Starting phenix.real_space_refine on Fri Aug 7 16:30:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lvi_63420/08_2026/9lvi_63420.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lvi_63420/08_2026/9lvi_63420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lvi_63420/08_2026/9lvi_63420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lvi_63420/08_2026/9lvi_63420.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lvi_63420/08_2026/9lvi_63420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lvi_63420/08_2026/9lvi_63420.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 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 97 5.16 5 C 14213 2.51 5 N 3669 2.21 5 O 4319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22298 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7314 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 46, 'TRANS': 908} Chain breaks: 15 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 6919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 6919 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 46, 'TRANS': 903} Chain breaks: 13 Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 673 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 8, 'ARG:plan': 7, 'PHE:plan': 6, 'TYR:plan': 11, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 336 Chain: "C" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7281 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 47, 'TRANS': 912} Chain breaks: 11 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 13, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 143 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.16, per 1000 atoms: 0.23 Number of scatterers: 22298 At special positions: 0 Unit cell: (129.48, 126.16, 176.79, 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 97 16.00 O 4319 8.00 N 3669 7.00 C 14213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5388 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 39 sheets defined 26.6% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.984A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.375A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.137A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.780A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.639A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.000A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.577A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.654A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.748A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.921A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.553A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.814A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.746A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.798A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.005A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.953A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.306A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.557A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.866A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.861A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.722A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.982A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.483A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.843A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.615A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.131A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.543A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.758A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.488A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.116A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.570A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.940A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.863A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.501A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.652A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 434 through 435 Processing sheet with id=AC3, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.167A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.296A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.718A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.718A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.581A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.123A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.861A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.706A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.981A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.552A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.745A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.412A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 1094 through 1097 893 hydrogen bonds defined for protein. 2463 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: 5.61 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5129 1.33 - 1.45: 5007 1.45 - 1.57: 12493 1.57 - 1.70: 2 1.70 - 1.82: 121 Bond restraints: 22752 Sorted by residual: bond pdb=" CA ILE B 402 " pdb=" C ILE B 402 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.23e-02 6.61e+03 1.43e+01 bond pdb=" N VAL C 171 " pdb=" CA VAL C 171 " ideal model delta sigma weight residual 1.458 1.414 0.044 1.17e-02 7.31e+03 1.43e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CA ASN B 87 " pdb=" C ASN B 87 " ideal model delta sigma weight residual 1.528 1.556 -0.029 8.80e-03 1.29e+04 1.06e+01 bond pdb=" C5 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 9.84e+00 ... (remaining 22747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 30483 2.36 - 4.72: 482 4.72 - 7.08: 38 7.08 - 9.44: 5 9.44 - 11.80: 2 Bond angle restraints: 31010 Sorted by residual: angle pdb=" N ILE B 418 " pdb=" CA ILE B 418 " pdb=" C ILE B 418 " ideal model delta sigma weight residual 111.58 99.78 11.80 1.06e+00 8.90e-01 1.24e+02 angle pdb=" N VAL B 407 " pdb=" CA VAL B 407 " pdb=" C VAL B 407 " ideal model delta sigma weight residual 110.72 103.49 7.23 1.01e+00 9.80e-01 5.12e+01 angle pdb=" C LEU B 229 " pdb=" N PRO B 230 " pdb=" CA PRO B 230 " ideal model delta sigma weight residual 119.84 112.29 7.55 1.25e+00 6.40e-01 3.64e+01 angle pdb=" N LYS B 417 " pdb=" CA LYS B 417 " pdb=" C LYS B 417 " ideal model delta sigma weight residual 111.04 119.62 -8.58 1.55e+00 4.16e-01 3.07e+01 angle pdb=" O VAL B 401 " pdb=" C VAL B 401 " pdb=" N ILE B 402 " ideal model delta sigma weight residual 121.96 126.29 -4.33 8.40e-01 1.42e+00 2.66e+01 ... (remaining 31005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.35: 13021 25.35 - 50.70: 894 50.70 - 76.05: 158 76.05 - 101.39: 79 101.39 - 126.74: 72 Dihedral angle restraints: 14224 sinusoidal: 5905 harmonic: 8319 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 178.27 -85.27 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -166.21 80.21 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.25 66.25 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 14221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.968: 3794 0.968 - 1.937: 1 1.937 - 2.905: 0 2.905 - 3.873: 0 3.873 - 4.841: 1 Chirality restraints: 3796 Sorted by residual: chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 2.44 -4.84 2.00e-01 2.50e+01 5.86e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -3.03 0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 3793 not shown) Planarity restraints: 3964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1312 " -0.328 2.00e-02 2.50e+03 2.80e-01 9.78e+02 pdb=" C7 NAG B1312 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1312 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG B1312 " 0.491 2.00e-02 2.50e+03 pdb=" O7 NAG B1312 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " 0.240 2.00e-02 2.50e+03 2.00e-01 5.00e+02 pdb=" C7 NAG C1311 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " -0.332 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " 0.071 2.00e-02 2.50e+03 5.79e-02 4.19e+01 pdb=" C7 NAG B1311 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " -0.091 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " -0.013 2.00e-02 2.50e+03 ... (remaining 3961 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 278 2.61 - 3.18: 20643 3.18 - 3.75: 34886 3.75 - 4.33: 48399 4.33 - 4.90: 80242 Nonbonded interactions: 184448 Sorted by model distance: nonbonded pdb=" O GLU C 309 " pdb=" OH TYR C 313 " model vdw 2.033 3.040 nonbonded pdb=" OE2 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.049 3.040 nonbonded pdb=" O4 NAG B1308 " pdb=" O7 NAG B1308 " model vdw 2.058 3.040 nonbonded pdb=" OG1 THR A 716 " pdb=" O GLN A1071 " model vdw 2.106 3.040 nonbonded pdb=" O GLU B 309 " pdb=" OH TYR B 313 " model vdw 2.115 3.040 ... (remaining 184443 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 165 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 201 through 212 or resid 222 through 22 \ 3 or (resid 224 and (name N or name CA or name C or name O or name CB )) or resi \ d 225 through 238 or (resid 239 and (name N or name CA or name C or name O or na \ me CB )) or resid 240 or resid 264 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 332 o \ r (resid 333 through 334 and (name N or name CA or name C or name O or name CB ) \ ) or resid 335 through 345 or (resid 346 through 360 and (name N or name CA or n \ ame C or name O or name CB )) or resid 361 or (resid 362 through 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 or (resid 366 through \ 368 and (name N or name CA or name C or name O or name CB )) or resid 369 or (r \ esid 370 through 372 and (name N or name CA or name C or name O or name CB )) or \ resid 373 through 374 or (resid 375 through 376 and (name N or name CA or name \ C or name O or name CB )) or resid 377 or (resid 378 and (name N or name CA or n \ ame C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA \ or name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (na \ me N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thr \ ough 390 and (name N or name CA or name C or name O or name CB )) or resid 391 t \ hrough 392 or (resid 393 through 402 and (name N or name CA or name C or name O \ or name CB )) or resid 403 through 406 or (resid 407 and (name N or name CA or n \ ame C or name O or name CB )) or resid 408 through 409 or (resid 410 through 411 \ and (name N or name CA or name C or name O or name CB )) or resid 412 through 4 \ 13 or (resid 414 through 415 and (name N or name CA or name C or name O or name \ CB )) or resid 416 or (resid 417 through 425 and (name N or name CA or name C or \ name O or name CB )) or resid 426 through 427 or (resid 428 through 430 and (na \ me N or name CA or name C or name O or name CB )) or resid 431 through 432 or (r \ esid 433 through 442 and (name N or name CA or name C or name O or name CB )) or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 3 or (resid 464 through 466 and (name N or name CA or name C or name O or name C \ B )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C or \ name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or name \ CA or name C or name O or name CB )) or resid 499 or (resid 500 through 503 and \ (name N or name CA or name C or name O or name CB )) or (resid 504 through 506 a \ nd (name N or name CA or name C or name O or name CB )) or resid 507 or (resid 5 \ 08 through 515 and (name N or name CA or name C or name O or name CB )) or (resi \ d 522 through 524 and (name N or name CA or name C or name O or name CB )) or re \ sid 525 through 528 or (resid 529 and (name N or name CA or name C or name O or \ name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA or name \ C or name O or name CB )) or resid 555 through 793 or (resid 794 and (name N or \ name CA or name C or name O or name CB )) or resid 795 or (resid 796 and (name \ N or name CA or name C or name O or name CB )) or resid 797 through 810 or (resi \ d 811 and (name N or name CA or name C or name O or name CB )) or resid 813 thro \ ugh 827 or resid 856 through 866 or (resid 867 through 868 and (name N or name C \ A or name C or name O or name CB )) or resid 869 through 939 or (resid 940 and ( \ name N or name CA or name C or name O or name CB )) or resid 941 through 984 or \ (resid 985 and (name N or name CA or name C or name O or name CB )) or resid 986 \ through 987 or (resid 988 through 989 and (name N or name CA or name C or name \ O or name CB )) or resid 990 through 1141 or (resid 1142 and (name N or name CA \ or name C or name O or name CB )) or resid 1143 through 1144 or (resid 1145 thro \ ugh 1146 and (name N or name CA or name C or name O or name CB )) or resid 1147 \ through 1309)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 165 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 201 through 210 or resid 216 or resid 222 through 240 or resid 264 throug \ h 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or \ resid 282 through 323 or (resid 324 and (name N or name CA or name C or name O o \ r name CB )) or resid 325 through 442 or resid 462 through 501 or resid 503 thro \ ugh 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) o \ r resid 569 through 570 or (resid 571 and (name N or name CA or name C or name O \ or name CB )) or resid 572 through 581 or (resid 582 through 583 and (name N or \ name CA or name C or name O or name CB )) or resid 584 through 585 or (resid 58 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 587 through \ 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) or re \ sid 615 through 618 or (resid 619 and (name N or name CA or name C or name O or \ name CB )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and ( \ name N or name CA or name C or name O or name CB )) or resid 746 through 810 or \ (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 813 \ through 827 or resid 856 through 866 or (resid 867 through 868 and (name N or n \ ame CA or name C or name O or name CB )) or resid 869 through 920 or (resid 921 \ and (name N or name CA or name C or name O or name CB )) or resid 922 through 93 \ 9 or (resid 940 and (name N or name CA or name C or name O or name CB )) or resi \ d 941 through 984 or (resid 985 and (name N or name CA or name C or name O or na \ me CB )) or resid 986 through 987 or (resid 988 through 989 and (name N or name \ CA or name C or name O or name CB )) or resid 990 through 1072 or (resid 1073 an \ d (name N or name CA or name C or name O or name CB )) or resid 1074 through 111 \ 7 or (resid 1118 and (name N or name CA or name C or name O or name CB )) or res \ id 1119 through 1143 or (resid 1144 through 1146 and (name N or name CA or name \ C or name O or name CB )) or resid 1147 through 1309)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 165 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201 through 210 or resid 212 or resid 222 t \ hrough 223 or (resid 224 and (name N or name CA or name C or name O or name CB ) \ ) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or nam \ e O or name CB )) or resid 240 or resid 264 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 332 or (resi \ d 333 through 334 and (name N or name CA or name C or name O or name CB )) or re \ sid 335 through 344 or (resid 345 through 360 and (name N or name CA or name C o \ r name O or name CB )) or resid 361 or (resid 362 through 364 and (name N or nam \ e CA or name C or name O or name CB )) or resid 365 or (resid 366 through 368 an \ d (name N or name CA or name C or name O or name CB )) or resid 369 or (resid 37 \ 0 through 372 and (name N or name CA or name C or name O or name CB )) or resid \ 373 through 374 or (resid 375 through 376 and (name N or name CA or name C or na \ me O or name CB )) or resid 377 through 379 or (resid 380 and (name N or name CA \ or name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (n \ ame N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 th \ rough 390 and (name N or name CA or name C or name O or name CB )) or resid 391 \ through 392 or (resid 393 through 402 and (name N or name CA or name C or name O \ or name CB )) or resid 403 through 405 or (resid 406 through 407 and (name N or \ name CA or name C or name O or name CB )) or resid 408 through 409 or (resid 41 \ 0 through 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 413 or (resid 414 through 415 and (name N or name CA or name C or na \ me O or name CB )) or (resid 416 through 425 and (name N or name CA or name C or \ name O or name CB )) or resid 426 or (resid 427 through 430 and (name N or name \ CA or name C or name O or name CB )) or resid 431 through 432 or (resid 433 thr \ ough 442 and (name N or name CA or name C or name O or name CB )) or resid 462 t \ hrough 463 or (resid 464 through 466 and (name N or name CA or name C or name O \ or name CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or n \ ame C or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N \ or name CA or name C or name O or name CB )) or resid 499 through 500 or (resid \ 501 and (name N or name CA or name C or name O or name CB )) or (resid 503 and \ (name N or name CA or name C or name O or name CB )) or (resid 504 through 506 a \ nd (name N or name CA or name C or name O or name CB )) or resid 507 or (resid 5 \ 08 through 515 and (name N or name CA or name C or name O or name CB )) or (resi \ d 522 through 524 and (name N or name CA or name C or name O or name CB )) or re \ sid 525 through 527 or (resid 528 through 529 and (name N or name CA or name C o \ r name O or name CB )) or resid 530 through 553 or (resid 554 and (name N or nam \ e CA or name C or name O or name CB )) or resid 555 through 567 or (resid 568 an \ d (name N or name CA or name C or name O or name CB )) or resid 569 through 570 \ or (resid 571 and (name N or name CA or name C or name O or name CB )) or resid \ 572 through 581 or (resid 582 through 583 and (name N or name CA or name C or na \ me O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 618 or (resid 619 and (n \ ame N or name CA or name C or name O or name CB )) or resid 620 through 645 or ( \ resid 646 through 647 and (name N or name CA or name C or name O or name CB )) o \ r resid 648 through 793 or (resid 794 and (name N or name CA or name C or name O \ or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C or na \ me O or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA \ or name C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and \ (name N or name CA or name C or name O or name CB )) or resid 1074 through 1117 \ or (resid 1118 and (name N or name CA or name C or name O or name CB )) or resid \ 1119 through 1141 or (resid 1142 and (name N or name CA or name C or name O or \ name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1147 through 1309)) } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.780 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.006 0.334 22843 Z= 0.295 Angle : 0.765 25.670 31244 Z= 0.400 Chirality : 0.095 4.841 3796 Planarity : 0.007 0.280 3922 Dihedral : 20.595 126.742 8728 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.80 % Allowed : 23.81 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2781 helix: 2.52 (0.21), residues: 661 sheet: -0.32 (0.21), residues: 530 loop : -1.74 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 403 TYR 0.035 0.001 TYR C 170 PHE 0.044 0.001 PHE C 377 TRP 0.022 0.001 TRP A 104 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.26 (22752) covalent geometry : angle 0.68436 / 0.38 (31010) SS BOND : bond 0.00426 / 0.27 ( 36) SS BOND : angle 1.21161 / 0.78 ( 72) hydrogen bonds : bond 0.11636 / 7.62 ( 881) hydrogen bonds : angle 6.72835 / 4.64 ( 2463) Misc. bond : bond 0.00351 / 0.18 ( 1) link_BETA1-4 : bond 0.00277 / 0.16 ( 12) link_BETA1-4 : angle 2.24843 / 1.27 ( 36) link_NAG-ASN : bond 0.06502 / 5.21 ( 42) link_NAG-ASN : angle 5.24343 / 3.72 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7678 (tt) REVERT: A 360 ASN cc_start: 0.8357 (t0) cc_final: 0.7963 (t0) REVERT: A 394 ASN cc_start: 0.7281 (t0) cc_final: 0.6721 (t0) REVERT: A 408 ARG cc_start: 0.8786 (ptm160) cc_final: 0.8363 (ppt90) REVERT: A 422 ASN cc_start: 0.8301 (m110) cc_final: 0.7612 (p0) REVERT: B 269 TYR cc_start: 0.8160 (m-80) cc_final: 0.7847 (m-80) REVERT: B 574 ASP cc_start: 0.7881 (t0) cc_final: 0.7674 (t0) outliers start: 18 outliers final: 10 residues processed: 189 average time/residue: 0.3940 time to fit residues: 90.1005 Evaluate side-chains 171 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain C residue 421 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 414 GLN B 564 GLN B 675 GLN C1071 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.092308 restraints weight = 38611.310| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.04 r_work: 0.3061 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22843 Z= 0.198 Angle : 0.703 16.102 31244 Z= 0.324 Chirality : 0.051 0.651 3796 Planarity : 0.004 0.068 3922 Dihedral : 15.077 108.352 4214 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.27 % Allowed : 22.17 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2781 helix: 2.60 (0.20), residues: 657 sheet: -0.42 (0.21), residues: 531 loop : -1.60 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 403 TYR 0.022 0.001 TYR A1138 PHE 0.021 0.002 PHE A 168 TRP 0.027 0.001 TRP A 104 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (22752) covalent geometry : angle 0.65984 / 0.31 (31010) SS BOND : bond 0.00390 / 0.24 ( 36) SS BOND : angle 1.34619 / 0.89 ( 72) hydrogen bonds : bond 0.04301 / 2.85 ( 881) hydrogen bonds : angle 5.66292 / 3.87 ( 2463) Misc. bond : bond 0.00437 / 0.23 ( 1) link_BETA1-4 : bond 0.00444 / 0.26 ( 12) link_BETA1-4 : angle 2.00553 / 1.21 ( 36) link_NAG-ASN : bond 0.00671 / 0.41 ( 42) link_NAG-ASN : angle 3.62582 / 2.51 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 181 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: A 324 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: A 360 ASN cc_start: 0.8575 (t0) cc_final: 0.8271 (t0) REVERT: A 408 ARG cc_start: 0.8491 (ptm160) cc_final: 0.8103 (ppt90) REVERT: A 529 LYS cc_start: 0.8010 (mmmm) cc_final: 0.7648 (mppt) REVERT: B 191 GLU cc_start: 0.8315 (mp0) cc_final: 0.7974 (mp0) REVERT: B 194 PHE cc_start: 0.8099 (m-10) cc_final: 0.7853 (m-10) REVERT: B 269 TYR cc_start: 0.8425 (m-80) cc_final: 0.8031 (m-80) REVERT: B 574 ASP cc_start: 0.8524 (t0) cc_final: 0.8173 (t0) REVERT: B 855 PHE cc_start: 0.7651 (m-10) cc_final: 0.7440 (m-10) REVERT: B 988 GLU cc_start: 0.8934 (pm20) cc_final: 0.8554 (pm20) outliers start: 74 outliers final: 20 residues processed: 237 average time/residue: 0.4417 time to fit residues: 126.7565 Evaluate side-chains 181 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 233 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 135 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 132 optimal weight: 50.0000 chunk 30 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 969 ASN C1083 HIS C1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.146446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.089105 restraints weight = 38507.315| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.09 r_work: 0.3070 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22843 Z= 0.189 Angle : 0.678 15.970 31244 Z= 0.311 Chirality : 0.049 0.626 3796 Planarity : 0.004 0.039 3922 Dihedral : 11.826 108.280 4203 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.72 % Allowed : 22.26 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2781 helix: 2.57 (0.20), residues: 657 sheet: -0.39 (0.21), residues: 553 loop : -1.60 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.018 0.001 TYR B1067 PHE 0.022 0.001 PHE B 92 TRP 0.029 0.001 TRP A 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (22752) covalent geometry : angle 0.63414 / 0.30 (31010) SS BOND : bond 0.00531 / 0.30 ( 36) SS BOND : angle 1.35276 / 0.88 ( 72) hydrogen bonds : bond 0.04165 / 2.76 ( 881) hydrogen bonds : angle 5.44687 / 3.70 ( 2463) Misc. bond : bond 0.00422 / 0.22 ( 1) link_BETA1-4 : bond 0.00345 / 0.21 ( 12) link_BETA1-4 : angle 2.02506 / 1.23 ( 36) link_NAG-ASN : bond 0.00591 / 0.35 ( 42) link_NAG-ASN : angle 3.57777 / 2.47 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 164 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6704 (tm) REVERT: A 314 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8369 (tm-30) REVERT: A 324 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: A 360 ASN cc_start: 0.8555 (t0) cc_final: 0.8305 (t0) REVERT: A 529 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7869 (mppt) REVERT: A 580 GLN cc_start: 0.7843 (pt0) cc_final: 0.7597 (pt0) REVERT: A 900 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8500 (mtm) REVERT: A 1017 GLU cc_start: 0.9111 (tt0) cc_final: 0.8853 (tm-30) REVERT: B 194 PHE cc_start: 0.8200 (m-10) cc_final: 0.7996 (m-10) REVERT: B 269 TYR cc_start: 0.8451 (m-80) cc_final: 0.8031 (m-80) REVERT: B 324 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: B 560 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8861 (mp) REVERT: B 574 ASP cc_start: 0.8525 (t0) cc_final: 0.8129 (t0) REVERT: B 855 PHE cc_start: 0.7742 (m-10) cc_final: 0.7527 (m-10) REVERT: B 985 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: B 988 GLU cc_start: 0.8984 (pm20) cc_final: 0.8555 (pm20) outliers start: 84 outliers final: 41 residues processed: 226 average time/residue: 0.4149 time to fit residues: 114.6241 Evaluate side-chains 199 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 274 optimal weight: 0.9980 chunk 275 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.150845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094415 restraints weight = 38508.261| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.04 r_work: 0.3097 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22843 Z= 0.139 Angle : 0.641 15.443 31244 Z= 0.295 Chirality : 0.048 0.571 3796 Planarity : 0.004 0.040 3922 Dihedral : 10.288 104.622 4201 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.58 % Allowed : 22.96 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.16), residues: 2781 helix: 2.62 (0.20), residues: 658 sheet: -0.27 (0.21), residues: 538 loop : -1.51 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.024 0.001 TYR A1138 PHE 0.025 0.001 PHE B 168 TRP 0.031 0.001 TRP A 104 HIS 0.003 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (22752) covalent geometry : angle 0.59708 / 0.28 (31010) SS BOND : bond 0.00318 / 0.19 ( 36) SS BOND : angle 1.28786 / 0.82 ( 72) hydrogen bonds : bond 0.03794 / 2.50 ( 881) hydrogen bonds : angle 5.26419 / 3.56 ( 2463) Misc. bond : bond 0.00418 / 0.22 ( 1) link_BETA1-4 : bond 0.00457 / 0.26 ( 12) link_BETA1-4 : angle 2.09479 / 1.28 ( 36) link_NAG-ASN : bond 0.00590 / 0.36 ( 42) link_NAG-ASN : angle 3.43831 / 2.41 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 171 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.8517 (t0) cc_final: 0.8273 (t0) REVERT: A 529 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7935 (mppt) REVERT: A 580 GLN cc_start: 0.7849 (pt0) cc_final: 0.7602 (pt0) REVERT: A 900 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8427 (mtm) REVERT: A 1017 GLU cc_start: 0.9100 (tt0) cc_final: 0.8846 (tm-30) REVERT: A 1101 HIS cc_start: 0.8205 (m90) cc_final: 0.7717 (m90) REVERT: B 200 TYR cc_start: 0.5668 (m-10) cc_final: 0.5442 (m-10) REVERT: B 324 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8430 (pm20) REVERT: B 560 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8910 (mp) REVERT: B 574 ASP cc_start: 0.8547 (t0) cc_final: 0.8120 (t0) REVERT: B 603 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8111 (t0) REVERT: B 985 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: B 988 GLU cc_start: 0.9011 (pm20) cc_final: 0.8573 (pm20) REVERT: C 118 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6403 (pt) outliers start: 81 outliers final: 40 residues processed: 232 average time/residue: 0.4347 time to fit residues: 122.7921 Evaluate side-chains 194 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 182 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 123 optimal weight: 40.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 751 ASN A 969 ASN B 207 HIS C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.145024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.087798 restraints weight = 38285.540| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.01 r_work: 0.3054 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22843 Z= 0.208 Angle : 0.668 16.060 31244 Z= 0.310 Chirality : 0.048 0.606 3796 Planarity : 0.004 0.049 3922 Dihedral : 9.586 103.375 4199 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.94 % Allowed : 23.27 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2781 helix: 2.46 (0.20), residues: 662 sheet: -0.44 (0.21), residues: 576 loop : -1.48 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 995 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.001 PHE B 92 TRP 0.038 0.001 TRP A 104 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (22752) covalent geometry : angle 0.62410 / 0.30 (31010) SS BOND : bond 0.00374 / 0.24 ( 36) SS BOND : angle 1.44709 / 0.92 ( 72) hydrogen bonds : bond 0.04219 / 2.80 ( 881) hydrogen bonds : angle 5.33409 / 3.61 ( 2463) Misc. bond : bond 0.00436 / 0.23 ( 1) link_BETA1-4 : bond 0.00363 / 0.21 ( 12) link_BETA1-4 : angle 2.15691 / 1.33 ( 36) link_NAG-ASN : bond 0.00539 / 0.32 ( 42) link_NAG-ASN : angle 3.51999 / 2.49 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 162 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8967 (t) cc_final: 0.8718 (m) REVERT: A 324 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: A 335 LEU cc_start: 0.8282 (tp) cc_final: 0.8015 (tm) REVERT: A 360 ASN cc_start: 0.8534 (t0) cc_final: 0.8291 (t0) REVERT: A 529 LYS cc_start: 0.8218 (mmmm) cc_final: 0.7984 (mppt) REVERT: A 567 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7210 (mmt-90) REVERT: A 580 GLN cc_start: 0.7925 (pt0) cc_final: 0.7658 (pt0) REVERT: A 900 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8526 (mtm) REVERT: A 1017 GLU cc_start: 0.9107 (tt0) cc_final: 0.8856 (tm-30) REVERT: A 1101 HIS cc_start: 0.8248 (m90) cc_final: 0.7768 (m90) REVERT: B 226 LEU cc_start: 0.8840 (tm) cc_final: 0.8583 (tm) REVERT: B 560 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9019 (mp) REVERT: B 574 ASP cc_start: 0.8573 (t0) cc_final: 0.8142 (t0) REVERT: B 603 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8208 (t0) REVERT: B 855 PHE cc_start: 0.7691 (m-10) cc_final: 0.7426 (m-10) REVERT: B 985 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8316 (m-30) REVERT: B 988 GLU cc_start: 0.9047 (pm20) cc_final: 0.8605 (pm20) REVERT: C 118 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6547 (pt) REVERT: C 314 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8460 (tm-30) REVERT: C 1050 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8128 (ppp) outliers start: 89 outliers final: 50 residues processed: 226 average time/residue: 0.3908 time to fit residues: 108.9835 Evaluate side-chains 207 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 176 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 74 optimal weight: 0.0670 chunk 14 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 188 ASN C1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.148520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092959 restraints weight = 38020.042| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.05 r_work: 0.3175 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22843 Z= 0.139 Angle : 0.637 15.736 31244 Z= 0.296 Chirality : 0.047 0.555 3796 Planarity : 0.004 0.129 3922 Dihedral : 9.083 101.486 4199 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.89 % Allowed : 23.54 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2781 helix: 2.55 (0.20), residues: 663 sheet: -0.30 (0.21), residues: 553 loop : -1.42 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 995 TYR 0.026 0.001 TYR A1138 PHE 0.031 0.001 PHE B 168 TRP 0.038 0.001 TRP A 104 HIS 0.004 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (22752) covalent geometry : angle 0.59349 / 0.29 (31010) SS BOND : bond 0.00317 / 0.19 ( 36) SS BOND : angle 1.16552 / 0.75 ( 72) hydrogen bonds : bond 0.03793 / 2.50 ( 881) hydrogen bonds : angle 5.20288 / 3.51 ( 2463) Misc. bond : bond 0.00410 / 0.22 ( 1) link_BETA1-4 : bond 0.00454 / 0.25 ( 12) link_BETA1-4 : angle 2.21432 / 1.36 ( 36) link_NAG-ASN : bond 0.00569 / 0.34 ( 42) link_NAG-ASN : angle 3.42730 / 2.41 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 167 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8444 (tm-30) REVERT: A 316 SER cc_start: 0.8980 (t) cc_final: 0.8663 (m) REVERT: A 324 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: A 335 LEU cc_start: 0.8249 (tp) cc_final: 0.8020 (tm) REVERT: A 360 ASN cc_start: 0.8529 (t0) cc_final: 0.8287 (t0) REVERT: A 529 LYS cc_start: 0.8234 (mmmm) cc_final: 0.8011 (mppt) REVERT: A 580 GLN cc_start: 0.7944 (pt0) cc_final: 0.7675 (pt0) REVERT: A 900 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8488 (mtm) REVERT: A 1101 HIS cc_start: 0.8286 (m90) cc_final: 0.7809 (m90) REVERT: B 34 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.6707 (mtp-110) REVERT: B 226 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8593 (tm) REVERT: B 319 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8701 (ttp-110) REVERT: B 324 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8483 (pm20) REVERT: B 560 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9000 (mp) REVERT: B 574 ASP cc_start: 0.8578 (t0) cc_final: 0.8148 (t0) REVERT: B 603 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8072 (t0) REVERT: B 855 PHE cc_start: 0.7597 (m-10) cc_final: 0.7335 (m-10) REVERT: B 988 GLU cc_start: 0.9062 (pm20) cc_final: 0.8636 (pm20) REVERT: C 314 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8512 (tm-30) REVERT: C 1050 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8014 (ppp) outliers start: 88 outliers final: 45 residues processed: 233 average time/residue: 0.3958 time to fit residues: 112.4538 Evaluate side-chains 210 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 151 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 188 ASN C1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.146865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090511 restraints weight = 37850.803| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.07 r_work: 0.3073 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22843 Z= 0.178 Angle : 0.648 15.881 31244 Z= 0.302 Chirality : 0.048 0.568 3796 Planarity : 0.004 0.041 3922 Dihedral : 8.783 100.279 4199 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.58 % Allowed : 24.34 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2781 helix: 2.54 (0.20), residues: 660 sheet: -0.38 (0.21), residues: 564 loop : -1.39 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 408 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE B 92 TRP 0.035 0.001 TRP A 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (22752) covalent geometry : angle 0.60506 / 0.29 (31010) SS BOND : bond 0.00357 / 0.22 ( 36) SS BOND : angle 1.30584 / 0.83 ( 72) hydrogen bonds : bond 0.03945 / 2.61 ( 881) hydrogen bonds : angle 5.22256 / 3.52 ( 2463) Misc. bond : bond 0.00423 / 0.22 ( 1) link_BETA1-4 : bond 0.00383 / 0.21 ( 12) link_BETA1-4 : angle 2.20442 / 1.36 ( 36) link_NAG-ASN : bond 0.00529 / 0.32 ( 42) link_NAG-ASN : angle 3.41827 / 2.40 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 162 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: A 316 SER cc_start: 0.8979 (t) cc_final: 0.8579 (m) REVERT: A 324 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: A 335 LEU cc_start: 0.8165 (tp) cc_final: 0.7930 (tm) REVERT: A 353 TRP cc_start: 0.7552 (p-90) cc_final: 0.7307 (p-90) REVERT: A 360 ASN cc_start: 0.8540 (t0) cc_final: 0.8316 (t0) REVERT: A 529 LYS cc_start: 0.8259 (mmmm) cc_final: 0.8043 (mppt) REVERT: A 580 GLN cc_start: 0.7989 (pt0) cc_final: 0.7717 (pt0) REVERT: A 900 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8503 (mtm) REVERT: A 1101 HIS cc_start: 0.8299 (m90) cc_final: 0.7807 (m90) REVERT: B 34 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.6720 (mtp-110) REVERT: B 226 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8625 (tm) REVERT: B 237 ARG cc_start: 0.7018 (mmm-85) cc_final: 0.6760 (mmm-85) REVERT: B 324 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: B 560 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8990 (mp) REVERT: B 574 ASP cc_start: 0.8594 (t0) cc_final: 0.8175 (t0) REVERT: B 603 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8127 (t0) REVERT: B 855 PHE cc_start: 0.7765 (m-10) cc_final: 0.7507 (m-10) REVERT: B 988 GLU cc_start: 0.9064 (pm20) cc_final: 0.8628 (pm20) REVERT: C 188 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7363 (p0) REVERT: C 314 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 902 MET cc_start: 0.8919 (mmt) cc_final: 0.8688 (mmp) REVERT: C 1050 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8049 (ppp) outliers start: 81 outliers final: 52 residues processed: 221 average time/residue: 0.3856 time to fit residues: 104.3842 Evaluate side-chains 217 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 155 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 228 optimal weight: 10.0000 chunk 102 optimal weight: 40.0000 chunk 273 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 267 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 123 optimal weight: 40.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 188 ASN C1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.147764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091659 restraints weight = 37665.229| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.06 r_work: 0.3146 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22843 Z= 0.130 Angle : 0.630 15.591 31244 Z= 0.292 Chirality : 0.047 0.546 3796 Planarity : 0.004 0.043 3922 Dihedral : 8.505 98.629 4199 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.19 % Allowed : 24.78 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 2781 helix: 2.62 (0.20), residues: 658 sheet: -0.23 (0.21), residues: 570 loop : -1.36 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.027 0.001 TYR A1138 PHE 0.031 0.001 PHE B 168 TRP 0.045 0.001 TRP A 104 HIS 0.003 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (22752) covalent geometry : angle 0.58752 / 0.28 (31010) SS BOND : bond 0.00313 / 0.19 ( 36) SS BOND : angle 1.16458 / 0.75 ( 72) hydrogen bonds : bond 0.03715 / 2.45 ( 881) hydrogen bonds : angle 5.16036 / 3.49 ( 2463) Misc. bond : bond 0.00407 / 0.21 ( 1) link_BETA1-4 : bond 0.00428 / 0.24 ( 12) link_BETA1-4 : angle 2.19165 / 1.35 ( 36) link_NAG-ASN : bond 0.00549 / 0.33 ( 42) link_NAG-ASN : angle 3.36677 / 2.36 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 163 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: A 316 SER cc_start: 0.8965 (t) cc_final: 0.8638 (m) REVERT: A 324 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: A 335 LEU cc_start: 0.8128 (tp) cc_final: 0.7908 (tm) REVERT: A 360 ASN cc_start: 0.8486 (t0) cc_final: 0.8271 (t0) REVERT: A 453 TYR cc_start: 0.6849 (p90) cc_final: 0.6154 (p90) REVERT: A 529 LYS cc_start: 0.8249 (mmmm) cc_final: 0.8044 (mppt) REVERT: A 580 GLN cc_start: 0.7989 (pt0) cc_final: 0.7714 (pt0) REVERT: A 900 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8490 (mtm) REVERT: A 1101 HIS cc_start: 0.8335 (m90) cc_final: 0.7842 (m90) REVERT: B 34 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6683 (mtp-110) REVERT: B 226 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8604 (tm) REVERT: B 234 ASN cc_start: 0.8588 (t0) cc_final: 0.8247 (p0) REVERT: B 324 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: B 560 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8967 (mp) REVERT: B 574 ASP cc_start: 0.8562 (t0) cc_final: 0.8135 (t0) REVERT: B 603 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8033 (t0) REVERT: B 790 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8509 (mtmm) REVERT: B 855 PHE cc_start: 0.7767 (m-10) cc_final: 0.7462 (m-10) REVERT: B 988 GLU cc_start: 0.9063 (pm20) cc_final: 0.8570 (pm20) REVERT: C 41 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6873 (mtpt) REVERT: C 314 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8523 (tm-30) REVERT: C 1050 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8029 (ppp) outliers start: 72 outliers final: 50 residues processed: 216 average time/residue: 0.3778 time to fit residues: 99.6001 Evaluate side-chains 215 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 154 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 11 optimal weight: 6.9990 chunk 103 optimal weight: 0.0470 chunk 91 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 233 optimal weight: 10.0000 chunk 110 optimal weight: 40.0000 chunk 161 optimal weight: 5.9990 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 207 HIS B 824 ASN C 188 ASN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.146058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089539 restraints weight = 37857.442| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.06 r_work: 0.3055 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22843 Z= 0.219 Angle : 0.666 16.331 31244 Z= 0.312 Chirality : 0.048 0.593 3796 Planarity : 0.004 0.041 3922 Dihedral : 8.287 96.603 4199 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.54 % Allowed : 24.47 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.16), residues: 2781 helix: 2.49 (0.20), residues: 659 sheet: -0.49 (0.21), residues: 581 loop : -1.36 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.018 0.001 TYR B1067 PHE 0.035 0.001 PHE B 565 TRP 0.040 0.002 TRP A 104 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (22752) covalent geometry : angle 0.62360 / 0.30 (31010) SS BOND : bond 0.00466 / 0.28 ( 36) SS BOND : angle 1.43220 / 0.91 ( 72) hydrogen bonds : bond 0.04237 / 2.81 ( 881) hydrogen bonds : angle 5.29519 / 3.58 ( 2463) Misc. bond : bond 0.00431 / 0.23 ( 1) link_BETA1-4 : bond 0.00356 / 0.20 ( 12) link_BETA1-4 : angle 2.12180 / 1.32 ( 36) link_NAG-ASN : bond 0.00500 / 0.30 ( 42) link_NAG-ASN : angle 3.42031 / 2.39 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 156 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6818 (m-10) cc_final: 0.6587 (m-10) REVERT: A 192 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.5120 (p90) REVERT: A 316 SER cc_start: 0.9031 (t) cc_final: 0.8803 (m) REVERT: A 324 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: A 335 LEU cc_start: 0.8105 (tp) cc_final: 0.7865 (tm) REVERT: A 360 ASN cc_start: 0.8506 (t0) cc_final: 0.8289 (t0) REVERT: A 453 TYR cc_start: 0.6831 (p90) cc_final: 0.6130 (p90) REVERT: A 529 LYS cc_start: 0.8281 (mmmm) cc_final: 0.8027 (mppt) REVERT: A 580 GLN cc_start: 0.8000 (pt0) cc_final: 0.7716 (pt0) REVERT: A 900 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8510 (mtm) REVERT: A 1101 HIS cc_start: 0.8301 (m90) cc_final: 0.7814 (m90) REVERT: B 34 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6841 (mtp-110) REVERT: B 226 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8628 (tm) REVERT: B 234 ASN cc_start: 0.8576 (t0) cc_final: 0.8296 (p0) REVERT: B 324 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: B 560 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8992 (mp) REVERT: B 574 ASP cc_start: 0.8575 (t0) cc_final: 0.8133 (t0) REVERT: B 603 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8204 (t0) REVERT: B 790 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8516 (mmmm) REVERT: B 988 GLU cc_start: 0.9064 (pm20) cc_final: 0.8622 (pm20) REVERT: C 226 LEU cc_start: 0.8631 (mt) cc_final: 0.8240 (OUTLIER) REVERT: C 314 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8517 (tm-30) REVERT: C 1050 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8082 (ppp) outliers start: 80 outliers final: 52 residues processed: 213 average time/residue: 0.3991 time to fit residues: 104.4797 Evaluate side-chains 214 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 153 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 37 optimal weight: 30.0000 chunk 246 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 131 optimal weight: 50.0000 chunk 125 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.144401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087100 restraints weight = 38293.386| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.07 r_work: 0.3025 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 22843 Z= 0.299 Angle : 0.715 17.316 31244 Z= 0.336 Chirality : 0.050 0.613 3796 Planarity : 0.004 0.056 3922 Dihedral : 8.242 94.440 4199 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.01 % Allowed : 25.04 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2781 helix: 2.31 (0.20), residues: 662 sheet: -0.60 (0.20), residues: 605 loop : -1.48 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 408 TYR 0.028 0.002 TYR A1138 PHE 0.040 0.002 PHE B 168 TRP 0.042 0.002 TRP A 104 HIS 0.006 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.30 (22752) covalent geometry : angle 0.67398 / 0.33 (31010) SS BOND : bond 0.00465 / 0.30 ( 36) SS BOND : angle 1.57107 / 0.99 ( 72) hydrogen bonds : bond 0.04586 / 3.04 ( 881) hydrogen bonds : angle 5.44205 / 3.69 ( 2463) Misc. bond : bond 0.00444 / 0.23 ( 1) link_BETA1-4 : bond 0.00383 / 0.22 ( 12) link_BETA1-4 : angle 2.07830 / 1.30 ( 36) link_NAG-ASN : bond 0.00491 / 0.30 ( 42) link_NAG-ASN : angle 3.50525 / 2.44 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 157 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6927 (m-10) cc_final: 0.6646 (m-10) REVERT: A 192 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.5402 (p90) REVERT: A 316 SER cc_start: 0.9133 (t) cc_final: 0.8904 (m) REVERT: A 324 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: A 329 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5852 (m-10) REVERT: A 335 LEU cc_start: 0.8100 (tp) cc_final: 0.7834 (tm) REVERT: A 360 ASN cc_start: 0.8521 (t0) cc_final: 0.8297 (t0) REVERT: A 453 TYR cc_start: 0.6864 (p90) cc_final: 0.6186 (p90) REVERT: A 580 GLN cc_start: 0.8052 (pt0) cc_final: 0.7757 (pt0) REVERT: A 900 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8521 (mtm) REVERT: A 1101 HIS cc_start: 0.8335 (m90) cc_final: 0.7896 (m90) REVERT: B 34 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.6986 (mtp-110) REVERT: B 226 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8674 (tm) REVERT: B 234 ASN cc_start: 0.8596 (t0) cc_final: 0.8311 (p0) REVERT: B 324 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: B 560 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8989 (mp) REVERT: B 574 ASP cc_start: 0.8642 (t0) cc_final: 0.8199 (t0) REVERT: B 603 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8324 (t0) REVERT: B 790 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8497 (mtmm) REVERT: B 988 GLU cc_start: 0.9051 (pm20) cc_final: 0.8615 (pm20) REVERT: C 226 LEU cc_start: 0.8677 (mt) cc_final: 0.8171 (mt) REVERT: C 314 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 902 MET cc_start: 0.8955 (mmt) cc_final: 0.8737 (mmp) REVERT: C 1050 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8199 (ppp) outliers start: 68 outliers final: 50 residues processed: 207 average time/residue: 0.4458 time to fit residues: 112.1084 Evaluate side-chains 213 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 206 optimal weight: 40.0000 chunk 168 optimal weight: 0.9990 chunk 265 optimal weight: 0.0270 chunk 46 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 230 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B1106 GLN B1134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090848 restraints weight = 37943.088| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.04 r_work: 0.3111 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22843 Z= 0.114 Angle : 0.648 16.115 31244 Z= 0.303 Chirality : 0.047 0.549 3796 Planarity : 0.004 0.057 3922 Dihedral : 7.897 92.187 4199 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.30 % Allowed : 25.88 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2781 helix: 2.54 (0.20), residues: 660 sheet: -0.37 (0.21), residues: 579 loop : -1.32 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 408 TYR 0.019 0.001 TYR B1067 PHE 0.031 0.001 PHE B 855 TRP 0.030 0.001 TRP A 104 HIS 0.003 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (22752) covalent geometry : angle 0.60732 / 0.29 (31010) SS BOND : bond 0.00302 / 0.18 ( 36) SS BOND : angle 1.13878 / 0.72 ( 72) hydrogen bonds : bond 0.03690 / 2.42 ( 881) hydrogen bonds : angle 5.16119 / 3.48 ( 2463) Misc. bond : bond 0.00380 / 0.20 ( 1) link_BETA1-4 : bond 0.00509 / 0.27 ( 12) link_BETA1-4 : angle 2.11906 / 1.31 ( 36) link_NAG-ASN : bond 0.00590 / 0.36 ( 42) link_NAG-ASN : angle 3.37839 / 2.35 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9384.14 seconds wall clock time: 160 minutes 9.08 seconds (9609.08 seconds total)