Starting phenix.real_space_refine on Fri Mar 6 16:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2f_23127/03_2026/7l2f_23127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2f_23127/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7l2f_23127/03_2026/7l2f_23127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2f_23127/03_2026/7l2f_23127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l2f_23127/03_2026/7l2f_23127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2f_23127/03_2026/7l2f_23127.map" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 11.31, per 1000 atoms: 0.35 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: 2.90 Conformation dependent library (CDL) restraints added in 1.9 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: 1.54 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: 7.87 Time building geometry restraints manager: 3.77 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 - 21.26: 19228 21.26 - 42.51: 1017 42.51 - 63.77: 113 63.77 - 85.03: 35 85.03 - 106.28: 9 Dihedral angle restraints: 20402 sinusoidal: 8870 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 20399 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: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 36.620 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 12.540 106.284 12882 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 covalent geometry : bond 0.00773 (32793) covalent geometry : angle 1.14922 (44629) SS BOND : bond 0.00892 ( 48) SS BOND : angle 1.81124 ( 96) hydrogen bonds : bond 0.20103 ( 1134) hydrogen bonds : angle 8.75301 ( 3156) link_BETA1-4 : bond 0.00401 ( 20) link_BETA1-4 : angle 1.39166 ( 60) link_NAG-ASN : bond 0.01124 ( 54) link_NAG-ASN : angle 4.44144 ( 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 : 1.057 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: 0.1981 time to fit residues: 142.4178 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 : 0.856 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.057353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.040643 restraints weight = 236991.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.042417 restraints weight = 104208.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.043554 restraints weight = 63401.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.044303 restraints weight = 46390.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.044767 restraints weight = 37975.057| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32915 Z= 0.153 Angle : 0.666 12.847 44947 Z= 0.340 Chirality : 0.045 0.358 5204 Planarity : 0.005 0.065 5671 Dihedral : 6.777 65.488 5863 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.16 % Allowed : 10.54 % 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: 1.29 (0.19), residues: 714 sheet: 0.54 (0.17), residues: 986 loop : -0.63 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.038 0.002 TYR A 365 PHE 0.054 0.002 PHE B 318 TRP 0.016 0.002 TRP A 886 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00334 (32793) covalent geometry : angle 0.65287 (44629) SS BOND : bond 0.00247 ( 48) SS BOND : angle 0.86765 ( 96) hydrogen bonds : bond 0.04957 ( 1134) hydrogen bonds : angle 6.54864 ( 3156) link_BETA1-4 : bond 0.00398 ( 20) link_BETA1-4 : angle 1.50551 ( 60) link_NAG-ASN : bond 0.00304 ( 54) link_NAG-ASN : angle 2.10163 ( 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 283 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 1.080 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: 0.8767 (ppp) cc_final: 0.8540 (ppp) REVERT: A 776 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9354 (ptpp) REVERT: A 1023 ASN cc_start: 0.9242 (m-40) cc_final: 0.8962 (m-40) REVERT: B 198 ASP cc_start: 0.7720 (t0) cc_final: 0.7511 (t0) REVERT: B 224 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8550 (tp30) REVERT: B 378 LYS cc_start: 0.8784 (tttt) cc_final: 0.8523 (ttmm) REVERT: B 763 LEU cc_start: 0.9721 (mp) cc_final: 0.9488 (mt) REVERT: B 1004 LEU cc_start: 0.9772 (mt) cc_final: 0.9390 (mt) REVERT: C 378 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8259 (mtpp) REVERT: C 988 GLU cc_start: 0.8284 (pm20) cc_final: 0.7993 (pm20) REVERT: C 1012 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8890 (mt) REVERT: C 1029 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.9162 (tpt) REVERT: H 67 PHE cc_start: 0.3544 (m-80) cc_final: 0.2907 (m-80) REVERT: H 98 ASP cc_start: 0.8042 (p0) cc_final: 0.7708 (p0) REVERT: G 98 ASP cc_start: 0.8133 (t0) cc_final: 0.7679 (p0) REVERT: J 46 LEU cc_start: 0.8830 (tp) cc_final: 0.8545 (mt) REVERT: J 96 LEU cc_start: 0.8286 (tt) cc_final: 0.7560 (tp) REVERT: I 64 LYS cc_start: 0.9474 (tppt) cc_final: 0.9249 (tppt) REVERT: I 66 ARG cc_start: 0.9230 (mtt-85) cc_final: 0.9011 (mtp180) REVERT: I 78 LEU cc_start: 0.8144 (pp) cc_final: 0.7774 (pp) REVERT: K 54 ARG cc_start: 0.6690 (mtt-85) cc_final: 0.6427 (mtt-85) outliers start: 40 outliers final: 18 residues processed: 268 average time/residue: 0.1916 time to fit residues: 83.3182 Evaluate side-chains 218 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 902 MET 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 45 LEU Chi-restraints excluded: chain I residue 68 THR 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: 2.9990 chunk 305 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 351 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 188 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.054456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.037872 restraints weight = 238079.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.039519 restraints weight = 108569.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.040596 restraints weight = 67394.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.041281 restraints weight = 49779.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.041736 restraints weight = 41073.447| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 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 = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32915 Z= 0.226 Angle : 0.672 13.298 44947 Z= 0.345 Chirality : 0.044 0.272 5204 Planarity : 0.004 0.055 5671 Dihedral : 5.945 59.559 5861 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.60 % Allowed : 10.89 % Favored : 87.51 % 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: -0.12 (0.13), residues: 3931 helix: 1.19 (0.19), residues: 713 sheet: 0.13 (0.16), residues: 1052 loop : -0.57 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 403 TYR 0.025 0.002 TYR G 79 PHE 0.025 0.002 PHE C1042 TRP 0.044 0.002 TRP I 52 HIS 0.018 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00487 (32793) covalent geometry : angle 0.66305 (44629) SS BOND : bond 0.00306 ( 48) SS BOND : angle 0.86827 ( 96) hydrogen bonds : bond 0.04575 ( 1134) hydrogen bonds : angle 6.20985 ( 3156) link_BETA1-4 : bond 0.00323 ( 20) link_BETA1-4 : angle 1.54257 ( 60) link_NAG-ASN : bond 0.00315 ( 54) link_NAG-ASN : angle 1.70348 ( 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 269 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 1.102 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: 0.8132 (t80) cc_final: 0.7834 (t80) REVERT: A 740 MET cc_start: 0.8807 (ppp) cc_final: 0.8580 (ppp) REVERT: A 869 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.9067 (ptp) REVERT: A 1023 ASN cc_start: 0.9274 (m-40) cc_final: 0.8989 (m-40) REVERT: A 1050 MET cc_start: 0.8212 (ptm) cc_final: 0.7540 (ptt) REVERT: B 198 ASP cc_start: 0.7908 (t0) cc_final: 0.7621 (t0) REVERT: B 312 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9417 (mt) REVERT: B 378 LYS cc_start: 0.8700 (tttt) cc_final: 0.8368 (ttmm) REVERT: B 1004 LEU cc_start: 0.9793 (mt) cc_final: 0.9415 (mt) REVERT: C 53 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8279 (t70) REVERT: C 378 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8312 (mtpp) REVERT: C 988 GLU cc_start: 0.8513 (pm20) cc_final: 0.8245 (pm20) REVERT: H 100 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8315 (t70) REVERT: L 46 LEU cc_start: 0.7947 (tp) cc_final: 0.7614 (mt) REVERT: G 101 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7721 (p0) REVERT: J 46 LEU cc_start: 0.8835 (tp) cc_final: 0.8563 (mt) REVERT: J 60 ASP cc_start: 0.9640 (p0) cc_final: 0.9287 (p0) REVERT: I 64 LYS cc_start: 0.9495 (tppt) cc_final: 0.9291 (tppt) REVERT: K 39 LYS cc_start: 0.8862 (pttm) cc_final: 0.8223 (pttm) REVERT: K 46 LEU cc_start: 0.7679 (tt) cc_final: 0.6918 (tp) REVERT: K 54 ARG cc_start: 0.7000 (mtt-85) cc_final: 0.6694 (mtt-85) outliers start: 55 outliers final: 26 residues processed: 255 average time/residue: 0.1887 time to fit residues: 78.1762 Evaluate side-chains 204 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 632 THR Chi-restraints excluded: chain A residue 707 TYR 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 16 VAL 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 78 LEU Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 68 THR 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: 0.7980 chunk 88 optimal weight: 7.9990 chunk 78 optimal weight: 0.0970 chunk 50 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 327 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 394 ASN C 777 ASN C1002 GLN C1036 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.055230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.038731 restraints weight = 226779.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.040370 restraints weight = 104745.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.041450 restraints weight = 65533.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042147 restraints weight = 48639.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.042600 restraints weight = 40134.090| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 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 = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32915 Z= 0.121 Angle : 0.593 15.025 44947 Z= 0.301 Chirality : 0.044 0.237 5204 Planarity : 0.004 0.048 5671 Dihedral : 5.393 57.312 5861 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.16 % Allowed : 12.40 % Favored : 86.43 % 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: -0.04 (0.13), residues: 3931 helix: 1.29 (0.20), residues: 723 sheet: 0.18 (0.16), residues: 1029 loop : -0.55 (0.12), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 19 TYR 0.019 0.001 TYR A 707 PHE 0.033 0.001 PHE B 318 TRP 0.016 0.001 TRP C 64 HIS 0.013 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00267 (32793) covalent geometry : angle 0.58538 (44629) SS BOND : bond 0.00316 ( 48) SS BOND : angle 0.80668 ( 96) hydrogen bonds : bond 0.04059 ( 1134) hydrogen bonds : angle 5.82879 ( 3156) link_BETA1-4 : bond 0.00379 ( 20) link_BETA1-4 : angle 1.34960 ( 60) link_NAG-ASN : bond 0.00191 ( 54) link_NAG-ASN : angle 1.48262 ( 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 232 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.125 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 18 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8570 (tt) REVERT: A 697 MET cc_start: 0.8503 (mmp) cc_final: 0.7976 (mmm) REVERT: A 869 MET cc_start: 0.9338 (mtp) cc_final: 0.9074 (ptp) REVERT: A 1005 GLN cc_start: 0.9451 (pm20) cc_final: 0.9139 (pm20) REVERT: A 1023 ASN cc_start: 0.9250 (m-40) cc_final: 0.8943 (m-40) REVERT: A 1050 MET cc_start: 0.8004 (ptm) cc_final: 0.7310 (ptt) REVERT: A 1107 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7733 (ttt180) REVERT: B 198 ASP cc_start: 0.7845 (t0) cc_final: 0.7503 (t0) REVERT: B 378 LYS cc_start: 0.8707 (tttt) cc_final: 0.8360 (ttmm) REVERT: B 697 MET cc_start: 0.8780 (tmm) cc_final: 0.7750 (tmm) REVERT: B 1004 LEU cc_start: 0.9760 (mt) cc_final: 0.9405 (mt) REVERT: B 1031 GLU cc_start: 0.8154 (tt0) cc_final: 0.7820 (tp30) REVERT: C 378 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8271 (mtpp) REVERT: C 988 GLU cc_start: 0.8392 (pm20) cc_final: 0.8162 (pm20) REVERT: C 1029 MET cc_start: 0.9239 (tpt) cc_final: 0.8968 (tpt) REVERT: H 28 THR cc_start: 0.8217 (t) cc_final: 0.7847 (m) REVERT: H 43 LYS cc_start: 0.7455 (mtmm) cc_final: 0.6721 (pttp) REVERT: H 100 ASP cc_start: 0.8680 (t0) cc_final: 0.8263 (t70) REVERT: G 101 ASP cc_start: 0.8117 (p0) cc_final: 0.7829 (p0) REVERT: J 46 LEU cc_start: 0.8887 (tp) cc_final: 0.8536 (mt) REVERT: I 64 LYS cc_start: 0.9477 (tppt) cc_final: 0.9254 (tppt) REVERT: I 67 PHE cc_start: 0.7078 (m-10) cc_final: 0.6799 (m-10) REVERT: I 75 LYS cc_start: 0.9518 (mmmt) cc_final: 0.9272 (ttpt) REVERT: K 46 LEU cc_start: 0.7823 (tt) cc_final: 0.7031 (tp) REVERT: K 54 ARG cc_start: 0.7010 (mtt-85) cc_final: 0.6653 (mtt-85) REVERT: K 103 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8306 (mmmt) outliers start: 40 outliers final: 21 residues processed: 226 average time/residue: 0.1711 time to fit residues: 65.0672 Evaluate side-chains 200 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 632 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 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 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 I residue 68 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: 7.9990 chunk 349 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 276 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 386 optimal weight: 30.0000 chunk 214 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.034464 restraints weight = 266174.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.036039 restraints weight = 117804.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.037080 restraints weight = 72847.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037750 restraints weight = 53771.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.038143 restraints weight = 44276.140| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 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 = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 0.008 0.073 32915 Z= 0.387 Angle : 0.795 11.382 44947 Z= 0.411 Chirality : 0.047 0.309 5204 Planarity : 0.005 0.065 5671 Dihedral : 5.960 56.206 5860 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.60 % Allowed : 12.84 % Favored : 85.56 % 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: -0.54 (0.13), residues: 3931 helix: 0.61 (0.19), residues: 721 sheet: -0.29 (0.15), residues: 1062 loop : -0.68 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.031 0.003 TYR A 707 PHE 0.048 0.003 PHE C1042 TRP 0.020 0.002 TRP B 353 HIS 0.017 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00831 (32793) covalent geometry : angle 0.78498 (44629) SS BOND : bond 0.00494 ( 48) SS BOND : angle 1.19224 ( 96) hydrogen bonds : bond 0.05016 ( 1134) hydrogen bonds : angle 6.40577 ( 3156) link_BETA1-4 : bond 0.00358 ( 20) link_BETA1-4 : angle 1.58997 ( 60) link_NAG-ASN : bond 0.00632 ( 54) link_NAG-ASN : angle 1.98551 ( 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 227 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8659 (tt) REVERT: A 423 TYR cc_start: 0.8251 (t80) cc_final: 0.7864 (t80) REVERT: A 740 MET cc_start: 0.8991 (ppp) cc_final: 0.8703 (ppp) REVERT: A 1023 ASN cc_start: 0.9388 (m-40) cc_final: 0.9115 (m-40) REVERT: A 1107 ARG cc_start: 0.8290 (ttt180) cc_final: 0.7893 (tpt-90) REVERT: B 41 LYS cc_start: 0.7726 (mttt) cc_final: 0.7131 (ttpt) REVERT: B 378 LYS cc_start: 0.8672 (tttt) cc_final: 0.8250 (ttmm) REVERT: B 697 MET cc_start: 0.8681 (tmm) cc_final: 0.7878 (tmm) REVERT: B 741 TYR cc_start: 0.8939 (t80) cc_final: 0.8627 (t80) REVERT: B 1004 LEU cc_start: 0.9809 (mt) cc_final: 0.9534 (mt) REVERT: B 1031 GLU cc_start: 0.8363 (tt0) cc_final: 0.7873 (tp30) REVERT: C 53 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8490 (t70) REVERT: C 378 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8328 (mtpp) REVERT: C 1029 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.9143 (tpt) REVERT: H 100 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8530 (t70) REVERT: L 61 ARG cc_start: 0.8720 (ptt-90) cc_final: 0.8492 (ptt90) REVERT: G 95 ASP cc_start: 0.7978 (t70) cc_final: 0.7054 (m-30) REVERT: G 101 ASP cc_start: 0.8367 (p0) cc_final: 0.8093 (p0) REVERT: J 46 LEU cc_start: 0.8888 (tp) cc_final: 0.8522 (tp) REVERT: I 67 PHE cc_start: 0.7463 (m-10) cc_final: 0.7236 (m-10) REVERT: K 54 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.6999 (mtt-85) REVERT: K 103 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8448 (mmmt) outliers start: 55 outliers final: 39 residues processed: 212 average time/residue: 0.1790 time to fit residues: 63.0183 Evaluate side-chains 196 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 632 THR Chi-restraints excluded: chain A residue 751 ASN 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 302 THR 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 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 392 PHE Chi-restraints excluded: chain C residue 516 GLU 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 H residue 102 VAL Chi-restraints excluded: chain G residue 37 VAL 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 I residue 68 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 39 LYS 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: 3.9990 chunk 344 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 250 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 314 GLN B 317 ASN C 764 ASN C 777 ASN ** C1002 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 = 0.3377 r_free = 0.3377 target = 0.052396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.035568 restraints weight = 276608.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.037264 restraints weight = 117075.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.038397 restraints weight = 70584.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.039124 restraints weight = 51144.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.039589 restraints weight = 41603.193| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 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 = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 32915 Z= 0.168 Angle : 0.617 13.766 44947 Z= 0.316 Chirality : 0.044 0.269 5204 Planarity : 0.004 0.046 5671 Dihedral : 5.479 55.997 5860 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.19 % Allowed : 14.09 % Favored : 84.72 % 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: -0.36 (0.13), residues: 3931 helix: 0.98 (0.19), residues: 731 sheet: -0.25 (0.16), residues: 1050 loop : -0.61 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 19 TYR 0.018 0.001 TYR C1138 PHE 0.027 0.002 PHE B 318 TRP 0.026 0.002 TRP I 52 HIS 0.012 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00367 (32793) covalent geometry : angle 0.61013 (44629) SS BOND : bond 0.00264 ( 48) SS BOND : angle 0.86616 ( 96) hydrogen bonds : bond 0.04222 ( 1134) hydrogen bonds : angle 5.90126 ( 3156) link_BETA1-4 : bond 0.00359 ( 20) link_BETA1-4 : angle 1.18331 ( 60) link_NAG-ASN : bond 0.00197 ( 54) link_NAG-ASN : angle 1.49443 ( 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 213 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.947 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 740 MET cc_start: 0.8849 (ppp) cc_final: 0.8505 (ppp) REVERT: A 869 MET cc_start: 0.9423 (mtp) cc_final: 0.9149 (ptp) REVERT: A 1023 ASN cc_start: 0.9357 (m-40) cc_final: 0.9066 (m110) REVERT: A 1050 MET cc_start: 0.7902 (ptm) cc_final: 0.7166 (ptt) REVERT: B 378 LYS cc_start: 0.8732 (tttt) cc_final: 0.8298 (ttmm) REVERT: B 697 MET cc_start: 0.8653 (tmm) cc_final: 0.7693 (tmm) REVERT: B 741 TYR cc_start: 0.8937 (t80) cc_final: 0.8620 (t80) REVERT: B 1004 LEU cc_start: 0.9783 (mt) cc_final: 0.9512 (mt) REVERT: B 1031 GLU cc_start: 0.8340 (tt0) cc_final: 0.7849 (tp30) REVERT: C 378 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8293 (mtpp) REVERT: C 1004 LEU cc_start: 0.9539 (mt) cc_final: 0.9221 (mt) REVERT: C 1012 LEU cc_start: 0.9115 (mt) cc_final: 0.8823 (mt) REVERT: H 28 THR cc_start: 0.8212 (t) cc_final: 0.7991 (m) REVERT: H 43 LYS cc_start: 0.8048 (mtmm) cc_final: 0.6630 (tmtt) REVERT: H 100 ASP cc_start: 0.8981 (t0) cc_final: 0.8648 (t70) REVERT: L 46 LEU cc_start: 0.8060 (mt) cc_final: 0.7810 (mt) REVERT: G 95 ASP cc_start: 0.7796 (t70) cc_final: 0.6922 (m-30) REVERT: G 100 ASP cc_start: 0.8949 (t0) cc_final: 0.8711 (m-30) REVERT: G 101 ASP cc_start: 0.8468 (p0) cc_final: 0.8203 (p0) REVERT: J 46 LEU cc_start: 0.8964 (tp) cc_final: 0.8636 (tp) REVERT: I 39 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8271 (tp-100) REVERT: I 100 ASP cc_start: 0.8414 (t0) cc_final: 0.8186 (t0) REVERT: K 54 ARG cc_start: 0.7367 (mtt-85) cc_final: 0.6914 (mtt-85) REVERT: K 103 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8330 (mmmt) outliers start: 41 outliers final: 30 residues processed: 202 average time/residue: 0.1928 time to fit residues: 65.7039 Evaluate side-chains 196 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 385 THR Chi-restraints excluded: chain A residue 632 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 47 VAL Chi-restraints excluded: chain B residue 87 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 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 516 GLU 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 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 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 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: 0.9980 chunk 152 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 386 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 327 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 306 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN C 764 ASN C 777 ASN ** C1002 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 = 0.3375 r_free = 0.3375 target = 0.052288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.035792 restraints weight = 233266.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.037398 restraints weight = 106441.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038445 restraints weight = 66372.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.039125 restraints weight = 49257.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.039555 restraints weight = 40557.865| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 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 = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32915 Z= 0.174 Angle : 0.604 13.687 44947 Z= 0.309 Chirality : 0.043 0.264 5204 Planarity : 0.004 0.047 5671 Dihedral : 5.340 55.423 5860 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.22 % Allowed : 14.03 % 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: -0.32 (0.13), residues: 3931 helix: 1.06 (0.20), residues: 726 sheet: -0.27 (0.16), residues: 1061 loop : -0.58 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.020 0.001 TYR A 741 PHE 0.021 0.001 PHE A 275 TRP 0.017 0.001 TRP C 64 HIS 0.018 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00378 (32793) covalent geometry : angle 0.59695 (44629) SS BOND : bond 0.00260 ( 48) SS BOND : angle 0.84001 ( 96) hydrogen bonds : bond 0.04147 ( 1134) hydrogen bonds : angle 5.81131 ( 3156) link_BETA1-4 : bond 0.00315 ( 20) link_BETA1-4 : angle 1.22843 ( 60) link_NAG-ASN : bond 0.00213 ( 54) link_NAG-ASN : angle 1.47105 ( 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 215 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.8223 (t80) cc_final: 0.7863 (t80) REVERT: A 740 MET cc_start: 0.8869 (ppp) cc_final: 0.8511 (ppp) REVERT: A 869 MET cc_start: 0.9420 (mtp) cc_final: 0.9143 (ptp) REVERT: A 1023 ASN cc_start: 0.9352 (m-40) cc_final: 0.9070 (m-40) REVERT: A 1050 MET cc_start: 0.8080 (ptm) cc_final: 0.7539 (ppp) REVERT: A 1107 ARG cc_start: 0.8256 (ttt180) cc_final: 0.7744 (tpt-90) REVERT: B 317 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8860 (t0) REVERT: B 378 LYS cc_start: 0.8708 (tttt) cc_final: 0.8271 (ttmm) REVERT: B 697 MET cc_start: 0.8633 (tmm) cc_final: 0.7669 (tmm) REVERT: B 741 TYR cc_start: 0.8979 (t80) cc_final: 0.8682 (t80) REVERT: B 1004 LEU cc_start: 0.9775 (mt) cc_final: 0.9502 (mt) REVERT: B 1031 GLU cc_start: 0.8363 (tt0) cc_final: 0.7832 (tp30) REVERT: C 378 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8288 (mtpp) REVERT: C 1004 LEU cc_start: 0.9549 (mt) cc_final: 0.9222 (mt) REVERT: C 1012 LEU cc_start: 0.9114 (mt) cc_final: 0.8815 (mt) REVERT: H 43 LYS cc_start: 0.8063 (mtmm) cc_final: 0.6639 (tmtt) REVERT: H 100 ASP cc_start: 0.8919 (t0) cc_final: 0.8613 (t70) REVERT: J 46 LEU cc_start: 0.8981 (tp) cc_final: 0.8627 (tp) REVERT: I 39 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8100 (tp-100) REVERT: I 66 ARG cc_start: 0.9233 (mtt-85) cc_final: 0.8957 (mtp180) REVERT: I 100 ASP cc_start: 0.8345 (t0) cc_final: 0.8103 (t0) REVERT: K 54 ARG cc_start: 0.7383 (mtt-85) cc_final: 0.6900 (mtt-85) REVERT: K 103 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8445 (mmmt) outliers start: 42 outliers final: 33 residues processed: 205 average time/residue: 0.1761 time to fit residues: 61.1055 Evaluate side-chains 195 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 751 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 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 B residue 1013 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 516 GLU 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 I residue 39 GLN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 1 GLU 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: 9.9990 chunk 182 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 363 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 358 optimal weight: 0.0670 chunk 118 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.051212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.034767 restraints weight = 260460.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036322 restraints weight = 118466.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.037342 restraints weight = 74004.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.038008 restraints weight = 54856.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.038443 restraints weight = 45255.497| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 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 = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 32915 Z= 0.265 Angle : 0.684 11.466 44947 Z= 0.351 Chirality : 0.044 0.282 5204 Planarity : 0.004 0.051 5671 Dihedral : 5.613 55.340 5860 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.37 % Allowed : 14.35 % Favored : 84.28 % 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: -0.46 (0.13), residues: 3931 helix: 1.02 (0.20), residues: 703 sheet: -0.36 (0.15), residues: 1084 loop : -0.67 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 319 TYR 0.020 0.002 TYR C1138 PHE 0.028 0.002 PHE B1089 TRP 0.018 0.002 TRP H 103 HIS 0.014 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00571 (32793) covalent geometry : angle 0.67585 (44629) SS BOND : bond 0.00347 ( 48) SS BOND : angle 0.98375 ( 96) hydrogen bonds : bond 0.04450 ( 1134) hydrogen bonds : angle 6.00606 ( 3156) link_BETA1-4 : bond 0.00277 ( 20) link_BETA1-4 : angle 1.32143 ( 60) link_NAG-ASN : bond 0.00390 ( 54) link_NAG-ASN : angle 1.66994 ( 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 206 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 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: A 423 TYR cc_start: 0.8289 (t80) cc_final: 0.7908 (t80) REVERT: A 1023 ASN cc_start: 0.9365 (m-40) cc_final: 0.9083 (m-40) REVERT: A 1050 MET cc_start: 0.8376 (ptm) cc_final: 0.7645 (ppp) REVERT: B 41 LYS cc_start: 0.8101 (mttt) cc_final: 0.7516 (ttpt) REVERT: B 378 LYS cc_start: 0.8715 (tttt) cc_final: 0.8264 (ttmm) REVERT: B 697 MET cc_start: 0.8694 (tmm) cc_final: 0.7756 (tmm) REVERT: B 1004 LEU cc_start: 0.9788 (mt) cc_final: 0.9481 (mt) REVERT: B 1031 GLU cc_start: 0.8324 (tt0) cc_final: 0.7814 (tp30) REVERT: C 53 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8476 (t70) REVERT: C 378 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8313 (mtpp) REVERT: C 1048 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7775 (t-170) REVERT: H 43 LYS cc_start: 0.8202 (mtmm) cc_final: 0.6788 (tmtt) REVERT: H 100 ASP cc_start: 0.8856 (t0) cc_final: 0.8612 (t70) REVERT: L 46 LEU cc_start: 0.8385 (mt) cc_final: 0.8159 (mt) REVERT: J 46 LEU cc_start: 0.8994 (tp) cc_final: 0.8469 (tp) REVERT: J 98 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6685 (t80) REVERT: I 39 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8209 (tp40) REVERT: I 66 ARG cc_start: 0.9273 (mtt-85) cc_final: 0.8981 (mtp-110) REVERT: K 54 ARG cc_start: 0.7507 (mtt-85) cc_final: 0.6728 (mtt-85) outliers start: 47 outliers final: 40 residues processed: 198 average time/residue: 0.1819 time to fit residues: 60.4412 Evaluate side-chains 192 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER 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 751 ASN 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 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 318 PHE 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 368 LEU Chi-restraints excluded: chain C residue 516 GLU 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 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: 10.0000 chunk 194 optimal weight: 1.9990 chunk 185 optimal weight: 0.2980 chunk 239 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 chunk 246 optimal weight: 6.9990 chunk 314 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.052573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.036310 restraints weight = 209289.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.037855 restraints weight = 99524.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.038865 restraints weight = 63347.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.039533 restraints weight = 47542.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.039952 restraints weight = 39436.427| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 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 = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4514 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= 0.122 Angle : 0.603 15.058 44947 Z= 0.305 Chirality : 0.044 0.250 5204 Planarity : 0.004 0.049 5671 Dihedral : 5.254 54.967 5860 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.05 % Allowed : 14.93 % 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: -0.29 (0.13), residues: 3931 helix: 1.20 (0.20), residues: 716 sheet: -0.23 (0.16), residues: 1065 loop : -0.60 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 77 TYR 0.018 0.001 TYR A 741 PHE 0.023 0.001 PHE A 275 TRP 0.025 0.002 TRP G 52 HIS 0.011 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00272 (32793) covalent geometry : angle 0.59676 (44629) SS BOND : bond 0.00227 ( 48) SS BOND : angle 0.82738 ( 96) hydrogen bonds : bond 0.03952 ( 1134) hydrogen bonds : angle 5.62781 ( 3156) link_BETA1-4 : bond 0.00389 ( 20) link_BETA1-4 : angle 1.13575 ( 60) link_NAG-ASN : bond 0.00190 ( 54) link_NAG-ASN : angle 1.32186 ( 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 : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8105 (mmm) REVERT: A 740 MET cc_start: 0.8938 (ppp) cc_final: 0.8537 (ppp) REVERT: A 869 MET cc_start: 0.9414 (mtp) cc_final: 0.9074 (ptp) REVERT: A 1023 ASN cc_start: 0.9378 (m-40) cc_final: 0.9082 (m-40) REVERT: A 1050 MET cc_start: 0.7872 (ptm) cc_final: 0.7595 (ppp) REVERT: A 1107 ARG cc_start: 0.8260 (ttt180) cc_final: 0.7762 (tpt-90) REVERT: B 41 LYS cc_start: 0.7808 (mttt) cc_final: 0.7226 (ttpt) REVERT: B 378 LYS cc_start: 0.8730 (tttt) cc_final: 0.8285 (ttmm) REVERT: B 697 MET cc_start: 0.8724 (tmm) cc_final: 0.7718 (tmm) REVERT: B 1004 LEU cc_start: 0.9763 (mt) cc_final: 0.9430 (mt) REVERT: B 1031 GLU cc_start: 0.8383 (tt0) cc_final: 0.7810 (tp30) REVERT: B 1092 GLU cc_start: 0.7795 (pm20) cc_final: 0.7314 (pm20) REVERT: C 53 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8477 (t70) REVERT: C 378 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8256 (mtpp) REVERT: C 780 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8940 (tm-30) REVERT: C 945 LEU cc_start: 0.9492 (mm) cc_final: 0.9271 (mp) REVERT: C 1004 LEU cc_start: 0.9547 (mt) cc_final: 0.9208 (mt) REVERT: C 1029 MET cc_start: 0.9357 (tpt) cc_final: 0.9026 (tpt) REVERT: H 43 LYS cc_start: 0.8257 (mtmm) cc_final: 0.6884 (tmtt) REVERT: H 100 ASP cc_start: 0.8778 (t0) cc_final: 0.8578 (t70) REVERT: L 46 LEU cc_start: 0.8224 (mt) cc_final: 0.7983 (mt) REVERT: J 46 LEU cc_start: 0.9052 (tp) cc_final: 0.8775 (tp) REVERT: I 39 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8212 (tp40) REVERT: I 58 TYR cc_start: 0.9194 (t80) cc_final: 0.8787 (t80) REVERT: I 66 ARG cc_start: 0.9273 (mtt-85) cc_final: 0.9024 (mtp-110) REVERT: K 54 ARG cc_start: 0.7345 (mtt-85) cc_final: 0.6839 (mtt-85) outliers start: 36 outliers final: 28 residues processed: 194 average time/residue: 0.1800 time to fit residues: 58.0103 Evaluate side-chains 184 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 1005 GLN 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 481 ASN 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 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 516 GLU 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 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: 4.9990 chunk 200 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 363 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 150 optimal weight: 0.0060 chunk 332 optimal weight: 30.0000 chunk 205 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.052994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.036154 restraints weight = 284673.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.037908 restraints weight = 117897.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.039066 restraints weight = 70411.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.039817 restraints weight = 50689.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.040312 restraints weight = 41019.844| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 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 = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4549 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= 0.117 Angle : 0.592 15.168 44947 Z= 0.298 Chirality : 0.044 0.407 5204 Planarity : 0.004 0.051 5671 Dihedral : 5.013 54.633 5860 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.84 % Allowed : 15.20 % 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: -0.19 (0.13), residues: 3931 helix: 1.34 (0.20), residues: 714 sheet: -0.14 (0.16), residues: 1082 loop : -0.57 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 71 TYR 0.020 0.001 TYR B 741 PHE 0.026 0.001 PHE I 67 TRP 0.015 0.001 TRP C 64 HIS 0.010 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00261 (32793) covalent geometry : angle 0.58662 (44629) SS BOND : bond 0.00215 ( 48) SS BOND : angle 0.76334 ( 96) hydrogen bonds : bond 0.03821 ( 1134) hydrogen bonds : angle 5.48549 ( 3156) link_BETA1-4 : bond 0.00366 ( 20) link_BETA1-4 : angle 1.19649 ( 60) link_NAG-ASN : bond 0.00152 ( 54) link_NAG-ASN : angle 1.27989 ( 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 189 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8001 (mmm) REVERT: A 740 MET cc_start: 0.8952 (ppp) cc_final: 0.8565 (ppp) REVERT: A 869 MET cc_start: 0.9407 (mtp) cc_final: 0.9069 (ptp) REVERT: A 1023 ASN cc_start: 0.9378 (m-40) cc_final: 0.9081 (m-40) REVERT: A 1050 MET cc_start: 0.8082 (ptm) cc_final: 0.7755 (ppp) REVERT: A 1107 ARG cc_start: 0.8194 (ttt180) cc_final: 0.7750 (tpt-90) REVERT: B 41 LYS cc_start: 0.7871 (mttt) cc_final: 0.7363 (ttpt) REVERT: B 378 LYS cc_start: 0.8698 (tttt) cc_final: 0.8253 (ttmm) REVERT: B 697 MET cc_start: 0.8664 (tmm) cc_final: 0.7635 (tmm) REVERT: B 1004 LEU cc_start: 0.9770 (mt) cc_final: 0.9413 (mt) REVERT: B 1031 GLU cc_start: 0.8389 (tt0) cc_final: 0.7843 (tp30) REVERT: B 1092 GLU cc_start: 0.7954 (pm20) cc_final: 0.7474 (pm20) REVERT: C 378 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8219 (mtpp) REVERT: C 780 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8949 (tm-30) REVERT: C 945 LEU cc_start: 0.9461 (mm) cc_final: 0.9241 (mp) REVERT: H 43 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7527 (pttp) REVERT: L 46 LEU cc_start: 0.8160 (mt) cc_final: 0.7887 (mt) REVERT: J 46 LEU cc_start: 0.8996 (tp) cc_final: 0.8752 (tp) REVERT: I 39 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8121 (tp40) REVERT: I 58 TYR cc_start: 0.9197 (t80) cc_final: 0.8778 (t80) REVERT: K 5 THR cc_start: 0.9090 (m) cc_final: 0.8830 (p) outliers start: 29 outliers final: 26 residues processed: 181 average time/residue: 0.1876 time to fit residues: 56.5661 Evaluate side-chains 178 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR 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 1104 VAL Chi-restraints excluded: chain C residue 29 THR 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 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: 2.9990 chunk 221 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 chunk 351 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 49 optimal weight: 0.0980 chunk 367 optimal weight: 7.9990 chunk 375 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.052686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035743 restraints weight = 322254.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.037563 restraints weight = 126362.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.038758 restraints weight = 73543.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.039545 restraints weight = 52106.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.040056 restraints weight = 41690.810| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 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 = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32915 Z= 0.136 Angle : 0.599 14.805 44947 Z= 0.301 Chirality : 0.044 0.423 5204 Planarity : 0.004 0.054 5671 Dihedral : 4.976 54.755 5860 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.02 % Allowed : 15.11 % Favored : 83.87 % 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: -0.16 (0.13), residues: 3931 helix: 1.36 (0.20), residues: 715 sheet: -0.14 (0.16), residues: 1074 loop : -0.55 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 77 TYR 0.019 0.001 TYR A 369 PHE 0.020 0.001 PHE A 275 TRP 0.014 0.001 TRP A 104 HIS 0.010 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00302 (32793) covalent geometry : angle 0.59342 (44629) SS BOND : bond 0.00213 ( 48) SS BOND : angle 0.74726 ( 96) hydrogen bonds : bond 0.03839 ( 1134) hydrogen bonds : angle 5.49595 ( 3156) link_BETA1-4 : bond 0.00346 ( 20) link_BETA1-4 : angle 1.19089 ( 60) link_NAG-ASN : bond 0.00155 ( 54) link_NAG-ASN : angle 1.27922 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7723.54 seconds wall clock time: 133 minutes 14.30 seconds (7994.30 seconds total)