Starting phenix.real_space_refine on Mon Aug 25 11:45:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmi_61603/08_2025/9jmi_61603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmi_61603/08_2025/9jmi_61603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jmi_61603/08_2025/9jmi_61603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmi_61603/08_2025/9jmi_61603.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmi_61603/08_2025/9jmi_61603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmi_61603/08_2025/9jmi_61603.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 174 5.16 5 C 17496 2.51 5 N 4524 2.21 5 O 5538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27732 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 8851 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 47, 'TRANS': 1083} Chain breaks: 9 Chain: "B" Number of atoms: 8851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 8851 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 47, 'TRANS': 1083} Chain breaks: 9 Chain: "C" Number of atoms: 8851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 8851 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 47, 'TRANS': 1083} Chain breaks: 9 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "R" 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: "S" 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: "T" 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: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 214 Unusual residues: {'FOL': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 214 Unusual residues: {'FOL': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 214 Unusual residues: {'FOL': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 7.80, per 1000 atoms: 0.28 Number of scatterers: 27732 At special positions: 0 Unit cell: (138.6, 149.16, 161.04, 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 174 16.00 O 5538 8.00 N 4524 7.00 C 17496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 396 " distance=2.04 Simple disulfide: pdb=" SG CYS A 414 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 572 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 642 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 638 " distance=2.03 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 699 " distance=2.06 Simple disulfide: pdb=" SG CYS A 713 " - pdb=" SG CYS A 722 " distance=2.03 Simple disulfide: pdb=" SG CYS A 785 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 790 " - pdb=" SG CYS A 796 " distance=2.04 Simple disulfide: pdb=" SG CYS A 892 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1097 " distance=2.02 Simple disulfide: pdb=" SG CYS A1136 " - pdb=" SG CYS A1143 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 396 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 572 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 515 " distance=2.02 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 642 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 638 " distance=2.03 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 699 " distance=2.03 Simple disulfide: pdb=" SG CYS B 713 " - pdb=" SG CYS B 722 " distance=2.03 Simple disulfide: pdb=" SG CYS B 785 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 790 " - pdb=" SG CYS B 796 " distance=2.04 Simple disulfide: pdb=" SG CYS B 892 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B1086 " - pdb=" SG CYS B1097 " distance=2.02 Simple disulfide: pdb=" SG CYS B1136 " - pdb=" SG CYS B1143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 225 " distance=2.05 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 338 " distance=2.03 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 396 " distance=2.03 Simple disulfide: pdb=" SG CYS C 414 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 426 " - pdb=" SG CYS C 572 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 515 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 642 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 638 " distance=2.03 Simple disulfide: pdb=" SG CYS C 667 " - pdb=" SG CYS C 699 " distance=2.04 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 722 " distance=2.03 Simple disulfide: pdb=" SG CYS C 785 " - pdb=" SG CYS C 807 " distance=2.03 Simple disulfide: pdb=" SG CYS C 790 " - pdb=" SG CYS C 796 " distance=2.04 Simple disulfide: pdb=" SG CYS C 892 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C1086 " - pdb=" SG CYS C1097 " distance=2.02 Simple disulfide: pdb=" SG CYS C1136 " - pdb=" SG CYS C1143 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 I 2 " - " BMA I 3 " " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A1402 " - " ASN A 58 " " NAG A1403 " - " ASN A 151 " " NAG A1404 " - " ASN A 183 " " NAG A1405 " - " ASN A 186 " " NAG A1406 " - " ASN A 201 " " NAG A1407 " - " ASN A 232 " " NAG A1408 " - " ASN A 476 " " NAG A1409 " - " ASN A 482 " " NAG A1410 " - " ASN A 609 " " NAG A1411 " - " ASN A 705 " " NAG A1412 " - " ASN A 764 " " NAG A1413 " - " ASN A 849 " " NAG A1414 " - " ASN A1188 " " NAG B1402 " - " ASN B 58 " " NAG B1403 " - " ASN B 151 " " NAG B1404 " - " ASN B 183 " " NAG B1405 " - " ASN B 186 " " NAG B1406 " - " ASN B 201 " " NAG B1407 " - " ASN B 232 " " NAG B1408 " - " ASN B 476 " " NAG B1409 " - " ASN B 482 " " NAG B1410 " - " ASN B 609 " " NAG B1411 " - " ASN B 705 " " NAG B1412 " - " ASN B 764 " " NAG B1413 " - " ASN B 849 " " NAG B1414 " - " ASN B1188 " " NAG C1402 " - " ASN C 151 " " NAG C1403 " - " ASN C 183 " " NAG C1404 " - " ASN C 186 " " NAG C1405 " - " ASN C 201 " " NAG C1406 " - " ASN C 232 " " NAG C1407 " - " ASN C 476 " " NAG C1408 " - " ASN C 482 " " NAG C1409 " - " ASN C 609 " " NAG C1410 " - " ASN C 705 " " NAG C1411 " - " ASN C 764 " " NAG C1412 " - " ASN C 849 " " NAG C1413 " - " ASN C1188 " " NAG C1414 " - " ASN C 58 " " NAG D 1 " - " ASN A 41 " " NAG E 1 " - " ASN A 97 " " NAG F 1 " - " ASN A 118 " " NAG G 1 " - " ASN A 158 " " NAG H 1 " - " ASN A 387 " " NAG I 1 " - " ASN A 399 " " NAG J 1 " - " ASN B 41 " " NAG K 1 " - " ASN B 97 " " NAG L 1 " - " ASN B 118 " " NAG M 1 " - " ASN B 158 " " NAG N 1 " - " ASN B 387 " " NAG O 1 " - " ASN B 399 " " NAG P 1 " - " ASN C 41 " " NAG Q 1 " - " ASN C 97 " " NAG R 1 " - " ASN C 118 " " NAG S 1 " - " ASN C 158 " " NAG T 1 " - " ASN C 387 " " NAG U 1 " - " ASN C 399 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB FOL A1401 " pdb=" CB FOL B1401 " pdb=" CB FOL C1401 " Number of C-beta restraints generated: 6360 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 54 sheets defined 27.1% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 212 through 219 removed outlier: 3.705A pdb=" N THR A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TRP A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 341 Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.825A pdb=" N VAL A 376 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 378 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.634A pdb=" N ALA A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 424' Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 613 through 616 Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.756A pdb=" N ILE A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 784 through 791 Processing helix chain 'A' and resid 793 through 801 removed outlier: 3.556A pdb=" N GLU A 801 " --> pdb=" O GLU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 805 through 833 Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.544A pdb=" N GLU A 854 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 878 removed outlier: 3.522A pdb=" N VAL A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 893 removed outlier: 3.944A pdb=" N GLU A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 920 through 934 Processing helix chain 'A' and resid 951 through 964 removed outlier: 3.704A pdb=" N GLY A 964 " --> pdb=" O MET A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 973 removed outlier: 3.725A pdb=" N LEU A 970 " --> pdb=" O THR A 966 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A 971 " --> pdb=" O GLN A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 991 Processing helix chain 'A' and resid 996 through 1018 removed outlier: 3.624A pdb=" N GLN A1000 " --> pdb=" O ASN A 996 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1021 No H-bonds generated for 'chain 'A' and resid 1019 through 1021' Processing helix chain 'A' and resid 1030 through 1038 Processing helix chain 'A' and resid 1039 through 1087 removed outlier: 3.867A pdb=" N GLU A1044 " --> pdb=" O THR A1040 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1175 No H-bonds generated for 'chain 'A' and resid 1173 through 1175' Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.544A pdb=" N TYR B 100 " --> pdb=" O ASN B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.923A pdb=" N TRP B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 341 Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 418 through 423 removed outlier: 3.935A pdb=" N ALA B 423 " --> pdb=" O PRO B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.511A pdb=" N MET B 441 " --> pdb=" O PRO B 438 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER B 443 " --> pdb=" O SER B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 474 through 481 Processing helix chain 'B' and resid 512 through 522 Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.835A pdb=" N LEU B 588 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.632A pdb=" N VAL B 676 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 677 " --> pdb=" O PRO B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 677' Processing helix chain 'B' and resid 678 through 688 removed outlier: 3.528A pdb=" N SER B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 791 Processing helix chain 'B' and resid 793 through 801 removed outlier: 3.625A pdb=" N GLU B 801 " --> pdb=" O GLU B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 805 through 833 Processing helix chain 'B' and resid 868 through 878 removed outlier: 3.818A pdb=" N VAL B 878 " --> pdb=" O LEU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 894 removed outlier: 3.644A pdb=" N LYS B 894 " --> pdb=" O ASP B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 920 through 934 removed outlier: 3.581A pdb=" N TYR B 927 " --> pdb=" O MET B 923 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 928 " --> pdb=" O GLU B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 962 removed outlier: 3.659A pdb=" N GLY B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 973 removed outlier: 3.518A pdb=" N LEU B 970 " --> pdb=" O THR B 966 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B 971 " --> pdb=" O GLN B 967 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 992 removed outlier: 3.856A pdb=" N THR B 990 " --> pdb=" O GLY B 986 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 991 " --> pdb=" O ALA B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1019 removed outlier: 3.557A pdb=" N GLN B1000 " --> pdb=" O ASN B 996 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B1002 " --> pdb=" O ALA B 998 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B1006 " --> pdb=" O VAL B1002 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B1019 " --> pdb=" O LYS B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1038 Processing helix chain 'B' and resid 1039 through 1087 removed outlier: 3.601A pdb=" N ASP B1048 " --> pdb=" O GLU B1044 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B1049 " --> pdb=" O VAL B1045 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B1050 " --> pdb=" O GLN B1046 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B1053 " --> pdb=" O ARG B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1175 No H-bonds generated for 'chain 'B' and resid 1173 through 1175' Processing helix chain 'B' and resid 1194 through 1198 Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 212 through 219 removed outlier: 3.759A pdb=" N THR C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 341 Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.825A pdb=" N VAL C 376 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 377 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 Processing helix chain 'C' and resid 418 through 424 removed outlier: 3.634A pdb=" N ALA C 423 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR C 424 " --> pdb=" O GLU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.563A pdb=" N MET C 441 " --> pdb=" O PRO C 438 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER C 443 " --> pdb=" O SER C 440 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 444 " --> pdb=" O MET C 441 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 445 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 474 through 481 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 583 through 588 removed outlier: 3.941A pdb=" N LEU C 588 " --> pdb=" O ASP C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 673 Processing helix chain 'C' and resid 678 through 687 removed outlier: 3.921A pdb=" N THR C 683 " --> pdb=" O ARG C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 791 Processing helix chain 'C' and resid 793 through 800 Processing helix chain 'C' and resid 801 through 804 removed outlier: 3.539A pdb=" N GLY C 804 " --> pdb=" O GLU C 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 801 through 804' Processing helix chain 'C' and resid 805 through 833 Processing helix chain 'C' and resid 840 through 845 Processing helix chain 'C' and resid 868 through 877 Processing helix chain 'C' and resid 887 through 893 removed outlier: 3.603A pdb=" N GLU C 891 " --> pdb=" O LYS C 887 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 892 " --> pdb=" O GLY C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 934 Processing helix chain 'C' and resid 951 through 962 removed outlier: 3.606A pdb=" N GLY C 962 " --> pdb=" O TYR C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 973 removed outlier: 3.542A pdb=" N LEU C 970 " --> pdb=" O THR C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 991 removed outlier: 3.660A pdb=" N ALA C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1018 removed outlier: 3.581A pdb=" N VAL C1006 " --> pdb=" O VAL C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1038 Processing helix chain 'C' and resid 1041 through 1087 removed outlier: 4.085A pdb=" N VAL C1045 " --> pdb=" O LEU C1041 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C1053 " --> pdb=" O ARG C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1173 through 1175 No H-bonds generated for 'chain 'C' and resid 1173 through 1175' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 67 removed outlier: 3.563A pdb=" N TYR A 312 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN A 311 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASP A 327 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 313 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 325 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU A 315 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 78 removed outlier: 5.804A pdb=" N VAL A 251 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR A 271 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 253 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 104 removed outlier: 4.040A pdb=" N GLN A 180 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 221 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 147 removed outlier: 4.557A pdb=" N VAL A 144 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 155 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 198 through 200 removed outlier: 3.804A pdb=" N SER A 287 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 200 " --> pdb=" O SER A 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 365 removed outlier: 4.674A pdb=" N ILE A 627 " --> pdb=" O MET A 639 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 619 " --> pdb=" O ILE A 627 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.707A pdb=" N SER A 389 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 429 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 411 " --> pdb=" O HIS A 470 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 489 through 496 removed outlier: 4.135A pdb=" N TYR A 489 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLY A 541 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS A 495 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR A 539 " --> pdb=" O CYS A 495 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 538 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY A 530 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE A 540 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR A 528 " --> pdb=" O ILE A 540 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 710 removed outlier: 6.899A pdb=" N HIS A 704 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N VAL A 740 " --> pdb=" O HIS A 704 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N THR A 706 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 747 through 748 removed outlier: 6.179A pdb=" N LEU A 747 " --> pdb=" O SER B 837 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 757 through 774 removed outlier: 6.645A pdb=" N GLU A 758 " --> pdb=" O THR A1130 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR A1130 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER A 760 " --> pdb=" O ASN A1128 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN A1128 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR A1126 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 764 " --> pdb=" O THR A1124 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N TYR A1121 " --> pdb=" O HIS A1102 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N HIS A1102 " --> pdb=" O TYR A1121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB7, first strand: chain 'A' and resid 836 through 837 removed outlier: 3.730A pdb=" N SER A 837 " --> pdb=" O LEU C 747 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1135 through 1136 Processing sheet with id=AB9, first strand: chain 'A' and resid 1143 through 1146 removed outlier: 4.093A pdb=" N CYS A1143 " --> pdb=" O VAL A1180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1149 through 1153 Processing sheet with id=AC2, first strand: chain 'B' and resid 26 through 27 removed outlier: 5.980A pdb=" N ASP B 26 " --> pdb=" O ILE B 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 60 through 67 removed outlier: 8.045A pdb=" N ASN B 311 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP B 327 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 313 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA B 325 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU B 315 " --> pdb=" O VAL B 323 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 75 through 77 removed outlier: 3.518A pdb=" N GLY B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL B 251 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 271 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 253 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.560A pdb=" N SER B 80 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 198 " --> pdb=" O SER B 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AC7, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AC8, first strand: chain 'B' and resid 120 through 121 removed outlier: 6.161A pdb=" N THR B 131 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 144 through 147 removed outlier: 4.615A pdb=" N VAL B 144 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 155 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 Processing sheet with id=AD2, first strand: chain 'B' and resid 362 through 365 removed outlier: 6.742A pdb=" N TYR B 363 " --> pdb=" O ASP B 595 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE B 627 " --> pdb=" O MET B 639 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 619 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 389 through 393 removed outlier: 3.768A pdb=" N SER B 389 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER B 429 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 472 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL B 409 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 489 through 496 removed outlier: 4.163A pdb=" N TYR B 489 " --> pdb=" O TYR B 545 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLY B 541 " --> pdb=" O SER B 493 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS B 495 " --> pdb=" O TYR B 539 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B 539 " --> pdb=" O CYS B 495 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE B 538 " --> pdb=" O GLY B 530 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY B 530 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE B 540 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR B 528 " --> pdb=" O ILE B 540 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 703 through 710 removed outlier: 6.565A pdb=" N PHE B 736 " --> pdb=" O HIS B 704 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR B 706 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU B 738 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP B 708 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 747 through 748 removed outlier: 6.120A pdb=" N LEU B 747 " --> pdb=" O SER C 837 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 757 through 774 removed outlier: 7.095A pdb=" N GLU B 758 " --> pdb=" O THR B1130 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR B1130 " --> pdb=" O GLU B 758 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER B 760 " --> pdb=" O ASN B1128 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASN B1128 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR B1126 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN B 764 " --> pdb=" O THR B1124 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 768 " --> pdb=" O GLY B1120 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR B1121 " --> pdb=" O HIS B1102 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N HIS B1102 " --> pdb=" O TYR B1121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AD9, first strand: chain 'B' and resid 1135 through 1136 Processing sheet with id=AE1, first strand: chain 'B' and resid 1143 through 1146 removed outlier: 4.637A pdb=" N CYS B1143 " --> pdb=" O VAL B1180 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1149 through 1153 removed outlier: 3.582A pdb=" N TYR B1150 " --> pdb=" O THR B1162 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 60 through 63 removed outlier: 7.269A pdb=" N GLU C 315 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AE5, first strand: chain 'C' and resid 75 through 78 removed outlier: 3.712A pdb=" N TYR C 303 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 109 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL C 251 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 271 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C 253 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.122A pdb=" N SER C 80 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU C 198 " --> pdb=" O SER C 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 103 through 104 removed outlier: 4.435A pdb=" N SER C 143 " --> pdb=" O HIS C 159 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N HIS C 159 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL C 145 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE C 157 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS C 147 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG C 155 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N TYR C 156 " --> pdb=" O PRO C 181 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN C 158 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU C 179 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 229 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 176 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE C 227 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL C 178 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N CYS C 225 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN C 180 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS C 223 " --> pdb=" O GLN C 180 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AE9, first strand: chain 'C' and resid 348 through 349 removed outlier: 3.571A pdb=" N SER C 657 " --> pdb=" O ASP C 652 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 362 through 365 removed outlier: 3.590A pdb=" N GLY C 628 " --> pdb=" O VAL C 619 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 389 through 393 removed outlier: 3.765A pdb=" N SER C 389 " --> pdb=" O TRP C 434 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP C 434 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 429 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 466 " --> pdb=" O CYS C 414 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS C 414 " --> pdb=" O THR C 466 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG C 468 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE C 412 " --> pdb=" O ARG C 468 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS C 470 " --> pdb=" O ASP C 410 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 489 through 496 removed outlier: 4.096A pdb=" N TYR C 489 " --> pdb=" O TYR C 545 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLY C 541 " --> pdb=" O SER C 493 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS C 495 " --> pdb=" O TYR C 539 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR C 539 " --> pdb=" O CYS C 495 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE C 538 " --> pdb=" O GLY C 530 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY C 530 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE C 540 " --> pdb=" O TYR C 528 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR C 528 " --> pdb=" O ILE C 540 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 703 through 710 removed outlier: 6.520A pdb=" N PHE C 736 " --> pdb=" O HIS C 704 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR C 706 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU C 738 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP C 708 " --> pdb=" O LEU C 738 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 757 through 775 removed outlier: 6.469A pdb=" N ASP C1125 " --> pdb=" O THR C 763 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE C 765 " --> pdb=" O PRO C1123 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE C 767 " --> pdb=" O TYR C1121 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR C1121 " --> pdb=" O PHE C 767 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 769 " --> pdb=" O VAL C1119 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C1119 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU C 771 " --> pdb=" O VAL C1117 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL C1117 " --> pdb=" O GLU C 771 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE C 773 " --> pdb=" O TYR C1115 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR C1115 " --> pdb=" O PHE C 773 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU C 775 " --> pdb=" O GLY C1113 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY C1113 " --> pdb=" O GLU C 775 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR C1121 " --> pdb=" O HIS C1102 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS C1102 " --> pdb=" O TYR C1121 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 781 through 783 Processing sheet with id=AF7, first strand: chain 'C' and resid 1135 through 1136 Processing sheet with id=AF8, first strand: chain 'C' and resid 1143 through 1146 removed outlier: 3.905A pdb=" N CYS C1143 " --> pdb=" O VAL C1180 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1149 through 1153 removed outlier: 3.535A pdb=" N TYR C1150 " --> pdb=" O THR C1162 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2727 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: 7.75 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4506 1.31 - 1.44: 8075 1.44 - 1.58: 15484 1.58 - 1.71: 0 1.71 - 1.85: 249 Bond restraints: 28314 Sorted by residual: bond pdb=" CA ASP A 224 " pdb=" C ASP A 224 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.34e-02 5.57e+03 3.17e+01 bond pdb=" C GLU A 411 " pdb=" O GLU A 411 " ideal model delta sigma weight residual 1.235 1.175 0.061 1.26e-02 6.30e+03 2.32e+01 bond pdb=" C CYS A 699 " pdb=" O CYS A 699 " ideal model delta sigma weight residual 1.234 1.190 0.044 1.19e-02 7.06e+03 1.36e+01 bond pdb=" CA GLU A 411 " pdb=" C GLU A 411 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.34e-02 5.57e+03 1.30e+01 bond pdb=" C GLY A 698 " pdb=" O GLY A 698 " ideal model delta sigma weight residual 1.232 1.191 0.041 1.19e-02 7.06e+03 1.18e+01 ... (remaining 28309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 37120 1.95 - 3.89: 1106 3.89 - 5.84: 151 5.84 - 7.78: 42 7.78 - 9.73: 8 Bond angle restraints: 38427 Sorted by residual: angle pdb=" N VAL A 409 " pdb=" CA VAL A 409 " pdb=" C VAL A 409 " ideal model delta sigma weight residual 108.12 116.42 -8.30 1.34e+00 5.57e-01 3.83e+01 angle pdb=" CA GLY A 698 " pdb=" C GLY A 698 " pdb=" N CYS A 699 " ideal model delta sigma weight residual 115.74 119.65 -3.91 7.30e-01 1.88e+00 2.87e+01 angle pdb=" C CYS A 699 " pdb=" N VAL A 700 " pdb=" CA VAL A 700 " ideal model delta sigma weight residual 123.06 116.40 6.66 1.38e+00 5.25e-01 2.33e+01 angle pdb=" N CYS A 667 " pdb=" CA CYS A 667 " pdb=" C CYS A 667 " ideal model delta sigma weight residual 111.28 116.54 -5.26 1.09e+00 8.42e-01 2.33e+01 angle pdb=" N MET B 988 " pdb=" CA MET B 988 " pdb=" C MET B 988 " ideal model delta sigma weight residual 111.36 116.32 -4.96 1.09e+00 8.42e-01 2.07e+01 ... (remaining 38422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 16415 21.77 - 43.54: 1268 43.54 - 65.31: 183 65.31 - 87.08: 62 87.08 - 108.85: 21 Dihedral angle restraints: 17949 sinusoidal: 8016 harmonic: 9933 Sorted by residual: dihedral pdb=" CB CYS C 667 " pdb=" SG CYS C 667 " pdb=" SG CYS C 699 " pdb=" CB CYS C 699 " ideal model delta sinusoidal sigma weight residual -86.00 -17.21 -68.79 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS B 713 " pdb=" SG CYS B 713 " pdb=" SG CYS B 722 " pdb=" CB CYS B 722 " ideal model delta sinusoidal sigma weight residual -86.00 -148.75 62.75 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual -86.00 -36.05 -49.95 1 1.00e+01 1.00e-02 3.42e+01 ... (remaining 17946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 4446 0.162 - 0.323: 26 0.323 - 0.485: 0 0.485 - 0.647: 0 0.647 - 0.809: 1 Chirality restraints: 4473 Sorted by residual: chirality pdb=" CG LEU B 752 " pdb=" CB LEU B 752 " pdb=" CD1 LEU B 752 " pdb=" CD2 LEU B 752 " both_signs ideal model delta sigma weight residual False -2.59 -1.78 -0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.88e+00 chirality pdb=" CA ASP A 410 " pdb=" N ASP A 410 " pdb=" C ASP A 410 " pdb=" CB ASP A 410 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 4470 not shown) Planarity restraints: 4926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 987 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ALA B 987 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA B 987 " -0.023 2.00e-02 2.50e+03 pdb=" N MET B 988 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 222 " -0.014 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C LEU B 222 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU B 222 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS B 223 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B1195 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO B1196 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B1196 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B1196 " -0.041 5.00e-02 4.00e+02 ... (remaining 4923 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5312 2.77 - 3.31: 23688 3.31 - 3.84: 45230 3.84 - 4.37: 52772 4.37 - 4.90: 94447 Nonbonded interactions: 221449 Sorted by model distance: nonbonded pdb=" O PRO A 68 " pdb=" OH TYR A 312 " model vdw 2.242 3.040 nonbonded pdb=" O PRO C 68 " pdb=" OH TYR C 312 " model vdw 2.252 3.040 nonbonded pdb=" O PRO B 68 " pdb=" OH TYR B 312 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR C 136 " pdb=" OE1 GLU C 240 " model vdw 2.289 3.040 nonbonded pdb=" O ARG A 38 " pdb=" OH TYR A 305 " model vdw 2.292 3.040 ... (remaining 221444 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.710 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.005 0.085 28440 Z= 0.258 Angle : 0.785 11.660 38757 Z= 0.400 Chirality : 0.052 0.809 4473 Planarity : 0.005 0.073 4869 Dihedral : 15.554 108.853 11445 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 0.14 % Allowed : 4.84 % Favored : 95.03 % Cbeta Deviations : 0.13 % 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 aren not related in a simple way. whole: -1.59 (0.13), residues: 3333 helix: -0.78 (0.16), residues: 807 sheet: -0.62 (0.20), residues: 675 loop : -1.33 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1178 TYR 0.043 0.002 TYR C 312 PHE 0.031 0.002 PHE B 757 TRP 0.012 0.001 TRP A 434 HIS 0.006 0.001 HIS A 669 Details of bonding type rmsd covalent geometry : bond 0.00530 (28314) covalent geometry : angle 0.76102 (38427) SS BOND : bond 0.00605 ( 48) SS BOND : angle 1.73842 ( 96) hydrogen bonds : bond 0.21862 ( 960) hydrogen bonds : angle 7.96665 ( 2727) link_BETA1-4 : bond 0.00523 ( 21) link_BETA1-4 : angle 1.54503 ( 63) link_NAG-ASN : bond 0.00283 ( 57) link_NAG-ASN : angle 2.63280 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 259 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 224 ASP cc_start: 0.8656 (t0) cc_final: 0.8245 (t70) REVERT: A 753 ASN cc_start: 0.6430 (t0) cc_final: 0.6192 (t0) REVERT: B 103 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 420 GLU cc_start: 0.7715 (pt0) cc_final: 0.7296 (pt0) REVERT: B 841 MET cc_start: 0.8882 (tmm) cc_final: 0.8563 (ttp) REVERT: C 81 MET cc_start: 0.7700 (ptp) cc_final: 0.7420 (ptp) REVERT: C 893 MET cc_start: 0.7341 (mmm) cc_final: 0.7092 (mmm) outliers start: 4 outliers final: 2 residues processed: 262 average time/residue: 0.1843 time to fit residues: 78.5740 Evaluate side-chains 238 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain B residue 415 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 532 ASN A1052 ASN B 791 ASN B 989 GLN B1174 ASN C 116 ASN C 190 HIS C 616 GLN C 734 ASN C 907 GLN C1140 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.094721 restraints weight = 36283.711| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.63 r_work: 0.2832 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28440 Z= 0.207 Angle : 0.631 19.523 38757 Z= 0.314 Chirality : 0.045 0.430 4473 Planarity : 0.004 0.052 4869 Dihedral : 8.416 61.333 5342 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.91 % Allowed : 8.39 % Favored : 90.69 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: -0.90 (0.14), residues: 3333 helix: 0.35 (0.18), residues: 801 sheet: -0.45 (0.19), residues: 741 loop : -1.07 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1178 TYR 0.040 0.002 TYR B 312 PHE 0.018 0.002 PHE C 757 TRP 0.014 0.001 TRP B 434 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00493 (28314) covalent geometry : angle 0.59524 (38427) SS BOND : bond 0.00443 ( 48) SS BOND : angle 1.34598 ( 96) hydrogen bonds : bond 0.05600 ( 960) hydrogen bonds : angle 5.60459 ( 2727) link_BETA1-4 : bond 0.00242 ( 21) link_BETA1-4 : angle 1.91657 ( 63) link_NAG-ASN : bond 0.00460 ( 57) link_NAG-ASN : angle 2.86929 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 250 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7836 (ptp-170) REVERT: A 224 ASP cc_start: 0.8252 (t0) cc_final: 0.7862 (t70) REVERT: A 621 ASP cc_start: 0.7628 (t0) cc_final: 0.7343 (t0) REVERT: A 1178 ARG cc_start: 0.8317 (mtm-85) cc_final: 0.7817 (mtm110) REVERT: B 266 MET cc_start: 0.9296 (mtm) cc_final: 0.9020 (mtm) REVERT: B 1154 ASN cc_start: 0.5859 (m-40) cc_final: 0.5580 (m110) REVERT: C 616 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.5291 (tm130) REVERT: C 956 ILE cc_start: 0.9166 (tt) cc_final: 0.8929 (tp) outliers start: 27 outliers final: 20 residues processed: 269 average time/residue: 0.1849 time to fit residues: 81.0185 Evaluate side-chains 245 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 616 GLN Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 1160 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 26 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 335 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 532 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.095275 restraints weight = 36168.785| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.56 r_work: 0.2830 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 28440 Z= 0.167 Angle : 0.586 18.839 38757 Z= 0.292 Chirality : 0.044 0.226 4473 Planarity : 0.004 0.045 4869 Dihedral : 7.249 57.005 5342 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 1.22 % Allowed : 9.61 % Favored : 89.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.14), residues: 3333 helix: 0.84 (0.19), residues: 783 sheet: -0.38 (0.19), residues: 741 loop : -0.98 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1178 TYR 0.025 0.001 TYR B 312 PHE 0.017 0.001 PHE C 757 TRP 0.013 0.001 TRP A 434 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00399 (28314) covalent geometry : angle 0.55162 (38427) SS BOND : bond 0.00438 ( 48) SS BOND : angle 1.53651 ( 96) hydrogen bonds : bond 0.04943 ( 960) hydrogen bonds : angle 5.26505 ( 2727) link_BETA1-4 : bond 0.00289 ( 21) link_BETA1-4 : angle 1.79056 ( 63) link_NAG-ASN : bond 0.00410 ( 57) link_NAG-ASN : angle 2.65421 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8192 (ptm160) cc_final: 0.7594 (ttm170) REVERT: A 621 ASP cc_start: 0.7616 (t0) cc_final: 0.7327 (t0) REVERT: A 1085 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7930 (tp30) REVERT: A 1178 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7681 (mtm110) REVERT: B 103 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8350 (mm-30) REVERT: B 266 MET cc_start: 0.9339 (mtm) cc_final: 0.8982 (mtm) REVERT: B 841 MET cc_start: 0.8735 (tmm) cc_final: 0.8325 (tmm) REVERT: C 81 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7358 (ptp) REVERT: C 616 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6314 (tm-30) REVERT: C 841 MET cc_start: 0.8758 (ttp) cc_final: 0.8466 (ttp) outliers start: 36 outliers final: 22 residues processed: 274 average time/residue: 0.1812 time to fit residues: 81.4345 Evaluate side-chains 246 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 1136 CYS Chi-restraints excluded: chain B residue 1160 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 616 GLN Chi-restraints excluded: chain C residue 1160 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 128 optimal weight: 0.4980 chunk 251 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 184 optimal weight: 0.0970 chunk 234 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 34 optimal weight: 0.0040 chunk 106 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.118526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.096029 restraints weight = 36010.766| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.60 r_work: 0.2890 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28440 Z= 0.111 Angle : 0.556 18.080 38757 Z= 0.277 Chirality : 0.042 0.316 4473 Planarity : 0.003 0.041 4869 Dihedral : 6.295 57.436 5342 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 1.25 % Allowed : 11.34 % Favored : 87.41 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.14), residues: 3333 helix: 1.15 (0.19), residues: 786 sheet: -0.30 (0.19), residues: 744 loop : -0.87 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1178 TYR 0.013 0.001 TYR B 312 PHE 0.012 0.001 PHE C1175 TRP 0.012 0.001 TRP B 434 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00250 (28314) covalent geometry : angle 0.52031 (38427) SS BOND : bond 0.00654 ( 48) SS BOND : angle 2.03226 ( 96) hydrogen bonds : bond 0.04264 ( 960) hydrogen bonds : angle 5.02773 ( 2727) link_BETA1-4 : bond 0.00326 ( 21) link_BETA1-4 : angle 1.62012 ( 63) link_NAG-ASN : bond 0.00413 ( 57) link_NAG-ASN : angle 2.44083 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7537 (ttm170) REVERT: A 58 ASN cc_start: 0.8076 (t0) cc_final: 0.7790 (t0) REVERT: A 621 ASP cc_start: 0.7590 (t0) cc_final: 0.7365 (t0) REVERT: A 960 MET cc_start: 0.8986 (mtm) cc_final: 0.8749 (mtp) REVERT: A 1094 ASN cc_start: 0.7793 (t0) cc_final: 0.7479 (t0) REVERT: A 1178 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.7794 (mtm110) REVERT: B 40 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8255 (tt) REVERT: B 224 ASP cc_start: 0.7416 (t70) cc_final: 0.7123 (t0) REVERT: B 266 MET cc_start: 0.9290 (mtm) cc_final: 0.9027 (mtm) REVERT: B 522 LEU cc_start: 0.7811 (mt) cc_final: 0.7572 (mp) REVERT: B 1070 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 1154 ASN cc_start: 0.6363 (m110) cc_final: 0.6116 (m-40) outliers start: 37 outliers final: 22 residues processed: 272 average time/residue: 0.1828 time to fit residues: 81.7476 Evaluate side-chains 252 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 1136 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 1160 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 196 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.091972 restraints weight = 36407.138| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.62 r_work: 0.2793 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 28440 Z= 0.199 Angle : 0.607 17.481 38757 Z= 0.301 Chirality : 0.045 0.236 4473 Planarity : 0.004 0.040 4869 Dihedral : 6.175 55.908 5339 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.90 % Allowed : 12.01 % Favored : 86.09 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.14), residues: 3333 helix: 1.08 (0.19), residues: 786 sheet: -0.34 (0.19), residues: 732 loop : -0.91 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1178 TYR 0.020 0.001 TYR A 594 PHE 0.019 0.002 PHE C 757 TRP 0.010 0.001 TRP B 434 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00482 (28314) covalent geometry : angle 0.57241 (38427) SS BOND : bond 0.00596 ( 48) SS BOND : angle 1.97071 ( 96) hydrogen bonds : bond 0.04889 ( 960) hydrogen bonds : angle 5.03103 ( 2727) link_BETA1-4 : bond 0.00251 ( 21) link_BETA1-4 : angle 1.71722 ( 63) link_NAG-ASN : bond 0.00406 ( 57) link_NAG-ASN : angle 2.58216 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8157 (ptm160) cc_final: 0.7579 (ttm170) REVERT: A 621 ASP cc_start: 0.7656 (t0) cc_final: 0.7377 (t0) REVERT: A 960 MET cc_start: 0.9034 (mtm) cc_final: 0.8748 (mtp) REVERT: A 1085 GLU cc_start: 0.8258 (tp30) cc_final: 0.8022 (tp30) REVERT: A 1178 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7699 (mtm110) REVERT: B 103 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8377 (mm-30) REVERT: B 224 ASP cc_start: 0.7778 (t70) cc_final: 0.7257 (t0) REVERT: B 266 MET cc_start: 0.9375 (mtm) cc_final: 0.9119 (mtm) REVERT: B 310 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8269 (pp) REVERT: B 522 LEU cc_start: 0.7890 (mt) cc_final: 0.7652 (mp) REVERT: C 81 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7430 (ptp) REVERT: C 310 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8512 (pp) REVERT: C 481 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7770 (pp) outliers start: 56 outliers final: 35 residues processed: 275 average time/residue: 0.1869 time to fit residues: 84.1931 Evaluate side-chains 261 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 1136 CYS Chi-restraints excluded: chain B residue 1160 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1160 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 204 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.090768 restraints weight = 36395.293| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.65 r_work: 0.2797 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 28440 Z= 0.252 Angle : 0.668 19.815 38757 Z= 0.330 Chirality : 0.047 0.256 4473 Planarity : 0.004 0.038 4869 Dihedral : 6.373 59.459 5339 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.23 % Allowed : 12.18 % Favored : 85.58 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.14), residues: 3333 helix: 0.95 (0.19), residues: 786 sheet: -0.42 (0.18), residues: 744 loop : -0.99 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1178 TYR 0.023 0.002 TYR A 594 PHE 0.037 0.002 PHE B 992 TRP 0.012 0.001 TRP A 434 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00611 (28314) covalent geometry : angle 0.63124 (38427) SS BOND : bond 0.00705 ( 48) SS BOND : angle 2.37180 ( 96) hydrogen bonds : bond 0.05197 ( 960) hydrogen bonds : angle 5.13159 ( 2727) link_BETA1-4 : bond 0.00259 ( 21) link_BETA1-4 : angle 1.79736 ( 63) link_NAG-ASN : bond 0.00466 ( 57) link_NAG-ASN : angle 2.71554 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 228 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8151 (ptm160) cc_final: 0.7606 (ttm170) REVERT: A 62 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7467 (tmm) REVERT: A 621 ASP cc_start: 0.7687 (t0) cc_final: 0.7408 (t0) REVERT: A 891 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: A 960 MET cc_start: 0.9020 (mtm) cc_final: 0.8710 (mtp) REVERT: A 1178 ARG cc_start: 0.8304 (mtm-85) cc_final: 0.7643 (mtm110) REVERT: B 103 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8404 (mm-30) REVERT: B 224 ASP cc_start: 0.7823 (t70) cc_final: 0.7351 (t70) REVERT: B 266 MET cc_start: 0.9376 (mtm) cc_final: 0.9119 (mtm) REVERT: B 310 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8341 (pp) REVERT: B 522 LEU cc_start: 0.8003 (mt) cc_final: 0.7772 (mp) REVERT: B 537 ILE cc_start: 0.8778 (mm) cc_final: 0.8553 (mm) REVERT: C 81 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7486 (ptp) REVERT: C 82 TYR cc_start: 0.7977 (m-10) cc_final: 0.7355 (m-80) REVERT: C 96 SER cc_start: 0.7953 (t) cc_final: 0.7603 (t) REVERT: C 310 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8574 (pp) REVERT: C 481 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7875 (pp) REVERT: C 616 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.5857 (tt0) outliers start: 66 outliers final: 52 residues processed: 275 average time/residue: 0.1749 time to fit residues: 80.1730 Evaluate side-chains 275 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 1136 CYS Chi-restraints excluded: chain B residue 1160 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 GLN Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1160 MET Chi-restraints excluded: chain C residue 1189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 238 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.096682 restraints weight = 35877.556| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.53 r_work: 0.2892 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28440 Z= 0.113 Angle : 0.571 18.219 38757 Z= 0.282 Chirality : 0.044 0.739 4473 Planarity : 0.003 0.039 4869 Dihedral : 5.682 57.727 5339 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 1.69 % Allowed : 13.13 % Favored : 85.18 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.14), residues: 3333 helix: 1.26 (0.19), residues: 789 sheet: -0.29 (0.18), residues: 738 loop : -0.88 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1178 TYR 0.014 0.001 TYR A 156 PHE 0.033 0.001 PHE B 992 TRP 0.011 0.001 TRP B1159 HIS 0.004 0.001 HIS B 704 Details of bonding type rmsd covalent geometry : bond 0.00252 (28314) covalent geometry : angle 0.52781 (38427) SS BOND : bond 0.00502 ( 48) SS BOND : angle 2.12290 ( 96) hydrogen bonds : bond 0.04145 ( 960) hydrogen bonds : angle 4.90870 ( 2727) link_BETA1-4 : bond 0.00296 ( 21) link_BETA1-4 : angle 1.52452 ( 63) link_NAG-ASN : bond 0.00569 ( 57) link_NAG-ASN : angle 2.80956 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7541 (ttm170) REVERT: A 621 ASP cc_start: 0.7561 (t0) cc_final: 0.7262 (t0) REVERT: A 1085 GLU cc_start: 0.8089 (tp30) cc_final: 0.7597 (tm-30) REVERT: A 1133 TYR cc_start: 0.7372 (m-80) cc_final: 0.7089 (m-80) REVERT: A 1178 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.7771 (mtm110) REVERT: B 224 ASP cc_start: 0.7784 (t70) cc_final: 0.7368 (t70) REVERT: B 310 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8645 (pp) REVERT: B 420 GLU cc_start: 0.7722 (pt0) cc_final: 0.7515 (tt0) REVERT: B 537 ILE cc_start: 0.8847 (mm) cc_final: 0.8627 (mm) REVERT: B 926 MET cc_start: 0.8718 (mtp) cc_final: 0.8429 (mtt) REVERT: C 310 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8549 (pp) REVERT: C 481 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8114 (pp) outliers start: 50 outliers final: 38 residues processed: 275 average time/residue: 0.1747 time to fit residues: 80.0161 Evaluate side-chains 259 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 1136 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 1189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 332 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 255 optimal weight: 0.0970 chunk 198 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 119 optimal weight: 0.0670 chunk 127 optimal weight: 10.0000 overall best weight: 1.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.094408 restraints weight = 36068.361| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.59 r_work: 0.2849 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28440 Z= 0.156 Angle : 0.605 18.711 38757 Z= 0.297 Chirality : 0.045 0.537 4473 Planarity : 0.003 0.038 4869 Dihedral : 5.556 56.352 5337 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 2.06 % Allowed : 12.93 % Favored : 85.01 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.14), residues: 3333 helix: 1.26 (0.19), residues: 789 sheet: -0.30 (0.18), residues: 738 loop : -0.89 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1178 TYR 0.014 0.001 TYR A 156 PHE 0.015 0.001 PHE C 757 TRP 0.010 0.001 TRP B 434 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00370 (28314) covalent geometry : angle 0.55805 (38427) SS BOND : bond 0.00540 ( 48) SS BOND : angle 2.55013 ( 96) hydrogen bonds : bond 0.04427 ( 960) hydrogen bonds : angle 4.88342 ( 2727) link_BETA1-4 : bond 0.00269 ( 21) link_BETA1-4 : angle 1.57980 ( 63) link_NAG-ASN : bond 0.00569 ( 57) link_NAG-ASN : angle 2.91153 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7556 (ttm170) REVERT: A 621 ASP cc_start: 0.7600 (t0) cc_final: 0.7254 (t0) REVERT: A 891 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6685 (pm20) REVERT: A 1085 GLU cc_start: 0.8126 (tp30) cc_final: 0.7791 (tm-30) REVERT: A 1133 TYR cc_start: 0.7438 (m-80) cc_final: 0.7169 (m-80) REVERT: A 1178 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7720 (mtm110) REVERT: B 224 ASP cc_start: 0.7804 (t70) cc_final: 0.7303 (t70) REVERT: B 310 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8580 (pp) REVERT: B 420 GLU cc_start: 0.7722 (pt0) cc_final: 0.7491 (tt0) REVERT: B 537 ILE cc_start: 0.8819 (mm) cc_final: 0.8592 (mm) REVERT: B 748 LYS cc_start: 0.8480 (tmmt) cc_final: 0.8175 (ttpt) REVERT: B 750 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: B 926 MET cc_start: 0.8746 (mtp) cc_final: 0.8439 (mtt) REVERT: B 1193 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6202 (pp) REVERT: C 310 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8544 (pp) REVERT: C 481 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8041 (pp) REVERT: C 616 GLN cc_start: 0.6705 (OUTLIER) cc_final: 0.6046 (tt0) outliers start: 61 outliers final: 44 residues processed: 272 average time/residue: 0.1745 time to fit residues: 77.3185 Evaluate side-chains 273 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 1143 CYS Chi-restraints excluded: chain B residue 1160 MET Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 616 GLN Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 1189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 103 optimal weight: 0.0770 chunk 205 optimal weight: 0.0370 chunk 29 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 317 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 196 optimal weight: 6.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.093925 restraints weight = 36162.247| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.83 r_work: 0.2828 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.002 0.035 28440 Z= 0.096 Angle : 0.553 18.067 38757 Z= 0.273 Chirality : 0.042 0.490 4473 Planarity : 0.003 0.039 4869 Dihedral : 5.062 57.399 5337 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 1.52 % Allowed : 13.57 % Favored : 84.91 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 3333 helix: 1.49 (0.19), residues: 786 sheet: -0.18 (0.19), residues: 738 loop : -0.84 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1178 TYR 0.014 0.001 TYR A 156 PHE 0.011 0.001 PHE A 302 TRP 0.013 0.001 TRP B1159 HIS 0.004 0.001 HIS B 704 Details of bonding type rmsd covalent geometry : bond 0.00211 (28314) covalent geometry : angle 0.50865 (38427) SS BOND : bond 0.00365 ( 48) SS BOND : angle 2.32410 ( 96) hydrogen bonds : bond 0.03792 ( 960) hydrogen bonds : angle 4.72473 ( 2727) link_BETA1-4 : bond 0.00339 ( 21) link_BETA1-4 : angle 1.40132 ( 63) link_NAG-ASN : bond 0.00549 ( 57) link_NAG-ASN : angle 2.71557 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8097 (ptm160) cc_final: 0.7586 (ttm170) REVERT: A 621 ASP cc_start: 0.7589 (t0) cc_final: 0.7145 (t0) REVERT: A 1085 GLU cc_start: 0.8123 (tp30) cc_final: 0.7480 (tm-30) REVERT: A 1133 TYR cc_start: 0.7584 (m-80) cc_final: 0.7362 (m-80) REVERT: A 1178 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7550 (mtm110) REVERT: B 224 ASP cc_start: 0.7900 (t70) cc_final: 0.7306 (t70) REVERT: B 310 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8329 (pp) REVERT: B 420 GLU cc_start: 0.7773 (pt0) cc_final: 0.7280 (tt0) REVERT: B 537 ILE cc_start: 0.8663 (mm) cc_final: 0.8455 (mm) REVERT: B 748 LYS cc_start: 0.8580 (tmmt) cc_final: 0.8311 (ttpt) REVERT: B 754 SER cc_start: 0.7075 (OUTLIER) cc_final: 0.6618 (p) REVERT: B 926 MET cc_start: 0.8703 (mtp) cc_final: 0.8345 (mtt) REVERT: B 1193 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5864 (pp) REVERT: C 310 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8274 (pp) REVERT: C 616 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6109 (tt0) outliers start: 45 outliers final: 26 residues processed: 275 average time/residue: 0.1561 time to fit residues: 71.5856 Evaluate side-chains 262 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 1160 MET Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 616 GLN Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 1189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 337 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.091037 restraints weight = 36404.164| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.64 r_work: 0.2778 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 28440 Z= 0.254 Angle : 0.678 18.306 38757 Z= 0.333 Chirality : 0.047 0.463 4473 Planarity : 0.004 0.036 4869 Dihedral : 5.635 56.473 5337 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 1.69 % Allowed : 13.67 % Favored : 84.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.14), residues: 3333 helix: 1.15 (0.19), residues: 789 sheet: -0.31 (0.18), residues: 735 loop : -0.90 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1178 TYR 0.026 0.002 TYR A 594 PHE 0.022 0.002 PHE C 757 TRP 0.010 0.001 TRP A 434 HIS 0.007 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00615 (28314) covalent geometry : angle 0.63293 (38427) SS BOND : bond 0.00631 ( 48) SS BOND : angle 2.70214 ( 96) hydrogen bonds : bond 0.05045 ( 960) hydrogen bonds : angle 4.97436 ( 2727) link_BETA1-4 : bond 0.00238 ( 21) link_BETA1-4 : angle 1.69276 ( 63) link_NAG-ASN : bond 0.00575 ( 57) link_NAG-ASN : angle 2.98038 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7592 (ttm170) REVERT: A 62 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7478 (tmm) REVERT: A 621 ASP cc_start: 0.7647 (t0) cc_final: 0.7385 (t0) REVERT: A 891 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6706 (pm20) REVERT: A 1085 GLU cc_start: 0.8302 (tp30) cc_final: 0.7594 (tp30) REVERT: A 1133 TYR cc_start: 0.7504 (m-80) cc_final: 0.7271 (m-80) REVERT: A 1178 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7635 (mtm110) REVERT: B 31 TYR cc_start: 0.8759 (m-80) cc_final: 0.8373 (m-80) REVERT: B 40 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8300 (tt) REVERT: B 224 ASP cc_start: 0.7924 (t70) cc_final: 0.7354 (t70) REVERT: B 266 MET cc_start: 0.9413 (mtm) cc_final: 0.9098 (mtm) REVERT: B 310 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8281 (pp) REVERT: B 537 ILE cc_start: 0.8784 (mm) cc_final: 0.8534 (mm) REVERT: B 748 LYS cc_start: 0.8599 (tmmt) cc_final: 0.8317 (ttpt) REVERT: B 750 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: B 754 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.6817 (p) REVERT: B 1193 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6117 (pp) REVERT: C 81 MET cc_start: 0.7916 (ptp) cc_final: 0.7457 (ptp) REVERT: C 82 TYR cc_start: 0.7953 (m-10) cc_final: 0.7315 (m-80) REVERT: C 96 SER cc_start: 0.7938 (t) cc_final: 0.7573 (t) REVERT: C 310 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8637 (pp) REVERT: C 481 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7834 (pp) REVERT: C 616 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.5942 (tt0) outliers start: 50 outliers final: 34 residues processed: 264 average time/residue: 0.1695 time to fit residues: 73.2963 Evaluate side-chains 270 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 1160 MET Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 616 GLN Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 1189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 165 optimal weight: 0.8980 chunk 330 optimal weight: 0.9990 chunk 225 optimal weight: 0.0870 chunk 324 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN C 259 ASN C1140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.092587 restraints weight = 36138.349| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.83 r_work: 0.2809 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28440 Z= 0.108 Angle : 0.572 17.568 38757 Z= 0.283 Chirality : 0.043 0.455 4473 Planarity : 0.003 0.039 4869 Dihedral : 5.182 58.422 5337 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 1.49 % Allowed : 13.81 % Favored : 84.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.15), residues: 3333 helix: 1.40 (0.19), residues: 789 sheet: -0.25 (0.18), residues: 738 loop : -0.82 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1178 TYR 0.017 0.001 TYR A 156 PHE 0.012 0.001 PHE C 757 TRP 0.014 0.001 TRP B1159 HIS 0.004 0.001 HIS B 704 Details of bonding type rmsd covalent geometry : bond 0.00246 (28314) covalent geometry : angle 0.52918 (38427) SS BOND : bond 0.00439 ( 48) SS BOND : angle 2.34066 ( 96) hydrogen bonds : bond 0.04015 ( 960) hydrogen bonds : angle 4.76889 ( 2727) link_BETA1-4 : bond 0.00315 ( 21) link_BETA1-4 : angle 1.43526 ( 63) link_NAG-ASN : bond 0.00528 ( 57) link_NAG-ASN : angle 2.73266 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6416.11 seconds wall clock time: 111 minutes 9.33 seconds (6669.33 seconds total)