc. bond : bond 0.00066 / 0.03 ( 1) link_BETA1-4 : bond 0.00653 / 0.45 ( 13) link_BETA1-4 : angle 2.39772 / 1.46 ( 39) link_NAG-ASN : bond 0.00431 / 0.33 ( 48) link_NAG-ASN : angle 2.48851 / 1.81 ( 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 279 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 207 time to evaluate : 0.907 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: 0.8880 (mm) cc_final: 0.8585 (mt) REVERT: A 153 MET cc_start: 0.6412 (mpp) cc_final: 0.6211 (pmm) REVERT: A 168 TYR cc_start: 0.8697 (t80) cc_final: 0.8246 (t80) REVERT: A 175 MET cc_start: 0.4635 (mtm) cc_final: 0.3688 (tpt) REVERT: A 853 PHE cc_start: 0.7762 (m-80) cc_final: 0.7377 (m-80) REVERT: A 952 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: A 1029 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: A 1108 TYR cc_start: 0.8851 (t80) cc_final: 0.8638 (t80) REVERT: B 135 PHE cc_start: 0.8080 (m-80) cc_final: 0.7457 (m-80) REVERT: B 175 MET cc_start: 0.4858 (pmm) cc_final: 0.2472 (pmm) REVERT: B 200 LYS cc_start: 0.7070 (mttp) cc_final: 0.6702 (mtmt) REVERT: B 407 GLN cc_start: 0.7374 (mt0) cc_final: 0.7152 (mt0) REVERT: B 527 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7738 (mttp) REVERT: B 561 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6000 (mm110) REVERT: B 579 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8342 (p) REVERT: B 955 GLN cc_start: 0.8219 (tp40) cc_final: 0.7918 (tt0) REVERT: B 986 GLU cc_start: 0.7606 (tp30) cc_final: 0.7253 (tp30) REVERT: B 1029 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: B 1111 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8085 (mt0) REVERT: C 49 HIS cc_start: 0.8025 (t-170) cc_final: 0.7723 (t-170) REVERT: C 168 TYR cc_start: 0.7281 (t80) cc_final: 0.6991 (t80) REVERT: C 240 LEU cc_start: 0.8043 (pt) cc_final: 0.7815 (pp) REVERT: C 327 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.5751 (t80) REVERT: C 352 ASN cc_start: 0.7088 (t0) cc_final: 0.6851 (t0) REVERT: C 576 ASP cc_start: 0.8271 (t0) cc_final: 0.7828 (t0) REVERT: C 880 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8724 (mp) REVERT: C 1048 MET cc_start: 0.8236 (ptt) cc_final: 0.7989 (ptt) outliers start: 72 outliers final: 43 residues processed: 261 average time/residue: 0.1487 time to fit residues: 64.4050 Evaluate side-chains 247 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 957 LEU 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 187 LEU Chi-restraints excluded: chain B residue 289 CYS 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 561 GLN 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 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 205 HIS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 306 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 236 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 313 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 214 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN B 785 GLN ** B 802 GLN ** 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 = 0.4191 r_free = 0.4191 target = 0.170493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108858 restraints weight = 40792.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111004 restraints weight = 26324.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111685 restraints weight = 16475.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112166 restraints weight = 14847.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112647 restraints weight = 14734.939| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3469 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= 0.161 Angle : 0.618 17.633 36097 Z= 0.300 Chirality : 0.046 0.435 4223 Planarity : 0.004 0.057 4567 Dihedral : 4.384 28.571 3417 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.48 % Allowed : 16.07 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3153 helix: 2.17 (0.20), residues: 661 sheet: -0.02 (0.21), residues: 608 loop : -1.57 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1105 TYR 0.016 0.001 TYR B1065 PHE 0.021 0.001 PHE C 560 TRP 0.015 0.001 TRP C 64 HIS 0.005 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (26342) covalent geometry : angle 0.59188 / 0.29 (35830) SS BOND : bond 0.00367 / 0.24 ( 42) SS BOND : angle 1.31744 / 0.90 ( 84) hydrogen bonds : bond 0.05237 / 3.47 ( 947) hydrogen bonds : angle 5.00600 / 3.47 ( 2625) Misc. bond : bond 0.00065 / 0.03 ( 1) link_BETA1-4 : bond 0.00669 / 0.46 ( 13) link_BETA1-4 : angle 2.39196 / 1.45 ( 39) link_NAG-ASN : bond 0.00407 / 0.31 ( 48) link_NAG-ASN : angle 2.48154 / 1.80 ( 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: 69 poor density : 204 time to evaluate : 0.828 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: 0.8922 (mm) cc_final: 0.8637 (mt) REVERT: A 153 MET cc_start: 0.6422 (mpp) cc_final: 0.6194 (pmm) REVERT: A 168 TYR cc_start: 0.8717 (t80) cc_final: 0.8247 (t80) REVERT: A 175 MET cc_start: 0.4728 (mtm) cc_final: 0.3661 (tpt) REVERT: A 853 PHE cc_start: 0.7655 (m-80) cc_final: 0.7275 (m-80) REVERT: A 952 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: A 1029 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: B 135 PHE cc_start: 0.8070 (m-80) cc_final: 0.7468 (m-80) REVERT: B 175 MET cc_start: 0.4962 (pmm) cc_final: 0.2051 (pmm) REVERT: B 407 GLN cc_start: 0.7342 (mt0) cc_final: 0.7118 (mt0) REVERT: B 527 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7729 (mtmm) REVERT: B 579 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8348 (p) REVERT: B 785 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: B 955 GLN cc_start: 0.8240 (tp40) cc_final: 0.7937 (tt0) REVERT: B 986 GLU cc_start: 0.7691 (tp30) cc_final: 0.7313 (tp30) REVERT: B 1029 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 1111 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8124 (mt0) REVERT: C 49 HIS cc_start: 0.8057 (t-170) cc_final: 0.7744 (t-170) REVERT: C 168 TYR cc_start: 0.7316 (t80) cc_final: 0.7026 (t80) REVERT: C 240 LEU cc_start: 0.8055 (pt) cc_final: 0.7817 (pp) REVERT: C 327 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.5834 (t80) REVERT: C 352 ASN cc_start: 0.7145 (t0) cc_final: 0.6888 (t0) REVERT: C 576 ASP cc_start: 0.8359 (t0) cc_final: 0.8009 (t0) REVERT: C 880 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8700 (mp) REVERT: C 1048 MET cc_start: 0.8215 (ptt) cc_final: 0.7918 (ptt) outliers start: 69 outliers final: 49 residues processed: 257 average time/residue: 0.1517 time to fit residues: 64.4738 Evaluate side-chains 246 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 952 GLN Chi-restraints excluded: chain A residue 957 LEU 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 187 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 401 ARG 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 785 GLN Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 LEU 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 194 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 306 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 71 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 277 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 154 optimal weight: 0.4980 chunk 41 optimal weight: 40.0000 chunk 314 optimal weight: 1.9990 chunk 167 optimal weight: 0.0270 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.171342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107774 restraints weight = 40871.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111818 restraints weight = 21906.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114423 restraints weight = 14967.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115850 restraints weight = 11968.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116846 restraints weight = 10517.328| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3551 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= 0.130 Angle : 0.609 17.520 36097 Z= 0.294 Chirality : 0.045 0.435 4223 Planarity : 0.004 0.057 4567 Dihedral : 4.318 27.886 3417 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.27 % Allowed : 16.58 % Favored : 81.16 % 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: 2.40 (0.20), residues: 654 sheet: 0.03 (0.21), residues: 601 loop : -1.53 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 188 TYR 0.015 0.001 TYR B1065 PHE 0.024 0.001 PHE A 372 TRP 0.013 0.001 TRP C 64 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (26342) covalent geometry : angle 0.58319 / 0.29 (35830) SS BOND : bond 0.00310 / 0.20 ( 42) SS BOND : angle 1.18858 / 0.80 ( 84) hydrogen bonds : bond 0.04826 / 3.20 ( 947) hydrogen bonds : angle 4.88996 / 3.39 ( 2625) Misc. bond : bond 0.00061 / 0.03 ( 1) link_BETA1-4 : bond 0.00702 / 0.49 ( 13) link_BETA1-4 : angle 2.39389 / 1.45 ( 39) link_NAG-ASN : bond 0.00416 / 0.32 ( 48) link_NAG-ASN : angle 2.41519 / 1.75 ( 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 262 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 199 time to evaluate : 0.943 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: 0.8968 (mm) cc_final: 0.8680 (mt) REVERT: A 134 GLN cc_start: 0.7446 (tp-100) cc_final: 0.6999 (tm-30) REVERT: A 168 TYR cc_start: 0.8809 (t80) cc_final: 0.8371 (t80) REVERT: A 175 MET cc_start: 0.4642 (mtm) cc_final: 0.3562 (tpt) REVERT: A 853 PHE cc_start: 0.7618 (m-80) cc_final: 0.7277 (m-80) REVERT: A 1029 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: B 135 PHE cc_start: 0.7821 (m-80) cc_final: 0.7203 (m-80) REVERT: B 175 MET cc_start: 0.4173 (pmm) cc_final: 0.2801 (pmm) REVERT: B 200 LYS cc_start: 0.7190 (mttp) cc_final: 0.6895 (mtmt) REVERT: B 955 GLN cc_start: 0.8191 (tp40) cc_final: 0.7869 (tt0) REVERT: B 986 GLU cc_start: 0.7653 (tp30) cc_final: 0.7166 (tp30) REVERT: B 1029 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: B 1111 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8116 (mt0) REVERT: C 49 HIS cc_start: 0.8026 (t-170) cc_final: 0.7764 (t-170) REVERT: C 168 TYR cc_start: 0.7392 (t80) cc_final: 0.7120 (t80) REVERT: C 240 LEU cc_start: 0.7891 (pt) cc_final: 0.7688 (pp) REVERT: C 327 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6116 (t80) REVERT: C 352 ASN cc_start: 0.7191 (t0) cc_final: 0.6924 (t0) REVERT: C 576 ASP cc_start: 0.8313 (t0) cc_final: 0.8007 (t0) REVERT: C 880 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8649 (mp) REVERT: C 1048 MET cc_start: 0.8268 (ptt) cc_final: 0.8030 (ptt) outliers start: 63 outliers final: 50 residues processed: 247 average time/residue: 0.1365 time to fit residues: 56.9034 Evaluate side-chains 248 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 957 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 LEU 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 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 401 ARG 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 909 VAL Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 992 ASP 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 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 306 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 143 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 299 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 171 GLN A 933 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN B1008 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.171763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110422 restraints weight = 41066.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112884 restraints weight = 24401.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113015 restraints weight = 18135.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113940 restraints weight = 14857.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114218 restraints weight = 14267.677| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 26446 Z= 0.254 Angle : 0.706 17.301 36097 Z= 0.347 Chirality : 0.048 0.434 4223 Planarity : 0.004 0.057 4567 Dihedral : 4.646 30.423 3417 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.37 % Allowed : 17.04 % Favored : 80.58 % 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: -0.84 (0.14), residues: 3153 helix: 1.81 (0.20), residues: 669 sheet: -0.16 (0.21), residues: 611 loop : -1.68 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 188 TYR 0.020 0.002 TYR B1065 PHE 0.027 0.002 PHE A 372 TRP 0.020 0.002 TRP A 884 HIS 0.008 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.25 (26342) covalent geometry : angle 0.67978 / 0.34 (35830) SS BOND : bond 0.00433 / 0.28 ( 42) SS BOND : angle 1.53676 / 1.05 ( 84) hydrogen bonds : bond 0.06362 / 4.23 ( 947) hydrogen bonds : angle 5.28315 / 3.65 ( 2625) Misc. bond : bond 0.00084 / 0.04 ( 1) link_BETA1-4 : bond 0.00631 / 0.45 ( 13) link_BETA1-4 : angle 2.42326 / 1.47 ( 39) link_NAG-ASN : bond 0.00429 / 0.31 ( 48) link_NAG-ASN : angle 2.61175 / 1.90 ( 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 268 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8197 (tptt) cc_final: 0.7880 (mmmt) REVERT: A 128 ILE cc_start: 0.8988 (mm) cc_final: 0.8738 (mt) REVERT: A 134 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7255 (tm-30) REVERT: A 168 TYR cc_start: 0.8830 (t80) cc_final: 0.8393 (t80) REVERT: A 175 MET cc_start: 0.4682 (mtm) cc_final: 0.3527 (tpt) REVERT: A 957 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8284 (tt) REVERT: A 1029 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: B 52 GLN cc_start: 0.8082 (tt0) cc_final: 0.7862 (pp30) REVERT: B 135 PHE cc_start: 0.8050 (m-80) cc_final: 0.7392 (m-80) REVERT: B 175 MET cc_start: 0.4714 (pmm) cc_final: 0.3136 (pmm) REVERT: B 200 LYS cc_start: 0.7283 (mttp) cc_final: 0.6940 (mtmt) REVERT: B 407 GLN cc_start: 0.7395 (mt0) cc_final: 0.7163 (mt0) REVERT: B 853 PHE cc_start: 0.7255 (m-10) cc_final: 0.7020 (m-10) REVERT: B 955 GLN cc_start: 0.8341 (tp40) cc_final: 0.8067 (tt0) REVERT: B 982 LEU cc_start: 0.8722 (mp) cc_final: 0.8458 (mt) REVERT: B 986 GLU cc_start: 0.7664 (tp30) cc_final: 0.7340 (tp30) REVERT: B 1029 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 1111 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8209 (mt0) REVERT: C 49 HIS cc_start: 0.8094 (t-170) cc_final: 0.7819 (t-170) REVERT: C 168 TYR cc_start: 0.7427 (t80) cc_final: 0.7173 (t80) REVERT: C 240 LEU cc_start: 0.8082 (pt) cc_final: 0.7842 (pp) REVERT: C 327 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6042 (t80) REVERT: C 352 ASN cc_start: 0.7286 (t0) cc_final: 0.7018 (t0) REVERT: C 576 ASP cc_start: 0.8397 (t0) cc_final: 0.8068 (t0) REVERT: C 880 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8784 (mp) REVERT: C 1048 MET cc_start: 0.8381 (ptt) cc_final: 0.8118 (ptt) outliers start: 66 outliers final: 53 residues processed: 256 average time/residue: 0.1554 time to fit residues: 66.0185 Evaluate side-chains 256 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP 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 709 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 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 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 401 ARG 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 893 GLN Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 992 ASP 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 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 306 VAL 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 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 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 Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 244 optimal weight: 9.9990 chunk 314 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 44 optimal weight: 40.0000 chunk 203 optimal weight: 0.4980 chunk 282 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.172104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108595 restraints weight = 40774.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112725 restraints weight = 21746.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115258 restraints weight = 14870.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116810 restraints weight = 11924.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117517 restraints weight = 10457.912| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26446 Z= 0.117 Angle : 0.618 17.437 36097 Z= 0.299 Chirality : 0.045 0.435 4223 Planarity : 0.004 0.060 4567 Dihedral : 4.394 28.594 3417 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.91 % Allowed : 17.40 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3153 helix: 2.22 (0.20), residues: 668 sheet: -0.09 (0.20), residues: 615 loop : -1.56 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 188 TYR 0.015 0.001 TYR B1065 PHE 0.043 0.001 PHE A 372 TRP 0.014 0.001 TRP C 64 HIS 0.006 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (26342) covalent geometry : angle 0.59367 / 0.29 (35830) SS BOND : bond 0.00301 / 0.20 ( 42) SS BOND : angle 1.15308 / 0.78 ( 84) hydrogen bonds : bond 0.04846 / 3.21 ( 947) hydrogen bonds : angle 4.95851 / 3.43 ( 2625) Misc. bond : bond 0.00058 / 0.03 ( 1) link_BETA1-4 : bond 0.00702 / 0.48 ( 13) link_BETA1-4 : angle 2.39934 / 1.45 ( 39) link_NAG-ASN : bond 0.00436 / 0.33 ( 48) link_NAG-ASN : angle 2.41027 / 1.74 ( 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 252 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 0.883 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: 0.9068 (mm) cc_final: 0.8774 (mt) REVERT: A 134 GLN cc_start: 0.7529 (tp-100) cc_final: 0.6965 (tm-30) REVERT: A 168 TYR cc_start: 0.8887 (t80) cc_final: 0.8448 (t80) REVERT: A 1029 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: B 135 PHE cc_start: 0.7834 (m-80) cc_final: 0.7230 (m-80) REVERT: B 175 MET cc_start: 0.4535 (pmm) cc_final: 0.2987 (pmm) REVERT: B 200 LYS cc_start: 0.7281 (mttp) cc_final: 0.6968 (mtmt) REVERT: B 955 GLN cc_start: 0.8207 (tp40) cc_final: 0.7918 (tt0) REVERT: B 986 GLU cc_start: 0.7535 (tp30) cc_final: 0.7254 (tp30) REVERT: B 1029 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: B 1111 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8145 (mt0) REVERT: C 49 HIS cc_start: 0.8016 (t-170) cc_final: 0.7754 (t-170) REVERT: C 168 TYR cc_start: 0.7443 (t80) cc_final: 0.7205 (t80) REVERT: C 240 LEU cc_start: 0.7886 (pt) cc_final: 0.7678 (pp) REVERT: C 327 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6300 (t80) REVERT: C 352 ASN cc_start: 0.7207 (t0) cc_final: 0.6936 (t0) REVERT: C 576 ASP cc_start: 0.8260 (t0) cc_final: 0.7949 (t0) REVERT: C 880 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8704 (mp) REVERT: C 1048 MET cc_start: 0.8228 (ptt) cc_final: 0.8012 (ptt) outliers start: 53 outliers final: 42 residues processed: 241 average time/residue: 0.1562 time to fit residues: 62.3173 Evaluate side-chains 239 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 957 LEU Chi-restraints excluded: chain A residue 975 LEU 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 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE 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 785 GLN Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 992 ASP 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 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 460 LYS 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 Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 280 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B 893 GLN ** C 99 ASN ** 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 = 0.4147 r_free = 0.4147 target = 0.166348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104751 restraints weight = 40676.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107371 restraints weight = 24073.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106961 restraints weight = 15320.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107672 restraints weight = 16872.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107609 restraints weight = 15689.184| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 26446 Z= 0.344 Angle : 0.780 16.775 36097 Z= 0.388 Chirality : 0.051 0.432 4223 Planarity : 0.005 0.060 4567 Dihedral : 4.822 31.263 3417 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.16 % Allowed : 17.44 % Favored : 80.40 % 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: -1.06 (0.14), residues: 3153 helix: 1.39 (0.20), residues: 684 sheet: -0.22 (0.20), residues: 614 loop : -1.78 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 188 TYR 0.021 0.002 TYR B1065 PHE 0.043 0.002 PHE A 372 TRP 0.024 0.002 TRP A 884 HIS 0.012 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00853 / 0.34 (26342) covalent geometry : angle 0.75555 / 0.38 (35830) SS BOND : bond 0.00495 / 0.31 ( 42) SS BOND : angle 1.71251 / 1.20 ( 84) hydrogen bonds : bond 0.07072 / 4.70 ( 947) hydrogen bonds : angle 5.49371 / 3.79 ( 2625) Misc. bond : bond 0.00099 / 0.05 ( 1) link_BETA1-4 : bond 0.00619 / 0.43 ( 13) link_BETA1-4 : angle 2.45455 / 1.49 ( 39) link_NAG-ASN : bond 0.00476 / 0.33 ( 48) link_NAG-ASN : angle 2.69418 / 1.95 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4368.32 seconds wall clock time: 76 minutes 49.28 seconds (4609.28 seconds total)