Starting phenix.real_space_refine on Fri Mar 6 00:35:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7df3_30660/03_2026/7df3_30660.cif Found real_map, /net/cci-nas-00/data/ceres_data/7df3_30660/03_2026/7df3_30660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7df3_30660/03_2026/7df3_30660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7df3_30660/03_2026/7df3_30660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7df3_30660/03_2026/7df3_30660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7df3_30660/03_2026/7df3_30660.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 120 5.16 5 C 16884 2.51 5 N 4341 2.21 5 O 5250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s 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: 26595 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "B" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "C" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.64, per 1000 atoms: 0.21 Number of scatterers: 26595 At special positions: 0 Unit cell: (145.86, 147.9, 174.42, 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 120 16.00 O 5250 8.00 N 4341 7.00 C 16884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.04 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 A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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 C 840 " - pdb=" SG CYS C 851 " 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=2.03 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG 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-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 61 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 61 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 149 " " NAG C1310 " - " ASN C 61 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 165 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 17 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 17 " " NAG T 1 " - " ASN C1134 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 165 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 17 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.2 seconds 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 51 sheets defined 23.3% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.641A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.570A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 836 through 843 removed outlier: 3.713A pdb=" N ASP A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.503A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.769A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.645A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.740A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 387 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 438 through 443 removed outlier: 3.640A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.569A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.713A pdb=" N ASP B 843 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.502A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.769A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.644A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1031 removed outlier: 3.740A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.640A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.569A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 836 through 843 removed outlier: 3.714A pdb=" N ASP C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.502A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.769A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.645A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 3.740A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 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 48 through 55 removed outlier: 3.679A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.503A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.271A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.654A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (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 325 through 328 removed outlier: 5.260A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.662A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.831A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.169A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.189A 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 807 through 808 removed outlier: 3.917A pdb=" N ARG A 815 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 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 48 through 55 removed outlier: 3.679A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.502A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.271A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 157 removed outlier: 3.654A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (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: 5.260A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.663A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.776A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.168A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 807 through 808 removed outlier: 3.917A pdb=" N ARG B 815 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 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 48 through 55 removed outlier: 3.678A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.503A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.271A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.654A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.261A 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: 3.663A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.168A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 807 through 808 removed outlier: 3.917A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 959 hydrogen bonds defined for protein. 2616 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: 6.56 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8428 1.34 - 1.46: 6524 1.46 - 1.58: 12075 1.58 - 1.70: 3 1.70 - 1.82: 150 Bond restraints: 27180 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" C2 NAG R 1 " ideal model delta sigma weight residual 1.532 1.630 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG Z 1 " pdb=" C2 NAG Z 1 " ideal model delta sigma weight residual 1.532 1.630 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG J 1 " pdb=" C2 NAG J 1 " ideal model delta sigma weight residual 1.532 1.630 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.236 0.098 2.34e-02 1.83e+03 1.75e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.236 0.098 2.34e-02 1.83e+03 1.75e+01 ... (remaining 27175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 36309 2.33 - 4.67: 594 4.67 - 7.00: 57 7.00 - 9.34: 9 9.34 - 11.67: 6 Bond angle restraints: 36975 Sorted by residual: angle pdb=" N ASN C 234 " pdb=" CA ASN C 234 " pdb=" C ASN C 234 " ideal model delta sigma weight residual 109.59 102.06 7.53 1.61e+00 3.86e-01 2.19e+01 angle pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" C ASN A 234 " ideal model delta sigma weight residual 109.59 102.07 7.52 1.61e+00 3.86e-01 2.18e+01 angle pdb=" N ASN B 234 " pdb=" CA ASN B 234 " pdb=" C ASN B 234 " ideal model delta sigma weight residual 109.59 102.07 7.52 1.61e+00 3.86e-01 2.18e+01 angle pdb=" C6 NAG T 2 " pdb=" C5 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 108.73 120.40 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C6 NAG D 2 " pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 108.73 120.40 -11.67 3.00e+00 1.11e-01 1.51e+01 ... (remaining 36970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16710 17.99 - 35.97: 339 35.97 - 53.96: 120 53.96 - 71.94: 27 71.94 - 89.93: 12 Dihedral angle restraints: 17208 sinusoidal: 7710 harmonic: 9498 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 17205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 4352 0.208 - 0.415: 40 0.415 - 0.623: 6 0.623 - 0.830: 0 0.830 - 1.038: 6 Chirality restraints: 4404 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 -2.23 -0.17 2.00e-02 2.50e+03 7.59e+01 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.49e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.42e+01 ... (remaining 4401 not shown) Planarity restraints: 4749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG A1304 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.503 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG C1304 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " 0.337 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B1304 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.178 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " 0.072 2.00e-02 2.50e+03 ... (remaining 4746 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 393 2.63 - 3.20: 24649 3.20 - 3.77: 42776 3.77 - 4.33: 60723 4.33 - 4.90: 97866 Nonbonded interactions: 226407 Sorted by model distance: nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.067 3.040 nonbonded pdb=" O3 NAG M 2 " pdb=" O7 NAG M 2 " model vdw 2.067 3.040 nonbonded pdb=" O3 NAG U 2 " pdb=" O7 NAG U 2 " model vdw 2.067 3.040 nonbonded pdb=" O3 NAG B1301 " pdb=" O7 NAG B1301 " model vdw 2.094 3.040 nonbonded pdb=" O3 NAG C1301 " pdb=" O7 NAG C1301 " model vdw 2.094 3.040 ... (remaining 226402 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' 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' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 25.120 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.004 0.098 27300 Z= 0.219 Angle : 0.863 45.037 37293 Z= 0.396 Chirality : 0.069 1.038 4404 Planarity : 0.016 0.287 4695 Dihedral : 8.697 89.926 10974 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.12), residues: 3234 helix: -2.80 (0.13), residues: 729 sheet: -0.73 (0.18), residues: 570 loop : -1.30 (0.12), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 466 TYR 0.025 0.002 TYR A 508 PHE 0.023 0.002 PHE B 275 TRP 0.028 0.002 TRP A 64 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00445 (27180) covalent geometry : angle 0.69725 (36975) SS BOND : bond 0.00372 ( 42) SS BOND : angle 0.90591 ( 84) hydrogen bonds : bond 0.25871 ( 947) hydrogen bonds : angle 9.82238 ( 2616) link_BETA1-4 : bond 0.00349 ( 24) link_BETA1-4 : angle 2.13018 ( 72) link_NAG-ASN : bond 0.01466 ( 54) link_NAG-ASN : angle 7.62227 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 832 time to evaluate : 0.788 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: A 309 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 772 VAL cc_start: 0.8657 (t) cc_final: 0.8395 (p) REVERT: A 955 ASN cc_start: 0.7620 (m-40) cc_final: 0.7418 (m-40) REVERT: B 88 ASP cc_start: 0.6566 (m-30) cc_final: 0.6326 (m-30) REVERT: B 111 ASP cc_start: 0.5447 (t0) cc_final: 0.5177 (t0) REVERT: B 271 GLN cc_start: 0.8219 (mt0) cc_final: 0.7985 (mt0) REVERT: B 309 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6350 (mp0) REVERT: B 772 VAL cc_start: 0.8848 (t) cc_final: 0.8594 (p) REVERT: B 1141 LEU cc_start: 0.7917 (tp) cc_final: 0.7696 (mt) REVERT: C 309 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6792 (mp0) REVERT: C 1101 HIS cc_start: 0.7172 (m90) cc_final: 0.6941 (m170) REVERT: C 1141 LEU cc_start: 0.7828 (tp) cc_final: 0.7624 (mt) outliers start: 0 outliers final: 3 residues processed: 832 average time/residue: 0.6179 time to fit residues: 601.3076 Evaluate side-chains 415 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 412 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 294 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 185 ASN A 196 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 474 GLN A 487 ASN A 580 GLN A 690 GLN A 762 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 969 ASN A1010 GLN A1119 ASN A1135 ASN B 99 ASN B 115 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 493 GLN B 613 GLN B 641 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 969 ASN B1010 GLN B1119 ASN B1135 ASN C 99 ASN C 115 GLN C 185 ASN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 675 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1083 HIS C1119 ASN C1135 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130273 restraints weight = 33109.545| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.08 r_work: 0.3419 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27300 Z= 0.221 Angle : 0.809 18.299 37293 Z= 0.400 Chirality : 0.053 0.709 4404 Planarity : 0.005 0.055 4695 Dihedral : 7.089 59.641 5145 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.22 % Favored : 96.60 % Rotamer: Outliers : 3.87 % Allowed : 11.44 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 3234 helix: -0.63 (0.17), residues: 738 sheet: -0.49 (0.17), residues: 726 loop : -1.28 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 466 TYR 0.032 0.002 TYR B 200 PHE 0.024 0.003 PHE B 347 TRP 0.025 0.002 TRP C 64 HIS 0.006 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00498 (27180) covalent geometry : angle 0.76196 (36975) SS BOND : bond 0.00470 ( 42) SS BOND : angle 1.81918 ( 84) hydrogen bonds : bond 0.05312 ( 947) hydrogen bonds : angle 6.44891 ( 2616) link_BETA1-4 : bond 0.00562 ( 24) link_BETA1-4 : angle 1.94517 ( 72) link_NAG-ASN : bond 0.00813 ( 54) link_NAG-ASN : angle 3.82264 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 405 time to evaluate : 1.152 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: A 111 ASP cc_start: 0.6590 (t0) cc_final: 0.6334 (t70) REVERT: A 113 LYS cc_start: 0.7844 (mttt) cc_final: 0.6782 (mmpt) REVERT: A 207 HIS cc_start: 0.7138 (t70) cc_final: 0.5313 (m170) REVERT: A 493 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: A 516 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: A 787 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7920 (mm-40) REVERT: A 957 GLN cc_start: 0.8635 (tt0) cc_final: 0.8411 (tt0) REVERT: A 977 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8747 (tp) REVERT: A 988 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7142 (tp30) REVERT: A 1086 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7714 (ptmt) REVERT: B 88 ASP cc_start: 0.7186 (m-30) cc_final: 0.6884 (m-30) REVERT: B 111 ASP cc_start: 0.6336 (t0) cc_final: 0.6075 (t0) REVERT: B 113 LYS cc_start: 0.7590 (mttt) cc_final: 0.6644 (mmpt) REVERT: B 271 GLN cc_start: 0.8639 (mt0) cc_final: 0.8364 (mt0) REVERT: B 309 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7304 (mp0) REVERT: B 326 ILE cc_start: 0.7919 (mm) cc_final: 0.7397 (pt) REVERT: B 378 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8286 (tptp) REVERT: B 487 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7440 (t0) REVERT: B 954 GLN cc_start: 0.8286 (mt0) cc_final: 0.7630 (pt0) REVERT: B 988 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7397 (tp30) REVERT: B 1086 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7881 (ptmt) REVERT: C 111 ASP cc_start: 0.6328 (t0) cc_final: 0.6102 (t0) REVERT: C 113 LYS cc_start: 0.7665 (mttt) cc_final: 0.6847 (mmpt) REVERT: C 309 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7381 (mp0) REVERT: C 408 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.6348 (ptt90) REVERT: C 440 ASN cc_start: 0.7845 (p0) cc_final: 0.7572 (m110) REVERT: C 444 LYS cc_start: 0.6770 (pttt) cc_final: 0.6368 (ptpt) REVERT: C 505 TYR cc_start: 0.7929 (t80) cc_final: 0.7357 (m-80) REVERT: C 572 THR cc_start: 0.8679 (p) cc_final: 0.8221 (t) REVERT: C 646 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7324 (ttp-110) REVERT: C 1086 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7913 (ptmt) outliers start: 110 outliers final: 26 residues processed: 480 average time/residue: 0.6282 time to fit residues: 351.7562 Evaluate side-chains 356 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 209 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 675 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN A1119 ASN B 137 ASN B 146 HIS B 245 HIS B 314 GLN B 487 ASN B 536 ASN B 580 GLN B 675 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 245 HIS C 314 GLN C 394 ASN C 580 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122827 restraints weight = 33003.971| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.05 r_work: 0.3310 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 27300 Z= 0.239 Angle : 0.750 12.397 37293 Z= 0.374 Chirality : 0.050 0.642 4404 Planarity : 0.005 0.044 4695 Dihedral : 6.940 59.024 5139 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.39 % Rotamer: Outliers : 4.01 % Allowed : 12.60 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.13), residues: 3234 helix: 0.05 (0.18), residues: 708 sheet: -0.57 (0.17), residues: 687 loop : -1.13 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 765 TYR 0.026 0.002 TYR B 200 PHE 0.028 0.002 PHE C 906 TRP 0.028 0.003 TRP C 64 HIS 0.006 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00546 (27180) covalent geometry : angle 0.71895 (36975) SS BOND : bond 0.00487 ( 42) SS BOND : angle 1.90114 ( 84) hydrogen bonds : bond 0.05122 ( 947) hydrogen bonds : angle 6.22144 ( 2616) link_BETA1-4 : bond 0.00481 ( 24) link_BETA1-4 : angle 1.92600 ( 72) link_NAG-ASN : bond 0.00622 ( 54) link_NAG-ASN : angle 2.81214 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 343 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6915 (mt) REVERT: A 113 LYS cc_start: 0.7961 (mttt) cc_final: 0.7313 (mtmm) REVERT: A 207 HIS cc_start: 0.7750 (t70) cc_final: 0.5686 (m170) REVERT: A 326 ILE cc_start: 0.7814 (mm) cc_final: 0.7603 (pt) REVERT: A 370 ASN cc_start: 0.6982 (m-40) cc_final: 0.6710 (m-40) REVERT: A 487 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7495 (t0) REVERT: A 516 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6593 (tm-30) REVERT: A 787 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7910 (mm-40) REVERT: A 921 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7810 (tppt) REVERT: A 935 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6538 (mp10) REVERT: A 957 GLN cc_start: 0.8665 (tt0) cc_final: 0.8443 (tt0) REVERT: A 977 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8700 (tp) REVERT: A 988 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7508 (tp30) REVERT: A 1086 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7840 (ptmt) REVERT: B 113 LYS cc_start: 0.7787 (mttt) cc_final: 0.6897 (mmpt) REVERT: B 271 GLN cc_start: 0.8680 (mt0) cc_final: 0.8451 (mt0) REVERT: B 440 ASN cc_start: 0.8124 (p0) cc_final: 0.7821 (m110) REVERT: B 487 ASN cc_start: 0.8305 (m-40) cc_final: 0.7695 (t0) REVERT: B 572 THR cc_start: 0.8626 (p) cc_final: 0.8280 (t) REVERT: B 922 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8545 (tp) REVERT: B 988 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7508 (tp30) REVERT: B 1086 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7890 (ptmt) REVERT: B 1122 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8593 (m) REVERT: C 113 LYS cc_start: 0.7938 (mttt) cc_final: 0.7131 (mmpt) REVERT: C 326 ILE cc_start: 0.7767 (mm) cc_final: 0.7510 (pt) REVERT: C 408 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.6358 (ptt90) REVERT: C 440 ASN cc_start: 0.7936 (p0) cc_final: 0.7626 (m-40) REVERT: C 444 LYS cc_start: 0.7029 (pttt) cc_final: 0.6538 (ptpt) REVERT: C 505 TYR cc_start: 0.8114 (t80) cc_final: 0.7580 (m-80) REVERT: C 569 ILE cc_start: 0.8299 (tp) cc_final: 0.7961 (pp) REVERT: C 572 THR cc_start: 0.8719 (p) cc_final: 0.8355 (t) REVERT: C 646 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7514 (mtm-85) REVERT: C 935 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6651 (mp10) REVERT: C 1019 ARG cc_start: 0.8480 (ttp-110) cc_final: 0.8092 (ttp-110) REVERT: C 1086 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7955 (ptmt) REVERT: C 1113 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8132 (mt0) outliers start: 114 outliers final: 42 residues processed: 423 average time/residue: 0.6535 time to fit residues: 322.1517 Evaluate side-chains 352 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 297 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 239 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 232 optimal weight: 0.0060 chunk 261 optimal weight: 0.4980 chunk 253 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 644 GLN A 675 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN B 137 ASN B 644 GLN B 675 GLN B 901 GLN B 954 GLN B 957 GLN C 394 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123151 restraints weight = 33087.348| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.08 r_work: 0.3336 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27300 Z= 0.148 Angle : 0.653 11.907 37293 Z= 0.329 Chirality : 0.049 0.718 4404 Planarity : 0.004 0.051 4695 Dihedral : 6.716 59.666 5139 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 4.05 % Allowed : 12.85 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3234 helix: 0.42 (0.19), residues: 714 sheet: -0.62 (0.17), residues: 681 loop : -1.07 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 765 TYR 0.025 0.002 TYR B 200 PHE 0.017 0.002 PHE A 643 TRP 0.022 0.002 TRP A 64 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00334 (27180) covalent geometry : angle 0.62405 (36975) SS BOND : bond 0.00498 ( 42) SS BOND : angle 1.78678 ( 84) hydrogen bonds : bond 0.04241 ( 947) hydrogen bonds : angle 6.01545 ( 2616) link_BETA1-4 : bond 0.00518 ( 24) link_BETA1-4 : angle 1.86597 ( 72) link_NAG-ASN : bond 0.00527 ( 54) link_NAG-ASN : angle 2.43448 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 343 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8470 (m-80) cc_final: 0.8254 (m-80) REVERT: A 113 LYS cc_start: 0.7860 (mttt) cc_final: 0.7106 (mmpt) REVERT: A 207 HIS cc_start: 0.7997 (t70) cc_final: 0.5879 (m170) REVERT: A 370 ASN cc_start: 0.7111 (m-40) cc_final: 0.6799 (m-40) REVERT: A 487 ASN cc_start: 0.8261 (m-40) cc_final: 0.7705 (t0) REVERT: A 493 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: A 516 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: A 554 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: A 787 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7891 (mm-40) REVERT: A 957 GLN cc_start: 0.8676 (tt0) cc_final: 0.8448 (tt0) REVERT: A 977 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8667 (tp) REVERT: A 988 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7569 (tp30) REVERT: A 1086 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7800 (ptmt) REVERT: B 113 LYS cc_start: 0.7889 (mttt) cc_final: 0.7021 (mmpt) REVERT: B 378 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8342 (tptp) REVERT: B 440 ASN cc_start: 0.8023 (p0) cc_final: 0.7768 (m-40) REVERT: B 487 ASN cc_start: 0.8270 (m-40) cc_final: 0.7679 (t0) REVERT: B 572 THR cc_start: 0.8680 (p) cc_final: 0.8351 (t) REVERT: B 814 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7044 (mttp) REVERT: B 922 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8524 (tp) REVERT: B 988 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7595 (tp30) REVERT: B 1086 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7855 (ptmt) REVERT: B 1113 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: C 113 LYS cc_start: 0.7932 (mttt) cc_final: 0.7113 (mmpt) REVERT: C 200 TYR cc_start: 0.7467 (m-80) cc_final: 0.7259 (m-80) REVERT: C 408 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.6269 (ptt90) REVERT: C 440 ASN cc_start: 0.7769 (p0) cc_final: 0.7509 (m110) REVERT: C 444 LYS cc_start: 0.6825 (pttt) cc_final: 0.6423 (ptpt) REVERT: C 505 TYR cc_start: 0.7979 (t80) cc_final: 0.7373 (m-80) REVERT: C 516 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: C 572 THR cc_start: 0.8668 (p) cc_final: 0.8357 (t) REVERT: C 646 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7463 (mtm-85) REVERT: C 1019 ARG cc_start: 0.8430 (ttp-110) cc_final: 0.8064 (ttp-110) REVERT: C 1086 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7839 (ptmt) REVERT: C 1113 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8138 (mt0) outliers start: 115 outliers final: 37 residues processed: 425 average time/residue: 0.6452 time to fit residues: 319.0416 Evaluate side-chains 348 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 263 optimal weight: 0.0870 chunk 309 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 295 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 764 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 955 ASN B 30 ASN B 137 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 954 GLN B 957 GLN C 644 GLN C 675 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124634 restraints weight = 32792.283| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.06 r_work: 0.3348 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27300 Z= 0.139 Angle : 0.621 9.881 37293 Z= 0.314 Chirality : 0.047 0.613 4404 Planarity : 0.004 0.059 4695 Dihedral : 6.381 55.763 5139 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.90 % Favored : 95.92 % Rotamer: Outliers : 3.87 % Allowed : 13.80 % Favored : 82.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3234 helix: 0.64 (0.19), residues: 717 sheet: -0.70 (0.17), residues: 690 loop : -0.94 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.021 0.001 TYR B 200 PHE 0.025 0.001 PHE B 643 TRP 0.020 0.002 TRP B 64 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00310 (27180) covalent geometry : angle 0.59316 (36975) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.82133 ( 84) hydrogen bonds : bond 0.04059 ( 947) hydrogen bonds : angle 5.83440 ( 2616) link_BETA1-4 : bond 0.00484 ( 24) link_BETA1-4 : angle 1.85779 ( 72) link_NAG-ASN : bond 0.00366 ( 54) link_NAG-ASN : angle 2.25584 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 336 time to evaluate : 0.997 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 59 PHE cc_start: 0.8420 (m-80) cc_final: 0.8205 (m-80) REVERT: A 113 LYS cc_start: 0.7828 (mttt) cc_final: 0.7065 (mmpt) REVERT: A 200 TYR cc_start: 0.7621 (m-80) cc_final: 0.7291 (m-80) REVERT: A 207 HIS cc_start: 0.7996 (t70) cc_final: 0.5851 (m-70) REVERT: A 370 ASN cc_start: 0.7153 (m-40) cc_final: 0.6826 (m-40) REVERT: A 461 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7260 (pp) REVERT: A 505 TYR cc_start: 0.8330 (m-10) cc_final: 0.7474 (t80) REVERT: A 554 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: A 787 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7850 (mm-40) REVERT: A 957 GLN cc_start: 0.8629 (tt0) cc_final: 0.8339 (tt0) REVERT: A 977 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 988 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7434 (tp30) REVERT: A 1086 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7783 (ptmt) REVERT: B 113 LYS cc_start: 0.7769 (mttt) cc_final: 0.6930 (mmpt) REVERT: B 378 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8340 (tptp) REVERT: B 440 ASN cc_start: 0.8031 (p0) cc_final: 0.7767 (m-40) REVERT: B 487 ASN cc_start: 0.8277 (m-40) cc_final: 0.7718 (t0) REVERT: B 572 THR cc_start: 0.8586 (p) cc_final: 0.8280 (t) REVERT: B 814 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7003 (mttp) REVERT: B 922 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8493 (tp) REVERT: B 973 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8172 (tp) REVERT: B 988 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7429 (tp30) REVERT: B 1086 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7868 (ptmt) REVERT: B 1113 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: C 113 LYS cc_start: 0.7926 (mttt) cc_final: 0.7055 (mmpt) REVERT: C 200 TYR cc_start: 0.7659 (m-80) cc_final: 0.7336 (m-80) REVERT: C 408 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.6238 (ptt90) REVERT: C 440 ASN cc_start: 0.7767 (p0) cc_final: 0.7554 (m-40) REVERT: C 444 LYS cc_start: 0.6695 (pttt) cc_final: 0.6349 (ptpt) REVERT: C 505 TYR cc_start: 0.7874 (t80) cc_final: 0.7370 (m-80) REVERT: C 516 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: C 569 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7684 (pp) REVERT: C 572 THR cc_start: 0.8651 (p) cc_final: 0.8364 (t) REVERT: C 646 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7392 (mtm-85) REVERT: C 1019 ARG cc_start: 0.8457 (ttp-110) cc_final: 0.8058 (ttp-110) REVERT: C 1086 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7768 (ptmt) REVERT: C 1113 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: C 1122 VAL cc_start: 0.8818 (t) cc_final: 0.8609 (m) outliers start: 110 outliers final: 40 residues processed: 412 average time/residue: 0.6652 time to fit residues: 319.3140 Evaluate side-chains 358 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 303 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 255 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 240 optimal weight: 0.0470 chunk 172 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 297 optimal weight: 0.5980 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 675 GLN A 804 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 137 ASN B 675 GLN B 913 GLN B 954 GLN B 957 GLN C 487 ASN C 675 GLN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122242 restraints weight = 33294.336| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.06 r_work: 0.3325 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27300 Z= 0.157 Angle : 0.627 10.372 37293 Z= 0.319 Chirality : 0.047 0.659 4404 Planarity : 0.004 0.055 4695 Dihedral : 6.363 55.511 5139 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.80 % Favored : 96.01 % Rotamer: Outliers : 3.80 % Allowed : 14.33 % Favored : 81.87 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3234 helix: 0.73 (0.19), residues: 723 sheet: -0.64 (0.18), residues: 681 loop : -0.90 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.020 0.002 TYR B 200 PHE 0.024 0.002 PHE B 643 TRP 0.024 0.002 TRP C 64 HIS 0.005 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00360 (27180) covalent geometry : angle 0.60056 (36975) SS BOND : bond 0.00448 ( 42) SS BOND : angle 2.02668 ( 84) hydrogen bonds : bond 0.04087 ( 947) hydrogen bonds : angle 5.80060 ( 2616) link_BETA1-4 : bond 0.00482 ( 24) link_BETA1-4 : angle 1.85970 ( 72) link_NAG-ASN : bond 0.00310 ( 54) link_NAG-ASN : angle 2.15249 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 325 time to evaluate : 1.076 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 59 PHE cc_start: 0.8551 (m-80) cc_final: 0.8316 (m-80) REVERT: A 113 LYS cc_start: 0.7910 (mttt) cc_final: 0.7167 (mmpt) REVERT: A 200 TYR cc_start: 0.7828 (m-80) cc_final: 0.7454 (m-80) REVERT: A 207 HIS cc_start: 0.8038 (t70) cc_final: 0.5879 (m-70) REVERT: A 370 ASN cc_start: 0.7085 (m-40) cc_final: 0.6719 (m-40) REVERT: A 461 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7485 (pp) REVERT: A 487 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7819 (t0) REVERT: A 505 TYR cc_start: 0.8344 (m-10) cc_final: 0.7538 (t80) REVERT: A 787 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7873 (mm-40) REVERT: A 957 GLN cc_start: 0.8637 (tt0) cc_final: 0.8417 (tt0) REVERT: A 977 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8686 (tp) REVERT: A 988 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7484 (tp30) REVERT: B 101 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 113 LYS cc_start: 0.7765 (mttt) cc_final: 0.7020 (mmpt) REVERT: B 378 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8352 (tptp) REVERT: B 408 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.6960 (ppt90) REVERT: B 440 ASN cc_start: 0.8057 (p0) cc_final: 0.7855 (m-40) REVERT: B 487 ASN cc_start: 0.8286 (m-40) cc_final: 0.7743 (t0) REVERT: B 505 TYR cc_start: 0.8038 (t80) cc_final: 0.7829 (t80) REVERT: B 572 THR cc_start: 0.8618 (p) cc_final: 0.8332 (t) REVERT: B 814 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7031 (mttp) REVERT: B 922 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8532 (tp) REVERT: B 973 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8242 (tp) REVERT: B 988 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7540 (tp30) REVERT: B 1086 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7862 (ptmt) REVERT: B 1113 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: C 113 LYS cc_start: 0.8097 (mttt) cc_final: 0.7318 (mmpt) REVERT: C 190 ARG cc_start: 0.8495 (mtt90) cc_final: 0.6590 (mmt-90) REVERT: C 200 TYR cc_start: 0.7962 (m-80) cc_final: 0.7660 (m-80) REVERT: C 408 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.6295 (ptt90) REVERT: C 440 ASN cc_start: 0.7845 (p0) cc_final: 0.7639 (m-40) REVERT: C 444 LYS cc_start: 0.6768 (pttt) cc_final: 0.6432 (ptpt) REVERT: C 505 TYR cc_start: 0.7888 (t80) cc_final: 0.7422 (m-80) REVERT: C 516 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: C 569 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7668 (pp) REVERT: C 572 THR cc_start: 0.8677 (p) cc_final: 0.8408 (t) REVERT: C 646 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7402 (mtm-85) REVERT: C 660 TYR cc_start: 0.8792 (m-10) cc_final: 0.8512 (m-80) REVERT: C 804 GLN cc_start: 0.7848 (mm110) cc_final: 0.7607 (mt0) REVERT: C 1019 ARG cc_start: 0.8409 (ttp-110) cc_final: 0.7995 (ttp-110) REVERT: C 1086 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7797 (ptmt) REVERT: C 1101 HIS cc_start: 0.7600 (m90) cc_final: 0.7173 (m170) outliers start: 108 outliers final: 54 residues processed: 401 average time/residue: 0.6419 time to fit residues: 300.2165 Evaluate side-chains 374 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 305 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 229 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 487 ASN A 675 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 137 ASN B 188 ASN B 580 GLN B 675 GLN B 872 GLN B 954 GLN B 957 GLN C 137 ASN C 173 GLN C 487 ASN C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1119 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120628 restraints weight = 32862.630| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.05 r_work: 0.3279 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 27300 Z= 0.200 Angle : 0.666 10.187 37293 Z= 0.339 Chirality : 0.048 0.638 4404 Planarity : 0.004 0.054 4695 Dihedral : 6.568 53.566 5139 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.61 % Rotamer: Outliers : 3.80 % Allowed : 14.89 % Favored : 81.31 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3234 helix: 0.66 (0.19), residues: 720 sheet: -0.54 (0.18), residues: 609 loop : -0.97 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 273 TYR 0.022 0.002 TYR B 200 PHE 0.023 0.002 PHE B 643 TRP 0.022 0.002 TRP A 64 HIS 0.006 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00462 (27180) covalent geometry : angle 0.64053 (36975) SS BOND : bond 0.00455 ( 42) SS BOND : angle 2.11494 ( 84) hydrogen bonds : bond 0.04338 ( 947) hydrogen bonds : angle 5.85220 ( 2616) link_BETA1-4 : bond 0.00462 ( 24) link_BETA1-4 : angle 1.93253 ( 72) link_NAG-ASN : bond 0.00431 ( 54) link_NAG-ASN : angle 2.14908 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 327 time to evaluate : 1.067 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 113 LYS cc_start: 0.8043 (mttt) cc_final: 0.7834 (mtmm) REVERT: A 370 ASN cc_start: 0.7303 (m-40) cc_final: 0.6962 (m-40) REVERT: A 461 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7840 (pp) REVERT: A 505 TYR cc_start: 0.8382 (m-10) cc_final: 0.7519 (t80) REVERT: A 787 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7963 (mm-40) REVERT: A 935 GLN cc_start: 0.7143 (mt0) cc_final: 0.6838 (mt0) REVERT: A 977 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8698 (tp) REVERT: A 988 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7507 (tp30) REVERT: A 1045 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7771 (ptmm) REVERT: A 1086 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7712 (ptmt) REVERT: B 66 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7597 (m90) REVERT: B 113 LYS cc_start: 0.7941 (mttt) cc_final: 0.7078 (mmpt) REVERT: B 231 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8027 (pp) REVERT: B 408 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.7053 (ppt90) REVERT: B 487 ASN cc_start: 0.8297 (m-40) cc_final: 0.7764 (t0) REVERT: B 505 TYR cc_start: 0.8178 (t80) cc_final: 0.7919 (t80) REVERT: B 572 THR cc_start: 0.8573 (p) cc_final: 0.8300 (t) REVERT: B 814 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6969 (mttp) REVERT: B 988 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7402 (tp30) REVERT: B 1086 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7895 (ptmt) REVERT: B 1113 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: C 113 LYS cc_start: 0.8221 (mttt) cc_final: 0.7349 (mmpt) REVERT: C 408 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.6331 (ptt90) REVERT: C 440 ASN cc_start: 0.8027 (p0) cc_final: 0.7696 (m-40) REVERT: C 444 LYS cc_start: 0.6903 (pttt) cc_final: 0.6541 (ptmt) REVERT: C 461 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7873 (pp) REVERT: C 505 TYR cc_start: 0.8001 (t80) cc_final: 0.7464 (m-80) REVERT: C 569 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7773 (pp) REVERT: C 572 THR cc_start: 0.8635 (p) cc_final: 0.8364 (t) REVERT: C 613 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: C 646 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7345 (ttp-110) REVERT: C 935 GLN cc_start: 0.6984 (mt0) cc_final: 0.6734 (mt0) REVERT: C 1019 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.8276 (ttp-110) REVERT: C 1101 HIS cc_start: 0.7639 (m90) cc_final: 0.7187 (m170) REVERT: C 1113 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8189 (mt0) outliers start: 108 outliers final: 57 residues processed: 402 average time/residue: 0.6710 time to fit residues: 313.7238 Evaluate side-chains 366 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 293 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 230 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 280 optimal weight: 0.1980 chunk 279 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 291 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 394 ASN A 487 ASN A 675 GLN A 856 ASN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 137 ASN B 394 ASN B 675 GLN B 872 GLN B 954 GLN B 957 GLN B 965 GLN C 394 ASN C 487 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121064 restraints weight = 32944.028| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.05 r_work: 0.3284 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27300 Z= 0.175 Angle : 0.706 17.134 37293 Z= 0.355 Chirality : 0.049 0.745 4404 Planarity : 0.004 0.069 4695 Dihedral : 6.599 59.866 5139 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.17 % Favored : 95.64 % Rotamer: Outliers : 3.94 % Allowed : 15.28 % Favored : 80.78 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.75 (0.14), residues: 3234 helix: 0.76 (0.19), residues: 723 sheet: -0.63 (0.18), residues: 597 loop : -0.94 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1091 TYR 0.016 0.002 TYR C 28 PHE 0.023 0.002 PHE B 643 TRP 0.023 0.002 TRP C 64 HIS 0.006 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00402 (27180) covalent geometry : angle 0.66518 (36975) SS BOND : bond 0.00473 ( 42) SS BOND : angle 3.70244 ( 84) hydrogen bonds : bond 0.04160 ( 947) hydrogen bonds : angle 5.82257 ( 2616) link_BETA1-4 : bond 0.00493 ( 24) link_BETA1-4 : angle 1.93462 ( 72) link_NAG-ASN : bond 0.00568 ( 54) link_NAG-ASN : angle 2.24192 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 308 time to evaluate : 1.067 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: A 153 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.5520 (pmt) REVERT: A 461 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7879 (pp) REVERT: A 505 TYR cc_start: 0.8366 (m-10) cc_final: 0.7534 (t80) REVERT: A 516 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: A 787 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7974 (mm-40) REVERT: A 977 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8668 (tp) REVERT: A 988 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7516 (tp30) REVERT: A 1086 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7747 (ptmt) REVERT: B 53 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7138 (t0) REVERT: B 66 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7584 (m90) REVERT: B 113 LYS cc_start: 0.8018 (mttt) cc_final: 0.7135 (mmpt) REVERT: B 231 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7979 (pp) REVERT: B 408 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7003 (ppt90) REVERT: B 487 ASN cc_start: 0.8237 (m-40) cc_final: 0.7703 (t0) REVERT: B 505 TYR cc_start: 0.8123 (t80) cc_final: 0.7910 (t80) REVERT: B 524 VAL cc_start: 0.8608 (t) cc_final: 0.8335 (t) REVERT: B 572 THR cc_start: 0.8601 (p) cc_final: 0.8325 (t) REVERT: B 973 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8295 (tp) REVERT: B 988 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7421 (tp30) REVERT: B 1113 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: C 111 ASP cc_start: 0.6461 (t0) cc_final: 0.6192 (t0) REVERT: C 408 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.6294 (ptt90) REVERT: C 440 ASN cc_start: 0.8012 (p0) cc_final: 0.7733 (m-40) REVERT: C 444 LYS cc_start: 0.6890 (pttt) cc_final: 0.6532 (ptmt) REVERT: C 461 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7822 (pp) REVERT: C 505 TYR cc_start: 0.7994 (t80) cc_final: 0.7459 (m-80) REVERT: C 516 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: C 569 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7709 (pp) REVERT: C 572 THR cc_start: 0.8606 (p) cc_final: 0.8340 (t) REVERT: C 646 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7299 (ttp-110) REVERT: C 1101 HIS cc_start: 0.7626 (m90) cc_final: 0.7173 (m170) REVERT: C 1113 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8160 (mt0) outliers start: 112 outliers final: 59 residues processed: 383 average time/residue: 0.6698 time to fit residues: 298.7091 Evaluate side-chains 357 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 282 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 76 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 394 ASN A 487 ASN A 675 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 137 ASN B 675 GLN B 954 GLN B 957 GLN C 487 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118983 restraints weight = 33071.945| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.11 r_work: 0.3282 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27300 Z= 0.166 Angle : 0.697 14.864 37293 Z= 0.350 Chirality : 0.049 0.896 4404 Planarity : 0.004 0.064 4695 Dihedral : 6.639 58.693 5139 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.11 % Favored : 95.70 % Rotamer: Outliers : 3.27 % Allowed : 16.02 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.74 (0.14), residues: 3234 helix: 0.71 (0.19), residues: 723 sheet: -0.62 (0.18), residues: 606 loop : -0.91 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.014 0.002 TYR B 28 PHE 0.023 0.002 PHE B 643 TRP 0.022 0.002 TRP C 64 HIS 0.008 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00384 (27180) covalent geometry : angle 0.65451 (36975) SS BOND : bond 0.00450 ( 42) SS BOND : angle 3.69931 ( 84) hydrogen bonds : bond 0.04115 ( 947) hydrogen bonds : angle 5.80160 ( 2616) link_BETA1-4 : bond 0.00461 ( 24) link_BETA1-4 : angle 1.90472 ( 72) link_NAG-ASN : bond 0.00682 ( 54) link_NAG-ASN : angle 2.31631 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 299 time to evaluate : 0.980 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 153 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.5426 (pmt) REVERT: A 461 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7919 (pp) REVERT: A 505 TYR cc_start: 0.8370 (m-10) cc_final: 0.7511 (t80) REVERT: A 787 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7942 (mm-40) REVERT: A 977 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8668 (tp) REVERT: A 988 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7472 (tp30) REVERT: A 1086 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7750 (ptmt) REVERT: B 66 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7568 (m90) REVERT: B 113 LYS cc_start: 0.8081 (mttt) cc_final: 0.7162 (mmpt) REVERT: B 231 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7960 (pp) REVERT: B 408 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.6955 (ppt90) REVERT: B 487 ASN cc_start: 0.8249 (m-40) cc_final: 0.7685 (t0) REVERT: B 524 VAL cc_start: 0.8584 (t) cc_final: 0.8328 (t) REVERT: B 572 THR cc_start: 0.8576 (p) cc_final: 0.8285 (t) REVERT: B 973 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8270 (tp) REVERT: B 988 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7396 (tp30) REVERT: B 1086 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7920 (ptmt) REVERT: B 1113 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: C 111 ASP cc_start: 0.6531 (t0) cc_final: 0.6278 (t0) REVERT: C 390 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7004 (pp) REVERT: C 408 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.6282 (ptt90) REVERT: C 440 ASN cc_start: 0.8017 (p0) cc_final: 0.7692 (m-40) REVERT: C 444 LYS cc_start: 0.6835 (pttt) cc_final: 0.6493 (ptmt) REVERT: C 461 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7864 (pp) REVERT: C 505 TYR cc_start: 0.7998 (t80) cc_final: 0.7429 (m-80) REVERT: C 516 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: C 569 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7705 (pp) REVERT: C 572 THR cc_start: 0.8594 (p) cc_final: 0.8332 (t) REVERT: C 646 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7302 (ttp-110) REVERT: C 1101 HIS cc_start: 0.7618 (m90) cc_final: 0.7151 (m170) REVERT: C 1113 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8134 (mt0) outliers start: 93 outliers final: 58 residues processed: 361 average time/residue: 0.6498 time to fit residues: 273.6541 Evaluate side-chains 361 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 286 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 278 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 283 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 487 ASN A 675 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN A1071 GLN B 370 ASN B 675 GLN B 872 GLN B 954 GLN B 957 GLN B 978 ASN C 487 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115916 restraints weight = 32913.106| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.10 r_work: 0.3208 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27300 Z= 0.235 Angle : 0.747 14.931 37293 Z= 0.377 Chirality : 0.049 0.586 4404 Planarity : 0.004 0.065 4695 Dihedral : 6.880 59.319 5139 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.27 % Favored : 95.58 % Rotamer: Outliers : 3.06 % Allowed : 16.37 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.82 (0.14), residues: 3234 helix: 0.58 (0.19), residues: 723 sheet: -0.51 (0.18), residues: 588 loop : -1.00 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1091 TYR 0.017 0.002 TYR B 495 PHE 0.022 0.002 PHE B 643 TRP 0.021 0.002 TRP C 64 HIS 0.008 0.002 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00546 (27180) covalent geometry : angle 0.70689 (36975) SS BOND : bond 0.00530 ( 42) SS BOND : angle 3.60682 ( 84) hydrogen bonds : bond 0.04478 ( 947) hydrogen bonds : angle 5.91965 ( 2616) link_BETA1-4 : bond 0.00433 ( 24) link_BETA1-4 : angle 1.97961 ( 72) link_NAG-ASN : bond 0.00727 ( 54) link_NAG-ASN : angle 2.41155 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 297 time to evaluate : 1.103 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 505 TYR cc_start: 0.8433 (m-10) cc_final: 0.7546 (t80) REVERT: A 516 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: A 787 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7997 (mm-40) REVERT: A 804 GLN cc_start: 0.8237 (mt0) cc_final: 0.7561 (mm-40) REVERT: A 935 GLN cc_start: 0.6873 (mm-40) cc_final: 0.6649 (mm-40) REVERT: A 977 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8715 (tp) REVERT: A 988 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7554 (tp30) REVERT: B 113 LYS cc_start: 0.8235 (mttt) cc_final: 0.7261 (mmpt) REVERT: B 118 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8897 (tp) REVERT: B 231 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8121 (pp) REVERT: B 408 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.6843 (ptt90) REVERT: B 487 ASN cc_start: 0.8211 (m-40) cc_final: 0.7650 (t0) REVERT: B 505 TYR cc_start: 0.8239 (t80) cc_final: 0.8009 (t80) REVERT: B 524 VAL cc_start: 0.8672 (t) cc_final: 0.8410 (t) REVERT: B 572 THR cc_start: 0.8554 (p) cc_final: 0.8267 (t) REVERT: B 973 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8401 (tp) REVERT: B 988 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7515 (tp30) REVERT: B 1113 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: C 111 ASP cc_start: 0.6750 (t0) cc_final: 0.6469 (t0) REVERT: C 408 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.6353 (ptt90) REVERT: C 440 ASN cc_start: 0.8195 (p0) cc_final: 0.7806 (m-40) REVERT: C 444 LYS cc_start: 0.6993 (pttt) cc_final: 0.6624 (ptmt) REVERT: C 461 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8011 (pp) REVERT: C 487 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8022 (t0) REVERT: C 516 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: C 569 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7820 (pp) REVERT: C 572 THR cc_start: 0.8588 (p) cc_final: 0.8334 (t) REVERT: C 646 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7342 (ttp-110) REVERT: C 1113 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8194 (mt0) outliers start: 87 outliers final: 54 residues processed: 355 average time/residue: 0.6427 time to fit residues: 265.4874 Evaluate side-chains 349 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 198 optimal weight: 0.2980 chunk 111 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 243 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 296 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 487 ASN A 675 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN B 460 ASN B 675 GLN B 690 GLN B 872 GLN B 957 GLN C 183 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1071 GLN C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118328 restraints weight = 32698.212| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.10 r_work: 0.3242 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27300 Z= 0.165 Angle : 0.696 13.306 37293 Z= 0.351 Chirality : 0.047 0.609 4404 Planarity : 0.004 0.064 4695 Dihedral : 6.660 59.442 5139 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Rotamer: Outliers : 2.99 % Allowed : 16.61 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.82 (0.14), residues: 3234 helix: 0.57 (0.19), residues: 741 sheet: -0.56 (0.18), residues: 588 loop : -0.99 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1091 TYR 0.016 0.002 TYR C 505 PHE 0.024 0.002 PHE B 643 TRP 0.025 0.002 TRP A 152 HIS 0.007 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00380 (27180) covalent geometry : angle 0.66002 (36975) SS BOND : bond 0.00424 ( 42) SS BOND : angle 3.33321 ( 84) hydrogen bonds : bond 0.04145 ( 947) hydrogen bonds : angle 5.87144 ( 2616) link_BETA1-4 : bond 0.00462 ( 24) link_BETA1-4 : angle 1.92310 ( 72) link_NAG-ASN : bond 0.00534 ( 54) link_NAG-ASN : angle 2.18444 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9930.94 seconds wall clock time: 169 minutes 54.46 seconds (10194.46 seconds total)