Starting phenix.real_space_refine on Mon Jul 6 03:24:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l2f_23127/07_2026/7l2f_23127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2f_23127/07_2026/7l2f_23127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l2f_23127/07_2026/7l2f_23127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2f_23127/07_2026/7l2f_23127.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2f_23127/07_2026/7l2f_23127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2f_23127/07_2026/7l2f_23127.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l2f_23127/07_2026/7l2f_23127.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l2f_23127/07_2026/7l2f_23127.cif" } resolution = 3.9 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= 0.003 sd= 0.017 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 132 5.16 5 C 20355 2.51 5 N 5263 2.21 5 O 6299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32049 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1088, 8509 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1088, 8509 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 bond proxies already assigned to first conformer: 8706 Chain: "B" Number of atoms: 8512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1088, 8509 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1088, 8509 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 bond proxies already assigned to first conformer: 8706 Chain: "C" Number of atoms: 8517 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1089, 8514 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 55, 'TRANS': 1033} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1089, 8514 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 55, 'TRANS': 1033} Chain breaks: 4 bond proxies already assigned to first conformer: 8711 Chain: "H" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1011 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 815 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1011 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "J" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 815 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "I" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1011 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 815 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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 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 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 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 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 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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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 chiralities: 3 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 11.95, per 1000 atoms: 0.37 Number of scatterers: 32049 At special positions: 0 Unit cell: (194.74, 190.46, 191.53, 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 132 16.00 O 6299 8.00 N 5263 7.00 C 20355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.99 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 61 " " NAG B1307 " - " ASN B 149 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 17 " " NAG B1311 " - " ASN B 282 " " NAG B1312 " - " ASN B 343 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 149 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 282 " " NAG C1312 " - " ASN C 17 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 122 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN B 122 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 234 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 2.1 seconds 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7376 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 66 sheets defined 21.6% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.498A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.555A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 752 through 783 removed outlier: 5.763A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.558A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.916A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.663A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.700A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.602A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.614A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.587A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.567A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.759A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.656A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.506A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 783 removed outlier: 5.065A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 853 through 857 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.585A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.709A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 942 Processing helix chain 'B' and resid 945 through 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.593A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.545A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.365A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.388A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.699A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.725A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 748 through 756 removed outlier: 3.586A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.531A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 800 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 853 through 857 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.714A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.753A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.661A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 942 removed outlier: 3.505A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 942 " --> pdb=" O LEU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.718A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.047A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.452A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100D removed outlier: 3.536A pdb=" N PHE H 100B" --> pdb=" O ASP H 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.721A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100D removed outlier: 3.536A pdb=" N PHE G 100B" --> pdb=" O ASP G 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.721A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 100D removed outlier: 3.535A pdb=" N PHE I 100B" --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.721A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.705A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.624A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.637A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.278A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 10.694A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.279A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.890A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.717A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.908A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.596A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.966A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.739A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.766A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.706A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.681A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.638A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.277A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.279A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.978A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.524A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.083A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.223A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.257A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.286A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.706A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.680A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.638A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.277A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 10.694A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.280A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.686A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.714A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.926A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.263A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.891A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.081A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.613A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.657A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.199A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.779A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.973A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.390A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.390A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.514A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.522A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 6 through 7 removed outlier: 3.972A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 18 " --> pdb=" O MET G 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET G 82 " --> pdb=" O LEU G 18 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.389A pdb=" N THR G 110 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR G 58 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.389A pdb=" N THR G 110 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.514A pdb=" N SER J 7 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.521A pdb=" N ALA J 34 " --> pdb=" O GLN J 89 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 6 through 7 removed outlier: 3.973A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 10 through 11 removed outlier: 4.389A pdb=" N THR I 110 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR I 58 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 10 through 11 removed outlier: 4.389A pdb=" N THR I 110 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.514A pdb=" N SER K 7 " --> pdb=" O SER K 22 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.521A pdb=" N ALA K 34 " --> pdb=" O GLN K 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3156 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: 9.43 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6803 1.33 - 1.46: 9210 1.46 - 1.58: 16612 1.58 - 1.71: 0 1.71 - 1.84: 168 Bond restraints: 32793 Sorted by residual: bond pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.74e+01 bond pdb=" C GLY C 526 " pdb=" N PRO C 527 " ideal model delta sigma weight residual 1.331 1.361 -0.030 7.90e-03 1.60e+04 1.40e+01 bond pdb=" N LEU I 18 " pdb=" CA LEU I 18 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.13e-02 7.83e+03 1.06e+01 bond pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta sigma weight residual 1.455 1.486 -0.031 9.60e-03 1.09e+04 1.04e+01 bond pdb=" N VAL C 289 " pdb=" CA VAL C 289 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.04e+01 ... (remaining 32788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 42486 2.58 - 5.16: 1991 5.16 - 7.75: 133 7.75 - 10.33: 14 10.33 - 12.91: 5 Bond angle restraints: 44629 Sorted by residual: angle pdb=" N ASN A1098 " pdb=" CA ASN A1098 " pdb=" C ASN A1098 " ideal model delta sigma weight residual 113.20 105.13 8.07 1.21e+00 6.83e-01 4.45e+01 angle pdb=" N GLY C 594 " pdb=" CA GLY C 594 " pdb=" C GLY C 594 " ideal model delta sigma weight residual 114.67 107.93 6.74 1.10e+00 8.26e-01 3.75e+01 angle pdb=" N GLY A 339 " pdb=" CA GLY A 339 " pdb=" C GLY A 339 " ideal model delta sigma weight residual 115.08 105.84 9.24 1.54e+00 4.22e-01 3.60e+01 angle pdb=" N PRO A 792 " pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 110.70 117.63 -6.93 1.22e+00 6.72e-01 3.23e+01 angle pdb=" N PHE C 592 " pdb=" CA PHE C 592 " pdb=" C PHE C 592 " ideal model delta sigma weight residual 111.28 105.74 5.54 1.09e+00 8.42e-01 2.58e+01 ... (remaining 44624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 17281 17.26 - 34.53: 1305 34.53 - 51.79: 213 51.79 - 69.05: 39 69.05 - 86.32: 14 Dihedral angle restraints: 18852 sinusoidal: 7320 harmonic: 11532 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 160.82 -67.82 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -150.32 64.32 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -135.66 49.66 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 18849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 5126 0.231 - 0.461: 72 0.461 - 0.692: 2 0.692 - 0.923: 2 0.923 - 1.154: 2 Chirality restraints: 5204 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.80e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 5201 not shown) Planarity restraints: 5725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG a 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG T 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.335 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A1307 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.051 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.200 2.00e-02 2.50e+03 ... (remaining 5722 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7102 2.79 - 3.32: 28400 3.32 - 3.85: 52485 3.85 - 4.37: 60591 4.37 - 4.90: 102662 Nonbonded interactions: 251240 Sorted by model distance: nonbonded pdb=" O ASP A 994 " pdb=" OG1 THR A 998 " model vdw 2.265 3.040 nonbonded pdb=" O GLY A 232 " pdb=" N ARG C 466 " model vdw 2.266 3.120 nonbonded pdb=" O ASP B 994 " pdb=" OG1 THR B 998 " model vdw 2.281 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.293 3.040 nonbonded pdb=" OG1 THR C 912 " pdb=" OD1 ASN C 914 " model vdw 2.315 3.040 ... (remaining 251235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 476 or resid 478 through 1312)) selection = (chain 'B' and (resid 14 through 476 or resid 478 through 1312)) selection = (chain 'C' and (resid 14 through 476 or resid 478 through 829 or resid 853 throu \ gh 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'a' } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.630 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.008 0.066 32915 Z= 0.540 Angle : 1.180 12.910 44947 Z= 0.785 Chirality : 0.085 1.154 5204 Planarity : 0.016 0.305 5671 Dihedral : 12.361 86.315 11332 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.47 % Allowed : 3.44 % Favored : 96.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 3931 helix: 0.91 (0.19), residues: 716 sheet: 0.47 (0.17), residues: 976 loop : -0.69 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 466 TYR 0.023 0.002 TYR C 741 PHE 0.036 0.002 PHE C 888 TRP 0.014 0.002 TRP C 886 HIS 0.024 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.54 (32793) covalent geometry : angle 1.14922 / 0.78 (44629) SS BOND : bond 0.00892 / 0.51 ( 48) SS BOND : angle 1.81124 / 1.27 ( 96) hydrogen bonds : bond 0.20103 / 12.95 ( 1134) hydrogen bonds : angle 8.75301 / 6.00 ( 3156) link_BETA1-4 : bond 0.00401 / 0.24 ( 20) link_BETA1-4 : angle 1.39166 / 1.00 ( 60) link_NAG-ASN : bond 0.01124 / 0.78 ( 54) link_NAG-ASN : angle 4.44144 / 3.01 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 442 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8095 (mt-10) REVERT: A 740 MET cc_start: 0.8631 (ppp) cc_final: 0.8419 (ppp) REVERT: A 776 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9367 (ptpp) REVERT: A 1023 ASN cc_start: 0.9299 (m110) cc_final: 0.9014 (m110) REVERT: B 338 PHE cc_start: 0.8596 (m-80) cc_final: 0.8384 (m-80) REVERT: B 378 LYS cc_start: 0.8739 (tttt) cc_final: 0.8413 (ttmm) REVERT: B 759 PHE cc_start: 0.9015 (t80) cc_final: 0.8769 (t80) REVERT: B 763 LEU cc_start: 0.9709 (mp) cc_final: 0.9504 (mt) REVERT: C 741 TYR cc_start: 0.8791 (t80) cc_final: 0.8421 (t80) REVERT: L 46 LEU cc_start: 0.7083 (tp) cc_final: 0.6649 (pp) REVERT: L 47 LEU cc_start: 0.6773 (mt) cc_final: 0.6548 (tp) REVERT: K 46 LEU cc_start: 0.7913 (tp) cc_final: 0.7477 (tt) outliers start: 16 outliers final: 3 residues processed: 457 average time/residue: 0.2227 time to fit residues: 159.9101 Evaluate side-chains 215 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 212 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 501 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1011 GLN A1023 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 173 GLN B 317 ASN B 787 GLN B 853 GLN B 856 ASN B1011 GLN B1054 GLN C 23 GLN C 52 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 607 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.057300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.040589 restraints weight = 237054.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.042360 restraints weight = 104249.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.043508 restraints weight = 63540.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.044243 restraints weight = 46366.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.044723 restraints weight = 37937.925| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32915 Z= 0.153 Angle : 0.665 13.051 44947 Z= 0.339 Chirality : 0.045 0.301 5204 Planarity : 0.005 0.064 5671 Dihedral : 4.667 28.927 4313 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.08 % Allowed : 10.63 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.13), residues: 3931 helix: 1.28 (0.19), residues: 712 sheet: 0.53 (0.17), residues: 986 loop : -0.62 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 995 TYR 0.033 0.002 TYR A 365 PHE 0.053 0.002 PHE B 318 TRP 0.017 0.002 TRP A 886 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (32793) covalent geometry : angle 0.65220 / 0.34 (44629) SS BOND : bond 0.00251 / 0.19 ( 48) SS BOND : angle 0.86701 / 0.63 ( 96) hydrogen bonds : bond 0.04883 / 3.13 ( 1134) hydrogen bonds : angle 6.52512 / 4.48 ( 3156) link_BETA1-4 : bond 0.00402 / 0.29 ( 20) link_BETA1-4 : angle 1.27881 / 0.81 ( 60) link_NAG-ASN : bond 0.00265 / 0.19 ( 54) link_NAG-ASN : angle 2.07699 / 1.41 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8769 (ppp) cc_final: 0.8539 (ppp) REVERT: A 776 LYS cc_start: 0.9624 (mmmt) cc_final: 0.9347 (ptpp) REVERT: A 1023 ASN cc_start: 0.9244 (m-40) cc_final: 0.8963 (m-40) REVERT: B 198 ASP cc_start: 0.7727 (t0) cc_final: 0.7521 (t0) REVERT: B 224 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8569 (tp30) REVERT: B 378 LYS cc_start: 0.8779 (tttt) cc_final: 0.8518 (ttmm) REVERT: B 763 LEU cc_start: 0.9720 (mp) cc_final: 0.9515 (mt) REVERT: B 1004 LEU cc_start: 0.9769 (mt) cc_final: 0.9388 (mt) REVERT: C 378 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8258 (mtpp) REVERT: C 988 GLU cc_start: 0.8282 (pm20) cc_final: 0.7993 (pm20) REVERT: C 1012 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8884 (mt) REVERT: C 1029 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9136 (tpt) REVERT: H 67 PHE cc_start: 0.3523 (m-80) cc_final: 0.2898 (m-80) REVERT: G 98 ASP cc_start: 0.8101 (t0) cc_final: 0.7637 (p0) REVERT: J 46 LEU cc_start: 0.8831 (tp) cc_final: 0.8546 (mt) REVERT: J 96 LEU cc_start: 0.8292 (tt) cc_final: 0.7564 (tp) REVERT: I 64 LYS cc_start: 0.9466 (tppt) cc_final: 0.9237 (tppt) REVERT: I 66 ARG cc_start: 0.9216 (mtt-85) cc_final: 0.9000 (mtp180) REVERT: I 78 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7739 (pp) REVERT: K 54 ARG cc_start: 0.6705 (mtt-85) cc_final: 0.6433 (mtt-85) outliers start: 37 outliers final: 17 residues processed: 267 average time/residue: 0.2125 time to fit residues: 92.0443 Evaluate side-chains 220 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 40 optimal weight: 3.9990 chunk 305 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 351 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 856 ASN C 23 GLN C 115 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS L 90 GLN G 35 HIS I 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.054225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.037663 restraints weight = 238570.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039289 restraints weight = 108993.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.040348 restraints weight = 67817.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041039 restraints weight = 50252.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.041481 restraints weight = 41469.694| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32915 Z= 0.240 Angle : 0.679 12.662 44947 Z= 0.349 Chirality : 0.044 0.252 5204 Planarity : 0.005 0.065 5671 Dihedral : 4.788 21.230 4311 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.66 % Allowed : 10.89 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 3931 helix: 1.17 (0.19), residues: 713 sheet: 0.11 (0.16), residues: 1053 loop : -0.57 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 19 TYR 0.030 0.002 TYR G 79 PHE 0.025 0.002 PHE B1089 TRP 0.012 0.002 TRP B 886 HIS 0.015 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (32793) covalent geometry : angle 0.67077 / 0.35 (44629) SS BOND : bond 0.00313 / 0.23 ( 48) SS BOND : angle 0.88350 / 0.63 ( 96) hydrogen bonds : bond 0.04639 / 2.99 ( 1134) hydrogen bonds : angle 6.23399 / 4.27 ( 3156) link_BETA1-4 : bond 0.00414 / 0.32 ( 20) link_BETA1-4 : angle 1.21757 / 0.79 ( 60) link_NAG-ASN : bond 0.00352 / 0.22 ( 54) link_NAG-ASN : angle 1.67954 / 1.13 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.8141 (t80) cc_final: 0.7838 (t80) REVERT: A 740 MET cc_start: 0.8811 (ppp) cc_final: 0.8574 (ppp) REVERT: A 869 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.9075 (ptp) REVERT: A 1023 ASN cc_start: 0.9278 (m-40) cc_final: 0.8995 (m-40) REVERT: A 1050 MET cc_start: 0.8236 (ptm) cc_final: 0.7570 (ptt) REVERT: B 198 ASP cc_start: 0.7919 (t0) cc_final: 0.7618 (t0) REVERT: B 312 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9422 (mt) REVERT: B 378 LYS cc_start: 0.8695 (tttt) cc_final: 0.8361 (ttmm) REVERT: B 1004 LEU cc_start: 0.9785 (mt) cc_final: 0.9416 (mt) REVERT: B 1031 GLU cc_start: 0.8134 (tt0) cc_final: 0.7920 (tt0) REVERT: C 53 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8296 (t70) REVERT: C 378 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8315 (mtpp) REVERT: C 988 GLU cc_start: 0.8546 (pm20) cc_final: 0.8272 (pm20) REVERT: H 100 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8317 (t70) REVERT: L 46 LEU cc_start: 0.7893 (tp) cc_final: 0.7536 (mt) REVERT: G 101 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7707 (p0) REVERT: J 46 LEU cc_start: 0.8839 (tp) cc_final: 0.8568 (mt) REVERT: J 60 ASP cc_start: 0.9643 (p0) cc_final: 0.9288 (p0) REVERT: I 64 LYS cc_start: 0.9493 (tppt) cc_final: 0.9292 (tppt) REVERT: K 39 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8215 (pttm) REVERT: K 46 LEU cc_start: 0.7680 (tt) cc_final: 0.6935 (tp) REVERT: K 54 ARG cc_start: 0.6951 (mtt-85) cc_final: 0.6557 (mtt-85) outliers start: 57 outliers final: 27 residues processed: 256 average time/residue: 0.2012 time to fit residues: 83.5929 Evaluate side-chains 208 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 148 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 327 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1002 GLN C1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.054582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.038120 restraints weight = 227445.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.039745 restraints weight = 105448.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.040798 restraints weight = 65962.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.041477 restraints weight = 49061.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041932 restraints weight = 40568.610| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32915 Z= 0.149 Angle : 0.604 14.523 44947 Z= 0.309 Chirality : 0.043 0.228 5204 Planarity : 0.004 0.048 5671 Dihedral : 4.602 20.164 4311 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.40 % Allowed : 12.29 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 3931 helix: 1.24 (0.20), residues: 721 sheet: 0.08 (0.16), residues: 1042 loop : -0.55 (0.12), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.020 0.001 TYR A 707 PHE 0.030 0.001 PHE B 318 TRP 0.015 0.001 TRP I 52 HIS 0.015 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (32793) covalent geometry : angle 0.59757 / 0.31 (44629) SS BOND : bond 0.00290 / 0.19 ( 48) SS BOND : angle 0.87686 / 0.60 ( 96) hydrogen bonds : bond 0.04134 / 2.65 ( 1134) hydrogen bonds : angle 5.89252 / 4.03 ( 3156) link_BETA1-4 : bond 0.00368 / 0.27 ( 20) link_BETA1-4 : angle 1.05371 / 0.68 ( 60) link_NAG-ASN : bond 0.00189 / 0.13 ( 54) link_NAG-ASN : angle 1.43747 / 0.97 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8531 (tt) REVERT: A 697 MET cc_start: 0.8549 (mmp) cc_final: 0.8041 (mmm) REVERT: A 740 MET cc_start: 0.8798 (ppp) cc_final: 0.8485 (ppp) REVERT: A 1023 ASN cc_start: 0.9267 (m-40) cc_final: 0.8970 (m-40) REVERT: A 1107 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7784 (ttt180) REVERT: B 198 ASP cc_start: 0.7887 (t0) cc_final: 0.7551 (t0) REVERT: B 378 LYS cc_start: 0.8717 (tttt) cc_final: 0.8357 (ttmm) REVERT: B 697 MET cc_start: 0.8780 (tmm) cc_final: 0.7756 (tmm) REVERT: B 1004 LEU cc_start: 0.9760 (mt) cc_final: 0.9464 (mt) REVERT: B 1031 GLU cc_start: 0.8048 (tt0) cc_final: 0.7769 (tt0) REVERT: C 53 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8249 (t70) REVERT: C 188 ASN cc_start: 0.7071 (OUTLIER) cc_final: 0.6862 (t0) REVERT: C 378 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8284 (mtpp) REVERT: C 988 GLU cc_start: 0.8431 (pm20) cc_final: 0.8202 (pm20) REVERT: H 28 THR cc_start: 0.8250 (t) cc_final: 0.7883 (m) REVERT: H 100 ASP cc_start: 0.8708 (t0) cc_final: 0.8284 (t70) REVERT: G 101 ASP cc_start: 0.8189 (p0) cc_final: 0.7887 (p0) REVERT: J 46 LEU cc_start: 0.8890 (tp) cc_final: 0.8551 (mt) REVERT: I 64 LYS cc_start: 0.9478 (tppt) cc_final: 0.9258 (tppt) REVERT: I 67 PHE cc_start: 0.7221 (m-10) cc_final: 0.6964 (m-10) REVERT: I 75 LYS cc_start: 0.9484 (mmmt) cc_final: 0.9280 (ttpt) REVERT: K 46 LEU cc_start: 0.7907 (tt) cc_final: 0.7107 (tp) REVERT: K 54 ARG cc_start: 0.7035 (mtt-85) cc_final: 0.6804 (mtt-85) REVERT: K 103 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8331 (mmmt) outliers start: 48 outliers final: 26 residues processed: 233 average time/residue: 0.1926 time to fit residues: 75.1019 Evaluate side-chains 204 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 258 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 386 optimal weight: 30.0000 chunk 214 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 804 GLN A 913 GLN A1054 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 613 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.051439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.034772 restraints weight = 264516.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.036383 restraints weight = 116866.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.037425 restraints weight = 72039.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038116 restraints weight = 53247.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.038550 restraints weight = 43752.255| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 32915 Z= 0.309 Angle : 0.743 11.509 44947 Z= 0.381 Chirality : 0.046 0.284 5204 Planarity : 0.005 0.064 5671 Dihedral : 5.152 24.068 4311 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.72 % Allowed : 12.93 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 3931 helix: 0.69 (0.19), residues: 733 sheet: -0.27 (0.16), residues: 1059 loop : -0.64 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 66 TYR 0.029 0.002 TYR A 707 PHE 0.036 0.003 PHE B1089 TRP 0.016 0.002 TRP H 103 HIS 0.015 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.31 (32793) covalent geometry : angle 0.73390 / 0.38 (44629) SS BOND : bond 0.00396 / 0.28 ( 48) SS BOND : angle 1.14384 / 0.83 ( 96) hydrogen bonds : bond 0.04766 / 3.10 ( 1134) hydrogen bonds : angle 6.28594 / 4.29 ( 3156) link_BETA1-4 : bond 0.00246 / 0.19 ( 20) link_BETA1-4 : angle 1.32787 / 0.88 ( 60) link_NAG-ASN : bond 0.00543 / 0.33 ( 54) link_NAG-ASN : angle 1.81974 / 1.23 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 423 TYR cc_start: 0.8181 (t80) cc_final: 0.7790 (t80) REVERT: A 740 MET cc_start: 0.8820 (ppp) cc_final: 0.8469 (ppp) REVERT: A 869 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.9166 (ptp) REVERT: A 1023 ASN cc_start: 0.9381 (m-40) cc_final: 0.9104 (m-40) REVERT: A 1029 MET cc_start: 0.9163 (mmm) cc_final: 0.8765 (tpp) REVERT: A 1107 ARG cc_start: 0.8260 (ttt180) cc_final: 0.7879 (tpt-90) REVERT: B 378 LYS cc_start: 0.8663 (tttt) cc_final: 0.8236 (ttmm) REVERT: B 697 MET cc_start: 0.8679 (tmm) cc_final: 0.7891 (tmm) REVERT: B 741 TYR cc_start: 0.8988 (t80) cc_final: 0.8657 (t80) REVERT: B 1004 LEU cc_start: 0.9807 (mt) cc_final: 0.9521 (mt) REVERT: B 1031 GLU cc_start: 0.8078 (tt0) cc_final: 0.7559 (tt0) REVERT: B 1092 GLU cc_start: 0.7825 (pm20) cc_final: 0.7508 (pm20) REVERT: C 53 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8481 (t70) REVERT: C 378 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8328 (mtpp) REVERT: C 988 GLU cc_start: 0.8671 (pm20) cc_final: 0.8431 (pm20) REVERT: C 1029 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9131 (tpt) REVERT: C 1042 PHE cc_start: 0.7679 (t80) cc_final: 0.7417 (t80) REVERT: H 43 LYS cc_start: 0.7878 (mtmm) cc_final: 0.6476 (tmtt) REVERT: H 100 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8587 (t70) REVERT: G 95 ASP cc_start: 0.7959 (t70) cc_final: 0.7173 (m-30) REVERT: G 101 ASP cc_start: 0.8399 (p0) cc_final: 0.8125 (p0) REVERT: J 46 LEU cc_start: 0.8885 (tp) cc_final: 0.8510 (tp) REVERT: J 98 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6719 (t80) REVERT: I 64 LYS cc_start: 0.9505 (tppt) cc_final: 0.9087 (mmtt) REVERT: K 54 ARG cc_start: 0.7387 (mtt-85) cc_final: 0.6964 (mtt-85) REVERT: K 103 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8378 (mmmt) outliers start: 59 outliers final: 41 residues processed: 211 average time/residue: 0.1920 time to fit residues: 68.1395 Evaluate side-chains 201 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 370 optimal weight: 30.0000 chunk 73 optimal weight: 0.6980 chunk 344 optimal weight: 8.9990 chunk 1 optimal weight: 0.0010 chunk 9 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 250 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 317 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 52 GLN B 188 ASN B 314 GLN B 317 ASN B 613 GLN C 394 ASN C 764 ASN C 777 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.053451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.036517 restraints weight = 274885.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.038275 restraints weight = 115430.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.039434 restraints weight = 69261.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.040167 restraints weight = 50034.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040661 restraints weight = 40755.052| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32915 Z= 0.114 Angle : 0.592 14.418 44947 Z= 0.301 Chirality : 0.044 0.229 5204 Planarity : 0.004 0.046 5671 Dihedral : 4.627 19.665 4311 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.19 % Allowed : 14.06 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 3931 helix: 1.20 (0.20), residues: 730 sheet: -0.10 (0.16), residues: 1027 loop : -0.54 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 71 TYR 0.018 0.001 TYR A 369 PHE 0.028 0.001 PHE B 318 TRP 0.018 0.001 TRP C 64 HIS 0.011 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (32793) covalent geometry : angle 0.58693 / 0.30 (44629) SS BOND : bond 0.00287 / 0.18 ( 48) SS BOND : angle 0.81459 / 0.58 ( 96) hydrogen bonds : bond 0.03976 / 2.57 ( 1134) hydrogen bonds : angle 5.68766 / 3.86 ( 3156) link_BETA1-4 : bond 0.00421 / 0.29 ( 20) link_BETA1-4 : angle 0.98129 / 0.65 ( 60) link_NAG-ASN : bond 0.00212 / 0.15 ( 54) link_NAG-ASN : angle 1.28697 / 0.86 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8549 (mmp) cc_final: 0.7953 (mmm) REVERT: A 740 MET cc_start: 0.8871 (ppp) cc_final: 0.8467 (ppp) REVERT: A 869 MET cc_start: 0.9416 (mtp) cc_final: 0.9089 (ptp) REVERT: A 1023 ASN cc_start: 0.9385 (m-40) cc_final: 0.9100 (m-40) REVERT: A 1050 MET cc_start: 0.7779 (ptm) cc_final: 0.7054 (ptt) REVERT: A 1107 ARG cc_start: 0.8221 (ttt180) cc_final: 0.7700 (tpt-90) REVERT: B 378 LYS cc_start: 0.8727 (tttt) cc_final: 0.8288 (ttmm) REVERT: B 697 MET cc_start: 0.8610 (tmm) cc_final: 0.7645 (tmm) REVERT: B 731 MET cc_start: 0.9453 (ptm) cc_final: 0.9165 (ptm) REVERT: B 741 TYR cc_start: 0.8946 (t80) cc_final: 0.8616 (t80) REVERT: B 1004 LEU cc_start: 0.9768 (mt) cc_final: 0.9471 (mt) REVERT: B 1031 GLU cc_start: 0.8161 (tt0) cc_final: 0.7584 (tt0) REVERT: B 1092 GLU cc_start: 0.7741 (pm20) cc_final: 0.7294 (pm20) REVERT: C 378 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8258 (mtpp) REVERT: C 780 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8955 (tm-30) REVERT: C 988 GLU cc_start: 0.8489 (pm20) cc_final: 0.8251 (pm20) REVERT: C 1004 LEU cc_start: 0.9544 (mt) cc_final: 0.9205 (mt) REVERT: C 1029 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9061 (tpt) REVERT: H 28 THR cc_start: 0.8133 (t) cc_final: 0.7927 (m) REVERT: H 43 LYS cc_start: 0.8020 (mtmm) cc_final: 0.6608 (tmtt) REVERT: H 100 ASP cc_start: 0.8943 (t0) cc_final: 0.8641 (t70) REVERT: L 46 LEU cc_start: 0.7915 (mt) cc_final: 0.7645 (mt) REVERT: G 100 ASP cc_start: 0.8964 (t0) cc_final: 0.8742 (m-30) REVERT: J 46 LEU cc_start: 0.8952 (tp) cc_final: 0.8637 (tp) REVERT: J 98 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6531 (t80) REVERT: I 39 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8194 (tp-100) REVERT: I 64 LYS cc_start: 0.9527 (tppt) cc_final: 0.9092 (mmtt) REVERT: I 66 ARG cc_start: 0.9248 (mtt-85) cc_final: 0.8979 (mtp-110) REVERT: I 67 PHE cc_start: 0.7287 (m-10) cc_final: 0.7080 (m-10) REVERT: I 100 ASP cc_start: 0.8441 (t0) cc_final: 0.8203 (t0) REVERT: K 54 ARG cc_start: 0.7300 (mtt-85) cc_final: 0.6866 (mtt-85) REVERT: K 103 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8353 (mmmt) outliers start: 41 outliers final: 25 residues processed: 214 average time/residue: 0.1909 time to fit residues: 69.1039 Evaluate side-chains 195 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 255 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 152 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 386 optimal weight: 40.0000 chunk 209 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 239 GLN B 317 ASN C 764 ASN C 777 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.051674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.035235 restraints weight = 236528.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.036774 restraints weight = 108844.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.037820 restraints weight = 68522.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.038490 restraints weight = 50872.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038922 restraints weight = 42079.814| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32915 Z= 0.243 Angle : 0.646 12.839 44947 Z= 0.331 Chirality : 0.043 0.254 5204 Planarity : 0.004 0.047 5671 Dihedral : 4.775 22.158 4310 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.19 % Allowed : 14.47 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 3931 helix: 1.03 (0.20), residues: 727 sheet: -0.28 (0.16), residues: 1080 loop : -0.55 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1107 TYR 0.021 0.002 TYR A 707 PHE 0.026 0.002 PHE B1089 TRP 0.014 0.002 TRP H 103 HIS 0.012 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (32793) covalent geometry : angle 0.63950 / 0.33 (44629) SS BOND : bond 0.00312 / 0.22 ( 48) SS BOND : angle 0.90142 / 0.66 ( 96) hydrogen bonds : bond 0.04297 / 2.80 ( 1134) hydrogen bonds : angle 5.88693 / 4.00 ( 3156) link_BETA1-4 : bond 0.00264 / 0.20 ( 20) link_BETA1-4 : angle 1.13658 / 0.76 ( 60) link_NAG-ASN : bond 0.00351 / 0.22 ( 54) link_NAG-ASN : angle 1.52966 / 1.02 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.8242 (t80) cc_final: 0.7943 (t80) REVERT: A 740 MET cc_start: 0.8886 (ppp) cc_final: 0.8490 (ppp) REVERT: A 1023 ASN cc_start: 0.9386 (m-40) cc_final: 0.9119 (m-40) REVERT: A 1107 ARG cc_start: 0.8229 (ttt180) cc_final: 0.7803 (ttt180) REVERT: B 317 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8850 (t0) REVERT: B 378 LYS cc_start: 0.8695 (tttt) cc_final: 0.8272 (ttmm) REVERT: B 697 MET cc_start: 0.8691 (tmm) cc_final: 0.7846 (tmm) REVERT: B 741 TYR cc_start: 0.9030 (t80) cc_final: 0.8725 (t80) REVERT: B 1004 LEU cc_start: 0.9795 (mt) cc_final: 0.9523 (mt) REVERT: B 1031 GLU cc_start: 0.8098 (tt0) cc_final: 0.7546 (tt0) REVERT: C 53 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8448 (t70) REVERT: C 378 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8299 (mtpp) REVERT: C 869 MET cc_start: 0.9241 (ptp) cc_final: 0.9022 (pmm) REVERT: C 988 GLU cc_start: 0.8649 (pm20) cc_final: 0.8421 (pm20) REVERT: C 1048 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7902 (t-170) REVERT: H 43 LYS cc_start: 0.8068 (mtmm) cc_final: 0.6665 (tmtt) REVERT: H 100 ASP cc_start: 0.8882 (t0) cc_final: 0.8607 (t70) REVERT: G 100 ASP cc_start: 0.8950 (t0) cc_final: 0.8720 (m-30) REVERT: J 46 LEU cc_start: 0.8958 (tp) cc_final: 0.8607 (tp) REVERT: J 98 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6642 (t80) REVERT: I 39 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8113 (tp-100) REVERT: I 64 LYS cc_start: 0.9503 (tppt) cc_final: 0.9123 (mmtt) REVERT: I 66 ARG cc_start: 0.9270 (mtt-85) cc_final: 0.8984 (mtp180) REVERT: I 100 ASP cc_start: 0.8356 (t0) cc_final: 0.8108 (t0) REVERT: K 54 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.6952 (mtt-85) REVERT: K 103 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8481 (mmmt) outliers start: 41 outliers final: 29 residues processed: 194 average time/residue: 0.1986 time to fit residues: 64.9706 Evaluate side-chains 194 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1048 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 327 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 358 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.051195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034797 restraints weight = 261047.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036338 restraints weight = 118221.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037349 restraints weight = 73871.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.038000 restraints weight = 54810.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038392 restraints weight = 45388.551| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 32915 Z= 0.271 Angle : 0.679 12.048 44947 Z= 0.349 Chirality : 0.044 0.273 5204 Planarity : 0.004 0.047 5671 Dihedral : 4.983 22.048 4310 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.16 % Allowed : 14.82 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 3931 helix: 0.98 (0.19), residues: 716 sheet: -0.40 (0.15), residues: 1087 loop : -0.67 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 319 TYR 0.024 0.002 TYR A 707 PHE 0.029 0.002 PHE B1089 TRP 0.019 0.002 TRP H 103 HIS 0.014 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.27 (32793) covalent geometry : angle 0.67167 / 0.35 (44629) SS BOND : bond 0.00343 / 0.25 ( 48) SS BOND : angle 0.98907 / 0.72 ( 96) hydrogen bonds : bond 0.04387 / 2.85 ( 1134) hydrogen bonds : angle 5.99285 / 4.07 ( 3156) link_BETA1-4 : bond 0.00312 / 0.23 ( 20) link_BETA1-4 : angle 1.10583 / 0.74 ( 60) link_NAG-ASN : bond 0.00352 / 0.22 ( 54) link_NAG-ASN : angle 1.59288 / 1.07 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.8278 (t80) cc_final: 0.7924 (t80) REVERT: A 697 MET cc_start: 0.8664 (mmp) cc_final: 0.7632 (mmm) REVERT: A 740 MET cc_start: 0.8892 (ppp) cc_final: 0.8502 (ppp) REVERT: A 869 MET cc_start: 0.9392 (mtp) cc_final: 0.9148 (ptp) REVERT: A 1023 ASN cc_start: 0.9357 (m-40) cc_final: 0.9084 (m-40) REVERT: A 1029 MET cc_start: 0.9051 (tpp) cc_final: 0.8608 (tpp) REVERT: A 1107 ARG cc_start: 0.8294 (ttt180) cc_final: 0.7905 (tpt-90) REVERT: B 41 LYS cc_start: 0.8118 (mttt) cc_final: 0.7500 (ttpt) REVERT: B 378 LYS cc_start: 0.8728 (tttt) cc_final: 0.8308 (ttmm) REVERT: B 697 MET cc_start: 0.8716 (tmm) cc_final: 0.7754 (tmm) REVERT: B 731 MET cc_start: 0.9439 (ptm) cc_final: 0.9150 (ptm) REVERT: B 1004 LEU cc_start: 0.9787 (mt) cc_final: 0.9473 (mt) REVERT: B 1031 GLU cc_start: 0.8065 (tt0) cc_final: 0.7534 (tt0) REVERT: B 1092 GLU cc_start: 0.7789 (pm20) cc_final: 0.7517 (pm20) REVERT: C 53 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8486 (t70) REVERT: C 378 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8322 (mtpp) REVERT: C 869 MET cc_start: 0.9191 (ptp) cc_final: 0.8982 (pmm) REVERT: C 988 GLU cc_start: 0.8691 (pm20) cc_final: 0.8453 (pm20) REVERT: C 1004 LEU cc_start: 0.9533 (mt) cc_final: 0.9208 (mt) REVERT: H 43 LYS cc_start: 0.8228 (mtmm) cc_final: 0.6833 (tmtt) REVERT: H 100 ASP cc_start: 0.8844 (t0) cc_final: 0.8612 (t70) REVERT: L 46 LEU cc_start: 0.8404 (mt) cc_final: 0.8182 (mt) REVERT: J 46 LEU cc_start: 0.9018 (tp) cc_final: 0.8514 (tp) REVERT: J 98 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6690 (t80) REVERT: I 39 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8160 (tp40) REVERT: I 52 TRP cc_start: 0.7356 (m-90) cc_final: 0.6616 (m100) REVERT: I 58 TYR cc_start: 0.9189 (t80) cc_final: 0.8887 (t80) REVERT: I 64 LYS cc_start: 0.9500 (tppt) cc_final: 0.9119 (mmtt) REVERT: I 66 ARG cc_start: 0.9399 (mtt-85) cc_final: 0.9084 (mtp-110) REVERT: I 67 PHE cc_start: 0.7405 (m-10) cc_final: 0.7178 (m-10) REVERT: K 54 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.6745 (mtt-85) outliers start: 40 outliers final: 34 residues processed: 198 average time/residue: 0.2099 time to fit residues: 68.7126 Evaluate side-chains 187 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 345 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 246 optimal weight: 6.9990 chunk 314 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN C 777 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.052430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.036187 restraints weight = 209659.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037720 restraints weight = 99687.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038734 restraints weight = 63437.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.039390 restraints weight = 47655.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.039821 restraints weight = 39610.285| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32915 Z= 0.126 Angle : 0.601 15.633 44947 Z= 0.303 Chirality : 0.044 0.245 5204 Planarity : 0.004 0.057 5671 Dihedral : 4.696 23.072 4310 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.05 % Allowed : 15.02 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 3931 helix: 1.24 (0.20), residues: 716 sheet: -0.26 (0.16), residues: 1068 loop : -0.62 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 54 TYR 0.018 0.001 TYR B 741 PHE 0.023 0.001 PHE A 275 TRP 0.018 0.001 TRP C 64 HIS 0.012 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (32793) covalent geometry : angle 0.59603 / 0.30 (44629) SS BOND : bond 0.00229 / 0.17 ( 48) SS BOND : angle 0.82942 / 0.59 ( 96) hydrogen bonds : bond 0.03943 / 2.56 ( 1134) hydrogen bonds : angle 5.64373 / 3.83 ( 3156) link_BETA1-4 : bond 0.00365 / 0.26 ( 20) link_BETA1-4 : angle 0.97643 / 0.65 ( 60) link_NAG-ASN : bond 0.00180 / 0.13 ( 54) link_NAG-ASN : angle 1.28594 / 0.86 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8594 (mmp) cc_final: 0.7598 (mmm) REVERT: A 740 MET cc_start: 0.8914 (ppp) cc_final: 0.8440 (ppp) REVERT: A 869 MET cc_start: 0.9420 (mtp) cc_final: 0.9097 (ptp) REVERT: A 1023 ASN cc_start: 0.9398 (m-40) cc_final: 0.9120 (m-40) REVERT: A 1050 MET cc_start: 0.8090 (ptm) cc_final: 0.7685 (ppp) REVERT: A 1107 ARG cc_start: 0.8265 (ttt180) cc_final: 0.7765 (tpt-90) REVERT: B 41 LYS cc_start: 0.7968 (mttt) cc_final: 0.7433 (ttpt) REVERT: B 378 LYS cc_start: 0.8695 (tttt) cc_final: 0.8249 (ttmm) REVERT: B 697 MET cc_start: 0.8659 (tmm) cc_final: 0.7675 (tmm) REVERT: B 731 MET cc_start: 0.9412 (ptm) cc_final: 0.9133 (ptm) REVERT: B 1004 LEU cc_start: 0.9771 (mt) cc_final: 0.9441 (mt) REVERT: B 1031 GLU cc_start: 0.8182 (tt0) cc_final: 0.7644 (tt0) REVERT: B 1092 GLU cc_start: 0.7876 (pm20) cc_final: 0.7506 (pm20) REVERT: C 378 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8260 (mtpp) REVERT: C 777 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.9012 (t0) REVERT: C 780 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8941 (tm-30) REVERT: C 869 MET cc_start: 0.9260 (ptp) cc_final: 0.9034 (pmm) REVERT: C 945 LEU cc_start: 0.9505 (mm) cc_final: 0.9265 (mp) REVERT: C 988 GLU cc_start: 0.8570 (pm20) cc_final: 0.8338 (pm20) REVERT: C 1004 LEU cc_start: 0.9524 (mt) cc_final: 0.9185 (mt) REVERT: C 1048 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7517 (t-170) REVERT: H 43 LYS cc_start: 0.8293 (mtmm) cc_final: 0.6965 (tmtt) REVERT: L 46 LEU cc_start: 0.8212 (mt) cc_final: 0.7975 (mt) REVERT: L 81 GLU cc_start: 0.9486 (tp30) cc_final: 0.9187 (pm20) REVERT: J 46 LEU cc_start: 0.9031 (tp) cc_final: 0.8775 (tp) REVERT: I 39 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8142 (tp40) REVERT: I 52 TRP cc_start: 0.7400 (m-90) cc_final: 0.6690 (m100) REVERT: I 58 TYR cc_start: 0.9176 (t80) cc_final: 0.8796 (t80) REVERT: I 64 LYS cc_start: 0.9503 (tppt) cc_final: 0.9098 (mmtt) REVERT: I 66 ARG cc_start: 0.9323 (mtt-85) cc_final: 0.9080 (mtp-110) REVERT: K 54 ARG cc_start: 0.7375 (mtt-85) cc_final: 0.6589 (mtt-85) outliers start: 36 outliers final: 32 residues processed: 193 average time/residue: 0.2066 time to fit residues: 66.3811 Evaluate side-chains 190 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1048 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 93 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 363 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 332 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 317 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.052764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035920 restraints weight = 284805.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037658 restraints weight = 118273.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.038826 restraints weight = 70656.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.039577 restraints weight = 50827.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.040049 restraints weight = 41187.741| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32915 Z= 0.118 Angle : 0.594 15.414 44947 Z= 0.299 Chirality : 0.043 0.220 5204 Planarity : 0.004 0.049 5671 Dihedral : 4.581 33.492 4310 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.96 % Allowed : 15.08 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 3931 helix: 1.33 (0.20), residues: 714 sheet: -0.12 (0.16), residues: 1061 loop : -0.62 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 54 TYR 0.020 0.001 TYR C1138 PHE 0.022 0.001 PHE A 275 TRP 0.016 0.001 TRP C 64 HIS 0.011 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (32793) covalent geometry : angle 0.58944 / 0.30 (44629) SS BOND : bond 0.00209 / 0.15 ( 48) SS BOND : angle 0.77576 / 0.56 ( 96) hydrogen bonds : bond 0.03842 / 2.49 ( 1134) hydrogen bonds : angle 5.55212 / 3.77 ( 3156) link_BETA1-4 : bond 0.00349 / 0.25 ( 20) link_BETA1-4 : angle 1.01362 / 0.67 ( 60) link_NAG-ASN : bond 0.00161 / 0.12 ( 54) link_NAG-ASN : angle 1.23970 / 0.82 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8519 (mmp) cc_final: 0.7493 (mmm) REVERT: A 740 MET cc_start: 0.8897 (ppp) cc_final: 0.8462 (ppp) REVERT: A 869 MET cc_start: 0.9412 (mtp) cc_final: 0.9092 (ptp) REVERT: A 1023 ASN cc_start: 0.9398 (m-40) cc_final: 0.9116 (m-40) REVERT: A 1029 MET cc_start: 0.9118 (tpp) cc_final: 0.8700 (tpp) REVERT: A 1050 MET cc_start: 0.8076 (ptm) cc_final: 0.7658 (ppp) REVERT: A 1107 ARG cc_start: 0.8232 (ttt180) cc_final: 0.7771 (tpt-90) REVERT: B 41 LYS cc_start: 0.8016 (mttt) cc_final: 0.7503 (ttpt) REVERT: B 378 LYS cc_start: 0.8690 (tttt) cc_final: 0.8245 (ttmm) REVERT: B 697 MET cc_start: 0.8653 (tmm) cc_final: 0.7717 (tmm) REVERT: B 731 MET cc_start: 0.9389 (ptm) cc_final: 0.9108 (ptm) REVERT: B 1004 LEU cc_start: 0.9782 (mt) cc_final: 0.9428 (mt) REVERT: B 1031 GLU cc_start: 0.8171 (tt0) cc_final: 0.7857 (tt0) REVERT: B 1092 GLU cc_start: 0.7924 (pm20) cc_final: 0.7534 (pm20) REVERT: C 378 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8234 (mtpp) REVERT: C 869 MET cc_start: 0.9228 (ptp) cc_final: 0.9014 (pmm) REVERT: C 945 LEU cc_start: 0.9469 (mm) cc_final: 0.9232 (mp) REVERT: C 988 GLU cc_start: 0.8530 (pm20) cc_final: 0.8271 (pm20) REVERT: C 1048 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7342 (t-170) REVERT: H 43 LYS cc_start: 0.8269 (mtmm) cc_final: 0.6936 (tmtt) REVERT: H 82 MET cc_start: 0.0512 (mmm) cc_final: 0.0203 (mmm) REVERT: L 46 LEU cc_start: 0.8196 (mt) cc_final: 0.7944 (mt) REVERT: L 81 GLU cc_start: 0.9496 (tp30) cc_final: 0.9218 (pm20) REVERT: G 98 ASP cc_start: 0.8482 (t70) cc_final: 0.8025 (p0) REVERT: J 46 LEU cc_start: 0.9018 (tp) cc_final: 0.8769 (tp) REVERT: I 39 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8080 (tp40) REVERT: I 52 TRP cc_start: 0.7346 (m-90) cc_final: 0.6632 (m100) REVERT: I 58 TYR cc_start: 0.9166 (t80) cc_final: 0.8755 (t80) REVERT: I 64 LYS cc_start: 0.9498 (tppt) cc_final: 0.9092 (mmtt) REVERT: I 66 ARG cc_start: 0.9342 (mtt-85) cc_final: 0.9102 (mtp-110) REVERT: K 54 ARG cc_start: 0.7350 (mtt-85) cc_final: 0.6838 (mtt-85) outliers start: 33 outliers final: 28 residues processed: 182 average time/residue: 0.2017 time to fit residues: 61.9001 Evaluate side-chains 182 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1048 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 44 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 351 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 367 optimal weight: 5.9990 chunk 375 optimal weight: 7.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.051442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034563 restraints weight = 326604.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036278 restraints weight = 132124.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037401 restraints weight = 78202.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038145 restraints weight = 56305.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.038575 restraints weight = 45504.760| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32915 Z= 0.233 Angle : 0.656 13.305 44947 Z= 0.333 Chirality : 0.044 0.254 5204 Planarity : 0.004 0.050 5671 Dihedral : 4.793 34.800 4310 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.08 % Allowed : 14.99 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 3931 helix: 1.18 (0.20), residues: 715 sheet: -0.29 (0.15), residues: 1095 loop : -0.61 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 54 TYR 0.023 0.002 TYR A 707 PHE 0.024 0.002 PHE B1089 TRP 0.015 0.002 TRP C 64 HIS 0.013 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 (32793) covalent geometry : angle 0.64912 / 0.33 (44629) SS BOND : bond 0.00316 / 0.22 ( 48) SS BOND : angle 0.89708 / 0.65 ( 96) hydrogen bonds : bond 0.04188 / 2.72 ( 1134) hydrogen bonds : angle 5.78782 / 3.93 ( 3156) link_BETA1-4 : bond 0.00321 / 0.24 ( 20) link_BETA1-4 : angle 1.12521 / 0.74 ( 60) link_NAG-ASN : bond 0.00308 / 0.19 ( 54) link_NAG-ASN : angle 1.50864 / 1.00 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8447.25 seconds wall clock time: 145 minutes 45.21 seconds (8745.21 seconds total)