Starting phenix.real_space_refine on Sun Jun 22 14:57:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wg9_32481/06_2025/7wg9_32481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg9_32481/06_2025/7wg9_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_32481/06_2025/7wg9_32481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg9_32481/06_2025/7wg9_32481.map" model { file = "/net/cci-nas-00/data/ceres_data/7wg9_32481/06_2025/7wg9_32481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg9_32481/06_2025/7wg9_32481.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25769 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.72, per 1000 atoms: 0.57 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: 6.21 Conformation dependent library (CDL) restraints added in 3.1 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: 3.48 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: 10.69 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8186 1.34 - 1.47: 6584 1.47 - 1.59: 11424 1.59 - 1.71: 1 1.71 - 1.83: 147 Bond restraints: 26342 Sorted by residual: bond pdb=" CA LEU B 177 " pdb=" C LEU B 177 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.34e-02 5.57e+03 4.48e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" CB PRO C 525 " pdb=" CG PRO C 525 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.14e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 26337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 35097 1.97 - 3.93: 665 3.93 - 5.90: 53 5.90 - 7.86: 12 7.86 - 9.83: 3 Bond angle restraints: 35830 Sorted by residual: angle pdb=" CA TRP C 152 " pdb=" CB TRP C 152 " pdb=" CG TRP C 152 " ideal model delta sigma weight residual 113.60 120.35 -6.75 1.90e+00 2.77e-01 1.26e+01 angle pdb=" C ALA A 568 " pdb=" N ASP A 569 " pdb=" CA ASP A 569 " ideal model delta sigma weight residual 122.46 127.32 -4.86 1.41e+00 5.03e-01 1.19e+01 angle pdb=" C LYS B 97 " pdb=" N SER B 98 " pdb=" CA SER B 98 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.21e+00 angle pdb=" C ALA C 568 " pdb=" N ASP C 569 " pdb=" CA ASP C 569 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.52e+00 angle pdb=" CA CYS A 536 " pdb=" CB CYS A 536 " pdb=" SG CYS A 536 " ideal model delta sigma weight residual 114.40 121.10 -6.70 2.30e+00 1.89e-01 8.48e+00 ... (remaining 35825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.66: 15087 19.66 - 39.31: 1119 39.31 - 58.97: 226 58.97 - 78.62: 57 78.62 - 98.28: 17 Dihedral angle restraints: 16506 sinusoidal: 7233 harmonic: 9273 Sorted by residual: dihedral pdb=" CB CYS B 289 " pdb=" SG CYS B 289 " pdb=" SG CYS B 299 " pdb=" CB CYS B 299 " ideal model delta sinusoidal sigma weight residual -86.00 -4.64 -81.36 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS B 478 " pdb=" SG CYS B 478 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual 93.00 173.47 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 149.89 -56.89 1 1.00e+01 1.00e-02 4.36e+01 ... (remaining 16503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4135 0.112 - 0.225: 84 0.225 - 0.337: 3 0.337 - 0.449: 0 0.449 - 0.562: 1 Chirality restraints: 4223 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 707 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C1096 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C1132 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 4220 not shown) Planarity restraints: 4615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 227 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO C 228 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 206 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO B 207 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 227 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO B 228 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.030 5.00e-02 4.00e+02 ... (remaining 4612 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 632 2.69 - 3.25: 25204 3.25 - 3.80: 39060 3.80 - 4.35: 49159 4.35 - 4.90: 83638 Nonbonded interactions: 197693 Sorted by model distance: nonbonded pdb=" OG SER B 436 " pdb=" OD2 ASP B 440 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR A 391 " pdb=" O GLU A 514 " model vdw 2.161 3.040 nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.181 3.040 nonbonded pdb=" NH1 ARG C1017 " pdb=" OD1 ASN C1021 " model vdw 2.211 3.120 nonbonded pdb=" O ASP B 440 " pdb=" ND2 ASN B 446 " model vdw 2.212 3.120 ... (remaining 197688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 14 through 1146 or resid 1301 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 57.670 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.140 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 26446 Z= 0.170 Angle : 0.647 19.948 36097 Z= 0.319 Chirality : 0.046 0.562 4223 Planarity : 0.004 0.073 4567 Dihedral : 14.257 98.277 10416 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (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 TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS B 146 PHE 0.015 0.001 PHE A 390 TYR 0.019 0.001 TYR B 168 ARG 0.007 0.000 ARG B 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 48) link_NAG-ASN : angle 2.73988 ( 144) link_BETA1-4 : bond 0.00814 ( 13) link_BETA1-4 : angle 3.16607 ( 39) hydrogen bonds : bond 0.14627 ( 947) hydrogen bonds : angle 6.79740 ( 2625) SS BOND : bond 0.00296 ( 42) SS BOND : angle 1.00615 ( 84) covalent geometry : bond 0.00342 (26342) covalent geometry : angle 0.61479 (35830) Misc. bond : bond 0.00132 ( 1) *********************** 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 : 2.747 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: 0.8172 (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: 0.8801 (p) REVERT: A 974 VAL cc_start: 0.8850 (t) cc_final: 0.8513 (t) REVERT: B 79 PHE cc_start: 0.6721 (t80) cc_final: 0.6424 (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: 0.6628 (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: 0.7582 (p0) REVERT: B 416 ILE cc_start: 0.8794 (pt) cc_final: 0.8512 (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: 0.7066 (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: 0.6739 (t80) REVERT: B 778 GLU cc_start: 0.7715 (tt0) cc_final: 0.7462 (pt0) REVERT: B 867 MET cc_start: 0.8509 (mtt) cc_final: 0.8255 (mtt) REVERT: B 915 TYR cc_start: 0.8544 (m-80) cc_final: 0.8212 (m-10) REVERT: B 1111 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8166 (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: 0.6430 (p0) REVERT: C 898 MET cc_start: 0.7490 (mtt) cc_final: 0.7244 (mtt) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.4219 time to fit residues: 330.6139 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 : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.0060 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 40.0000 chunk 249 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN A 911 GLN A 933 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 899 GLN C 924 GLN C1008 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.171259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108747 restraints weight = 41089.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110165 restraints weight = 26798.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111484 restraints weight = 18101.422| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 26446 Z= 0.243 Angle : 0.747 18.569 36097 Z= 0.367 Chirality : 0.050 0.443 4223 Planarity : 0.005 0.058 4567 Dihedral : 8.174 72.924 4698 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.30 % Allowed : 9.17 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3153 helix: 1.75 (0.20), residues: 662 sheet: -0.36 (0.20), residues: 611 loop : -1.73 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 434 HIS 0.010 0.002 HIS A1062 PHE 0.024 0.002 PHE A 904 TYR 0.021 0.002 TYR B1065 ARG 0.005 0.001 ARG C1012 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 48) link_NAG-ASN : angle 2.87370 ( 144) link_BETA1-4 : bond 0.00644 ( 13) link_BETA1-4 : angle 2.62802 ( 39) hydrogen bonds : bond 0.06331 ( 947) hydrogen bonds : angle 5.52156 ( 2625) SS BOND : bond 0.01374 ( 42) SS BOND : angle 2.07155 ( 84) covalent geometry : bond 0.00590 (26342) covalent geometry : angle 0.71468 (35830) Misc. bond : bond 0.00091 ( 1) *********************** 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 313 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 249 time to evaluate : 2.757 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: 0.8746 (mm) cc_final: 0.8467 (mt) REVERT: A 152 TRP cc_start: 0.6002 (t-100) cc_final: 0.5579 (t-100) REVERT: A 153 MET cc_start: 0.6907 (mpp) cc_final: 0.6064 (pmm) REVERT: A 168 TYR cc_start: 0.8509 (t80) cc_final: 0.8112 (t80) REVERT: A 327 PHE cc_start: 0.7724 (m-10) cc_final: 0.7476 (m-10) REVERT: A 578 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8433 (mm-40) REVERT: A 853 PHE cc_start: 0.7798 (m-10) cc_final: 0.7581 (m-80) REVERT: A 1029 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: B 81 ASN cc_start: 0.7660 (p0) cc_final: 0.7452 (p0) REVERT: B 135 PHE cc_start: 0.7999 (m-80) cc_final: 0.7605 (m-80) REVERT: B 264 TYR cc_start: 0.6334 (m-80) cc_final: 0.6077 (m-80) REVERT: B 407 GLN cc_start: 0.7675 (mt0) cc_final: 0.7421 (mp10) REVERT: B 415 LYS cc_start: 0.8879 (mttt) cc_final: 0.8593 (mmmt) REVERT: B 416 ILE cc_start: 0.8698 (pt) cc_final: 0.8498 (pt) REVERT: B 527 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7713 (mttp) REVERT: B 705 TYR cc_start: 0.8133 (t80) cc_final: 0.7597 (t80) REVERT: B 867 MET cc_start: 0.8920 (mtt) cc_final: 0.8718 (mtm) REVERT: B 974 VAL cc_start: 0.8588 (t) cc_final: 0.8346 (t) REVERT: B 977 ASP cc_start: 0.7743 (t0) cc_final: 0.7464 (t0) REVERT: B 1111 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8197 (mt0) REVERT: C 240 LEU cc_start: 0.7732 (pt) cc_final: 0.7491 (pp) REVERT: C 352 ASN cc_start: 0.7391 (t0) cc_final: 0.7182 (t0) REVERT: C 376 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8604 (ttpp) REVERT: C 390 PHE cc_start: 0.8597 (m-10) cc_final: 0.8291 (m-80) REVERT: C 576 ASP cc_start: 0.8089 (t0) cc_final: 0.7729 (t0) REVERT: C 880 ILE cc_start: 0.9107 (mt) cc_final: 0.8898 (mt) REVERT: C 902 TYR cc_start: 0.7283 (m-10) cc_final: 0.7061 (m-10) REVERT: C 1048 MET cc_start: 0.8136 (ptt) cc_final: 0.7924 (ptt) outliers start: 64 outliers final: 40 residues processed: 292 average time/residue: 0.3460 time to fit residues: 166.0851 Evaluate side-chains 243 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 2.959 ------------------------------------------------------------------------------- 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 618 VAL 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 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 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 773 ASP Chi-restraints excluded: chain B residue 996 THR 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 201 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 919 LYS Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1008 GLN Chi-restraints excluded: chain C residue 1028 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 298 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 150 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN A 933 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 HIS ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.173489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116063 restraints weight = 40830.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115514 restraints weight = 23208.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115957 restraints weight = 16314.845| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26446 Z= 0.123 Angle : 0.615 19.314 36097 Z= 0.297 Chirality : 0.045 0.436 4223 Planarity : 0.004 0.070 4567 Dihedral : 7.475 66.029 4698 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.12 % Allowed : 11.97 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3153 helix: 2.19 (0.20), residues: 664 sheet: -0.13 (0.21), residues: 580 loop : -1.60 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 434 HIS 0.005 0.001 HIS B 653 PHE 0.026 0.001 PHE C 560 TYR 0.025 0.001 TYR C 419 ARG 0.015 0.000 ARG C 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 48) link_NAG-ASN : angle 2.72193 ( 144) link_BETA1-4 : bond 0.00799 ( 13) link_BETA1-4 : angle 2.71663 ( 39) hydrogen bonds : bond 0.05015 ( 947) hydrogen bonds : angle 5.15519 ( 2625) SS BOND : bond 0.00289 ( 42) SS BOND : angle 1.53630 ( 84) covalent geometry : bond 0.00282 (26342) covalent geometry : angle 0.58127 (35830) Misc. bond : bond 0.00057 ( 1) *********************** 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 278 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8582 (t80) cc_final: 0.8167 (t80) REVERT: A 171 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8282 (tp40) REVERT: A 952 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: A 1029 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: B 135 PHE cc_start: 0.7924 (m-80) cc_final: 0.7205 (m-80) REVERT: B 200 LYS cc_start: 0.7240 (mttp) cc_final: 0.6915 (mtmt) REVERT: B 264 TYR cc_start: 0.6577 (m-80) cc_final: 0.6323 (m-80) REVERT: B 407 GLN cc_start: 0.7574 (mt0) cc_final: 0.7367 (mt0) REVERT: B 527 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7709 (mttp) REVERT: B 705 TYR cc_start: 0.8051 (t80) cc_final: 0.7456 (t80) REVERT: B 853 PHE cc_start: 0.7076 (m-10) cc_final: 0.6845 (m-10) REVERT: B 876 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8053 (tt) REVERT: B 955 GLN cc_start: 0.8272 (tp40) cc_final: 0.8015 (tt0) REVERT: B 977 ASP cc_start: 0.7805 (t0) cc_final: 0.7504 (t0) REVERT: B 1029 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: B 1111 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8170 (mt0) REVERT: C 49 HIS cc_start: 0.7949 (t-170) cc_final: 0.7700 (t70) REVERT: C 168 TYR cc_start: 0.7005 (t80) cc_final: 0.6689 (t80) REVERT: C 240 LEU cc_start: 0.7719 (pt) cc_final: 0.7491 (pp) REVERT: C 325 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7888 (t) REVERT: C 352 ASN cc_start: 0.7269 (t0) cc_final: 0.6228 (p0) REVERT: C 557 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7704 (t80) REVERT: C 576 ASP cc_start: 0.8061 (t0) cc_final: 0.7591 (t0) outliers start: 59 outliers final: 30 residues processed: 259 average time/residue: 0.3452 time to fit residues: 147.5344 Evaluate side-chains 228 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain 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 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 LEU 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 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 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 549 VAL Chi-restraints excluded: chain C residue 557 PHE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 24 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B 923 ASN C 66 HIS C1008 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.171377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109563 restraints weight = 41234.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110779 restraints weight = 25172.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112016 restraints weight = 17336.032| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26446 Z= 0.167 Angle : 0.632 18.753 36097 Z= 0.306 Chirality : 0.046 0.436 4223 Planarity : 0.004 0.076 4567 Dihedral : 7.126 59.270 4698 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.59 % Allowed : 13.45 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3153 helix: 2.16 (0.20), residues: 653 sheet: -0.07 (0.21), residues: 599 loop : -1.62 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 884 HIS 0.006 0.001 HIS C1062 PHE 0.021 0.002 PHE C 560 TYR 0.017 0.001 TYR B1065 ARG 0.005 0.000 ARG B 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 48) link_NAG-ASN : angle 2.72506 ( 144) link_BETA1-4 : bond 0.00710 ( 13) link_BETA1-4 : angle 2.68721 ( 39) hydrogen bonds : bond 0.05436 ( 947) hydrogen bonds : angle 5.12083 ( 2625) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.55601 ( 84) covalent geometry : bond 0.00405 (26342) covalent geometry : angle 0.59929 (35830) Misc. bond : bond 0.00065 ( 1) *********************** 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 291 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 219 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8842 (mm) cc_final: 0.8546 (mt) REVERT: A 153 MET cc_start: 0.6338 (mpp) cc_final: 0.5759 (pmm) REVERT: A 168 TYR cc_start: 0.8614 (t80) cc_final: 0.8201 (t80) REVERT: A 952 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: A 1029 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: B 135 PHE cc_start: 0.8059 (m-80) cc_final: 0.7389 (m-80) REVERT: B 200 LYS cc_start: 0.7173 (mttp) cc_final: 0.6823 (mtmt) REVERT: B 296 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: B 415 LYS cc_start: 0.8898 (mttt) cc_final: 0.8628 (mmmt) REVERT: B 527 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7712 (mttp) REVERT: B 876 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8138 (tt) REVERT: B 955 GLN cc_start: 0.8327 (tp40) cc_final: 0.8029 (tt0) REVERT: B 977 ASP cc_start: 0.8072 (t0) cc_final: 0.7795 (t0) REVERT: B 1029 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: B 1111 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8162 (mt0) REVERT: C 49 HIS cc_start: 0.8036 (t-170) cc_final: 0.7749 (t-170) REVERT: C 188 ARG cc_start: 0.7363 (mpp80) cc_final: 0.6930 (mpp80) REVERT: C 240 LEU cc_start: 0.7854 (pt) cc_final: 0.7620 (pp) REVERT: C 325 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7950 (t) REVERT: C 327 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.5525 (t80) REVERT: C 352 ASN cc_start: 0.7380 (t0) cc_final: 0.7165 (t0) REVERT: C 547 THR cc_start: 0.8522 (p) cc_final: 0.8320 (p) REVERT: C 576 ASP cc_start: 0.8175 (t0) cc_final: 0.7937 (t0) REVERT: C 880 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8775 (mp) outliers start: 72 outliers final: 38 residues processed: 272 average time/residue: 0.3560 time to fit residues: 157.5068 Evaluate side-chains 245 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain 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 296 GLU Chi-restraints excluded: chain B residue 348 VAL 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 664 ILE Chi-restraints excluded: chain B residue 697 LEU 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 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 205 HIS Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN Chi-restraints excluded: chain C residue 1008 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 235 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 GLN 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 785 GLN C 911 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.169127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105305 restraints weight = 41075.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108941 restraints weight = 24774.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109641 restraints weight = 16859.080| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26446 Z= 0.222 Angle : 0.669 19.038 36097 Z= 0.327 Chirality : 0.047 0.451 4223 Planarity : 0.004 0.068 4567 Dihedral : 7.050 57.909 4698 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.20 % Allowed : 14.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3153 helix: 1.87 (0.20), residues: 662 sheet: -0.12 (0.20), residues: 614 loop : -1.71 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 884 HIS 0.007 0.001 HIS C1062 PHE 0.021 0.002 PHE A 92 TYR 0.019 0.001 TYR B1065 ARG 0.007 0.000 ARG B 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 48) link_NAG-ASN : angle 2.79016 ( 144) link_BETA1-4 : bond 0.00711 ( 13) link_BETA1-4 : angle 2.74847 ( 39) hydrogen bonds : bond 0.05988 ( 947) hydrogen bonds : angle 5.25054 ( 2625) SS BOND : bond 0.00428 ( 42) SS BOND : angle 1.51269 ( 84) covalent geometry : bond 0.00546 (26342) covalent geometry : angle 0.63695 (35830) Misc. bond : bond 0.00068 ( 1) *********************** 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 292 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 203 time to evaluate : 2.776 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: 0.8897 (mm) cc_final: 0.8629 (mt) REVERT: A 153 MET cc_start: 0.6402 (mpp) cc_final: 0.6168 (pmm) REVERT: A 168 TYR cc_start: 0.8633 (t80) cc_final: 0.8269 (t80) REVERT: A 952 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7622 (mt0) REVERT: A 1029 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: B 135 PHE cc_start: 0.8113 (m-80) cc_final: 0.7487 (m-80) REVERT: B 200 LYS cc_start: 0.7178 (mttp) cc_final: 0.6803 (mtmt) REVERT: B 523 CYS cc_start: 0.6501 (OUTLIER) cc_final: 0.5920 (m) REVERT: B 527 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7771 (mttp) REVERT: B 579 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 876 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8159 (tt) REVERT: B 955 GLN cc_start: 0.8378 (tp40) cc_final: 0.8041 (tt0) REVERT: B 1029 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: B 1111 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8142 (mt0) REVERT: C 49 HIS cc_start: 0.8069 (t-170) cc_final: 0.7749 (t-170) REVERT: C 168 TYR cc_start: 0.7124 (t80) cc_final: 0.6851 (t80) REVERT: C 240 LEU cc_start: 0.7985 (pt) cc_final: 0.7767 (pp) REVERT: C 327 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.5583 (t80) REVERT: C 352 ASN cc_start: 0.7398 (t0) cc_final: 0.7168 (t0) REVERT: C 390 PHE cc_start: 0.8817 (m-80) cc_final: 0.8411 (m-80) REVERT: C 527 LYS cc_start: 0.6930 (tptt) cc_final: 0.6539 (mmtm) REVERT: C 576 ASP cc_start: 0.8281 (t0) cc_final: 0.7810 (t0) REVERT: C 880 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8722 (mp) outliers start: 89 outliers final: 49 residues processed: 272 average time/residue: 0.3774 time to fit residues: 168.8539 Evaluate side-chains 246 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 54 LEU 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 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 523 CYS 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 876 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 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 201 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 360 VAL 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 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1029 GLU 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 165 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 267 optimal weight: 5.9990 chunk 240 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.171812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113318 restraints weight = 40825.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113691 restraints weight = 22801.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113467 restraints weight = 17071.792| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3322 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= 0.121 Angle : 0.606 18.858 36097 Z= 0.291 Chirality : 0.045 0.440 4223 Planarity : 0.004 0.058 4567 Dihedral : 6.712 57.745 4698 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.19 % Allowed : 16.58 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3153 helix: 2.25 (0.20), residues: 658 sheet: -0.02 (0.21), residues: 603 loop : -1.58 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.005 0.001 HIS C 205 PHE 0.021 0.001 PHE A 92 TYR 0.015 0.001 TYR B1065 ARG 0.006 0.000 ARG B 565 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 48) link_NAG-ASN : angle 2.64359 ( 144) link_BETA1-4 : bond 0.00801 ( 13) link_BETA1-4 : angle 2.73766 ( 39) hydrogen bonds : bond 0.04842 ( 947) hydrogen bonds : angle 4.95848 ( 2625) SS BOND : bond 0.00302 ( 42) SS BOND : angle 1.26088 ( 84) covalent geometry : bond 0.00279 (26342) covalent geometry : angle 0.57402 (35830) Misc. bond : bond 0.00045 ( 1) *********************** 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 267 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 2.629 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: 0.8968 (mm) cc_final: 0.8676 (mt) REVERT: A 134 GLN cc_start: 0.7356 (tp-100) cc_final: 0.6791 (tm-30) REVERT: A 135 PHE cc_start: 0.7981 (m-80) cc_final: 0.7739 (m-10) REVERT: A 168 TYR cc_start: 0.8739 (t80) cc_final: 0.8331 (t80) REVERT: A 853 PHE cc_start: 0.7748 (m-80) cc_final: 0.7332 (m-80) REVERT: A 952 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: A 1029 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: A 1108 TYR cc_start: 0.8824 (t80) cc_final: 0.8615 (t80) REVERT: B 135 PHE cc_start: 0.8017 (m-80) cc_final: 0.7427 (m-80) REVERT: B 200 LYS cc_start: 0.7189 (mttp) cc_final: 0.6840 (mtmt) REVERT: B 527 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7770 (mttp) REVERT: B 579 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8349 (p) REVERT: B 876 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8088 (tt) REVERT: B 955 GLN cc_start: 0.8333 (tp40) cc_final: 0.7933 (tt0) REVERT: B 1029 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: B 1111 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8116 (mt0) REVERT: C 49 HIS cc_start: 0.8044 (t-170) cc_final: 0.7738 (t-170) REVERT: C 64 TRP cc_start: 0.8201 (t60) cc_final: 0.7907 (t60) REVERT: C 168 TYR cc_start: 0.7026 (t80) cc_final: 0.6727 (t80) REVERT: C 188 ARG cc_start: 0.7802 (mpp80) cc_final: 0.7087 (mtp85) REVERT: C 240 LEU cc_start: 0.7972 (pt) cc_final: 0.7749 (pp) REVERT: C 327 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.5653 (t80) REVERT: C 352 ASN cc_start: 0.7347 (t0) cc_final: 0.7126 (t0) REVERT: C 390 PHE cc_start: 0.8832 (m-80) cc_final: 0.8476 (m-80) REVERT: C 576 ASP cc_start: 0.8316 (t0) cc_final: 0.7881 (t0) REVERT: C 880 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8760 (mp) outliers start: 61 outliers final: 38 residues processed: 251 average time/residue: 0.3340 time to fit residues: 140.3242 Evaluate side-chains 244 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 900 MET 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 187 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 664 ILE 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 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 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 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 261 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 258 optimal weight: 0.2980 chunk 225 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 311 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.171661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110072 restraints weight = 41123.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112102 restraints weight = 25126.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113229 restraints weight = 15807.356| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3442 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= 0.130 Angle : 0.606 18.674 36097 Z= 0.291 Chirality : 0.045 0.442 4223 Planarity : 0.004 0.057 4567 Dihedral : 6.553 57.915 4698 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.27 % Allowed : 16.72 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3153 helix: 2.32 (0.20), residues: 659 sheet: 0.07 (0.21), residues: 624 loop : -1.54 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.005 0.001 HIS C 205 PHE 0.021 0.001 PHE A 92 TYR 0.015 0.001 TYR B1065 ARG 0.006 0.000 ARG B 565 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 48) link_NAG-ASN : angle 2.59461 ( 144) link_BETA1-4 : bond 0.00767 ( 13) link_BETA1-4 : angle 2.70954 ( 39) hydrogen bonds : bond 0.04815 ( 947) hydrogen bonds : angle 4.90257 ( 2625) SS BOND : bond 0.00308 ( 42) SS BOND : angle 1.28369 ( 84) covalent geometry : bond 0.00306 (26342) covalent geometry : angle 0.57558 (35830) Misc. bond : bond 0.00046 ( 1) *********************** 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 271 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 2.883 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: 0.8888 (mm) cc_final: 0.8605 (mt) REVERT: A 168 TYR cc_start: 0.8734 (t80) cc_final: 0.8357 (t80) REVERT: A 853 PHE cc_start: 0.7608 (m-80) cc_final: 0.7252 (m-80) REVERT: A 952 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: A 1029 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: B 135 PHE cc_start: 0.8055 (m-80) cc_final: 0.7474 (m-80) REVERT: B 200 LYS cc_start: 0.7124 (mttp) cc_final: 0.6775 (mtmt) REVERT: B 415 LYS cc_start: 0.9033 (mttt) cc_final: 0.8741 (mmmt) REVERT: B 527 LYS cc_start: 0.8020 (mmtm) cc_final: 0.7722 (mtmm) REVERT: B 579 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.7417 (p) REVERT: B 785 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: B 876 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8103 (tt) REVERT: B 955 GLN cc_start: 0.8296 (tp40) cc_final: 0.7893 (tt0) REVERT: B 1029 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: B 1111 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8098 (mt0) REVERT: C 49 HIS cc_start: 0.8034 (t-170) cc_final: 0.7741 (t-170) REVERT: C 64 TRP cc_start: 0.8132 (t60) cc_final: 0.7721 (t60) REVERT: C 168 TYR cc_start: 0.6941 (t80) cc_final: 0.6618 (t80) REVERT: C 240 LEU cc_start: 0.7963 (pt) cc_final: 0.7741 (pp) REVERT: C 327 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5683 (t80) REVERT: C 352 ASN cc_start: 0.7321 (t0) cc_final: 0.7090 (t0) REVERT: C 390 PHE cc_start: 0.8839 (m-80) cc_final: 0.8563 (m-80) REVERT: C 576 ASP cc_start: 0.8314 (t0) cc_final: 0.7867 (t0) REVERT: C 880 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8699 (mp) outliers start: 63 outliers final: 44 residues processed: 254 average time/residue: 0.3544 time to fit residues: 149.1737 Evaluate side-chains 248 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL 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 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 900 MET 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 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 785 GLN 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 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 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE 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 425 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN Chi-restraints excluded: chain C residue 1029 GLU 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 89 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 226 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN C1008 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.168626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104931 restraints weight = 40888.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108643 restraints weight = 24037.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109303 restraints weight = 17450.297| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26446 Z= 0.223 Angle : 0.676 18.573 36097 Z= 0.329 Chirality : 0.047 0.454 4223 Planarity : 0.004 0.057 4567 Dihedral : 6.736 58.343 4698 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.70 % Allowed : 16.76 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3153 helix: 1.92 (0.20), residues: 668 sheet: -0.11 (0.20), residues: 629 loop : -1.65 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 884 HIS 0.008 0.001 HIS C1062 PHE 0.025 0.002 PHE A 372 TYR 0.018 0.001 TYR B1065 ARG 0.005 0.000 ARG B 565 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 48) link_NAG-ASN : angle 2.69624 ( 144) link_BETA1-4 : bond 0.00751 ( 13) link_BETA1-4 : angle 2.73584 ( 39) hydrogen bonds : bond 0.05933 ( 947) hydrogen bonds : angle 5.15039 ( 2625) SS BOND : bond 0.00434 ( 42) SS BOND : angle 1.48999 ( 84) covalent geometry : bond 0.00549 (26342) covalent geometry : angle 0.64662 (35830) Misc. bond : bond 0.00068 ( 1) *********************** 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 279 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 204 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8224 (tptt) cc_final: 0.7890 (mmmt) REVERT: A 128 ILE cc_start: 0.8891 (mm) cc_final: 0.8643 (mt) REVERT: A 134 GLN cc_start: 0.7723 (tp-100) cc_final: 0.6842 (tm-30) REVERT: A 153 MET cc_start: 0.6452 (pmm) cc_final: 0.6120 (pmm) REVERT: A 168 TYR cc_start: 0.8711 (t80) cc_final: 0.8353 (t80) REVERT: A 175 MET cc_start: 0.5498 (mpp) cc_final: 0.3780 (tpt) REVERT: A 952 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: A 1029 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7214 (mt-10) REVERT: B 135 PHE cc_start: 0.8112 (m-80) cc_final: 0.7494 (m-80) REVERT: B 415 LYS cc_start: 0.9099 (mttt) cc_final: 0.8723 (mmmt) REVERT: B 527 LYS cc_start: 0.8181 (mmtm) cc_final: 0.7784 (mtmm) REVERT: B 579 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8024 (p) REVERT: B 876 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 955 GLN cc_start: 0.8359 (tp40) cc_final: 0.7947 (tt0) REVERT: B 1029 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 1111 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8190 (mt0) REVERT: C 49 HIS cc_start: 0.8073 (t-170) cc_final: 0.7786 (t-170) REVERT: C 51 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8173 (t) REVERT: C 64 TRP cc_start: 0.8150 (t60) cc_final: 0.7849 (t60) REVERT: C 168 TYR cc_start: 0.7138 (t80) cc_final: 0.6819 (t80) REVERT: C 188 ARG cc_start: 0.7917 (mpp80) cc_final: 0.7085 (mtp85) REVERT: C 240 LEU cc_start: 0.8072 (pt) cc_final: 0.7830 (pp) REVERT: C 327 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.5887 (t80) REVERT: C 352 ASN cc_start: 0.7374 (t0) cc_final: 0.7133 (t0) REVERT: C 390 PHE cc_start: 0.8895 (m-80) cc_final: 0.8614 (m-80) REVERT: C 576 ASP cc_start: 0.8390 (t0) cc_final: 0.7926 (t0) REVERT: C 880 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8730 (mp) outliers start: 75 outliers final: 56 residues processed: 260 average time/residue: 0.3421 time to fit residues: 147.1159 Evaluate side-chains 257 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 193 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 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 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 900 MET 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 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 40 ASP 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 201 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 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 876 LEU Chi-restraints excluded: chain B residue 909 VAL 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 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE 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 425 ASP 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 557 PHE Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 732 THR 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 1003 GLN Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 76 optimal weight: 5.9990 chunk 306 optimal weight: 0.6980 chunk 277 optimal weight: 0.9980 chunk 289 optimal weight: 0.0570 chunk 6 optimal weight: 0.0670 chunk 168 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 237 optimal weight: 0.5980 chunk 202 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 302 optimal weight: 0.1980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.174001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110757 restraints weight = 40567.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114887 restraints weight = 21608.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117545 restraints weight = 14706.442| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26446 Z= 0.106 Angle : 0.600 18.677 36097 Z= 0.289 Chirality : 0.045 0.446 4223 Planarity : 0.004 0.060 4567 Dihedral : 6.410 57.683 4698 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.73 % Allowed : 17.76 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3153 helix: 2.46 (0.20), residues: 660 sheet: 0.01 (0.20), residues: 638 loop : -1.48 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 434 HIS 0.005 0.001 HIS C 205 PHE 0.031 0.001 PHE A 372 TYR 0.014 0.001 TYR B1065 ARG 0.005 0.000 ARG B 565 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 48) link_NAG-ASN : angle 2.52758 ( 144) link_BETA1-4 : bond 0.00842 ( 13) link_BETA1-4 : angle 2.75584 ( 39) hydrogen bonds : bond 0.04317 ( 947) hydrogen bonds : angle 4.81034 ( 2625) SS BOND : bond 0.00280 ( 42) SS BOND : angle 1.11769 ( 84) covalent geometry : bond 0.00233 (26342) covalent geometry : angle 0.57081 (35830) Misc. bond : bond 0.00026 ( 1) *********************** 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 263 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9025 (mm) cc_final: 0.8730 (mt) REVERT: A 134 GLN cc_start: 0.7253 (tp-100) cc_final: 0.6591 (tm-30) REVERT: A 153 MET cc_start: 0.6405 (pmm) cc_final: 0.6056 (pmm) REVERT: A 154 GLU cc_start: 0.5627 (OUTLIER) cc_final: 0.4884 (tm-30) REVERT: A 168 TYR cc_start: 0.8793 (t80) cc_final: 0.8475 (t80) REVERT: A 175 MET cc_start: 0.4954 (mpp) cc_final: 0.3987 (tpt) REVERT: A 853 PHE cc_start: 0.7556 (m-80) cc_final: 0.7237 (m-80) REVERT: A 880 ILE cc_start: 0.8503 (pt) cc_final: 0.8249 (mt) REVERT: A 952 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7495 (mt0) REVERT: A 1029 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: B 135 PHE cc_start: 0.7831 (m-80) cc_final: 0.7217 (m-80) REVERT: B 175 MET cc_start: 0.5333 (pmm) cc_final: 0.4382 (pmm) REVERT: B 579 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 955 GLN cc_start: 0.8254 (tp40) cc_final: 0.7775 (tt0) REVERT: B 1029 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: B 1111 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8134 (mt0) REVERT: C 49 HIS cc_start: 0.7974 (t-170) cc_final: 0.7765 (t-170) REVERT: C 168 TYR cc_start: 0.7185 (t80) cc_final: 0.6897 (t80) REVERT: C 188 ARG cc_start: 0.7699 (mpp80) cc_final: 0.7167 (mpp80) REVERT: C 240 LEU cc_start: 0.7874 (pt) cc_final: 0.7666 (pp) REVERT: C 327 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6318 (t80) REVERT: C 352 ASN cc_start: 0.7269 (t0) cc_final: 0.7035 (t0) REVERT: C 390 PHE cc_start: 0.8753 (m-80) cc_final: 0.8465 (m-80) REVERT: C 576 ASP cc_start: 0.8261 (t0) cc_final: 0.8008 (t0) REVERT: C 880 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8700 (mp) outliers start: 48 outliers final: 34 residues processed: 250 average time/residue: 0.3425 time to fit residues: 141.8642 Evaluate side-chains 239 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 952 GLN 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 62 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS 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 975 LEU 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 201 ILE 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 513 PHE Chi-restraints excluded: chain C residue 557 PHE Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN Chi-restraints excluded: chain C residue 1029 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 60 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 270 optimal weight: 0.1980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.172460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112164 restraints weight = 40548.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113736 restraints weight = 24642.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113994 restraints weight = 18536.648| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26446 Z= 0.129 Angle : 0.610 18.250 36097 Z= 0.291 Chirality : 0.045 0.443 4223 Planarity : 0.004 0.062 4567 Dihedral : 6.363 57.888 4698 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.55 % Allowed : 18.52 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3153 helix: 2.46 (0.20), residues: 661 sheet: 0.00 (0.20), residues: 633 loop : -1.46 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 64 HIS 0.005 0.001 HIS C 205 PHE 0.038 0.001 PHE A 372 TYR 0.014 0.001 TYR B1065 ARG 0.005 0.000 ARG B 565 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 48) link_NAG-ASN : angle 2.51461 ( 144) link_BETA1-4 : bond 0.00768 ( 13) link_BETA1-4 : angle 2.68714 ( 39) hydrogen bonds : bond 0.04679 ( 947) hydrogen bonds : angle 4.82641 ( 2625) SS BOND : bond 0.00292 ( 42) SS BOND : angle 1.15880 ( 84) covalent geometry : bond 0.00305 (26342) covalent geometry : angle 0.58158 (35830) Misc. bond : bond 0.00040 ( 1) ********************** 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 243 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 2.600 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 97 LYS cc_start: 0.8184 (tptt) cc_final: 0.7856 (mmmt) REVERT: A 128 ILE cc_start: 0.9030 (mm) cc_final: 0.8760 (mt) REVERT: A 134 GLN cc_start: 0.7381 (tp-100) cc_final: 0.6623 (tm-30) REVERT: A 154 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5157 (tm-30) REVERT: A 168 TYR cc_start: 0.8807 (t80) cc_final: 0.8464 (t80) REVERT: A 175 MET cc_start: 0.5004 (mpp) cc_final: 0.4179 (tpt) REVERT: A 952 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: A 1029 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: B 135 PHE cc_start: 0.7877 (m-80) cc_final: 0.7235 (m-80) REVERT: B 175 MET cc_start: 0.5268 (pmm) cc_final: 0.4371 (pmm) REVERT: B 415 LYS cc_start: 0.9054 (mttt) cc_final: 0.8791 (mmmt) REVERT: B 579 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8141 (p) REVERT: B 955 GLN cc_start: 0.8280 (tp40) cc_final: 0.7820 (tt0) REVERT: B 1029 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: B 1111 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8170 (mt0) REVERT: C 49 HIS cc_start: 0.8015 (t-170) cc_final: 0.7790 (t-170) REVERT: C 168 TYR cc_start: 0.7194 (t80) cc_final: 0.6895 (t80) REVERT: C 188 ARG cc_start: 0.7697 (mpp80) cc_final: 0.7124 (mpp80) REVERT: C 240 LEU cc_start: 0.7999 (pt) cc_final: 0.7765 (pp) REVERT: C 327 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6308 (t80) REVERT: C 352 ASN cc_start: 0.7253 (t0) cc_final: 0.7017 (t0) REVERT: C 576 ASP cc_start: 0.8348 (t0) cc_final: 0.7931 (t0) REVERT: C 880 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8754 (mp) outliers start: 43 outliers final: 34 residues processed: 231 average time/residue: 0.3687 time to fit residues: 139.3507 Evaluate side-chains 232 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 952 GLN 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 62 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS 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 695 MET 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 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE 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 513 PHE Chi-restraints excluded: chain C residue 557 PHE Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN Chi-restraints excluded: chain C residue 1029 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 299 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 283 optimal weight: 2.9990 chunk 231 optimal weight: 0.0020 chunk 257 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.173803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113091 restraints weight = 40686.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115165 restraints weight = 30831.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115831 restraints weight = 18389.280| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26446 Z= 0.110 Angle : 0.602 18.340 36097 Z= 0.287 Chirality : 0.044 0.452 4223 Planarity : 0.004 0.052 4567 Dihedral : 6.225 57.827 4698 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.83 % Allowed : 18.30 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3153 helix: 2.62 (0.20), residues: 655 sheet: 0.07 (0.20), residues: 644 loop : -1.41 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 434 HIS 0.005 0.001 HIS C 205 PHE 0.044 0.001 PHE A 372 TYR 0.014 0.001 TYR B1065 ARG 0.006 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 48) link_NAG-ASN : angle 2.46658 ( 144) link_BETA1-4 : bond 0.00792 ( 13) link_BETA1-4 : angle 2.69033 ( 39) hydrogen bonds : bond 0.04289 ( 947) hydrogen bonds : angle 4.71840 ( 2625) SS BOND : bond 0.00264 ( 42) SS BOND : angle 1.06512 ( 84) covalent geometry : bond 0.00251 (26342) covalent geometry : angle 0.57426 (35830) Misc. bond : bond 0.00031 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8486.56 seconds wall clock time: 148 minutes 12.04 seconds (8892.04 seconds total)