Starting phenix.real_space_refine on Sat Feb 7 18:04:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l15_62734/02_2026/9l15_62734.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l15_62734/02_2026/9l15_62734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l15_62734/02_2026/9l15_62734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l15_62734/02_2026/9l15_62734.map" model { file = "/net/cci-nas-00/data/ceres_data/9l15_62734/02_2026/9l15_62734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l15_62734/02_2026/9l15_62734.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 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 141 5.16 5 C 21899 2.51 5 N 5657 2.21 5 O 6812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 221 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34509 Number of models: 1 Model: "" Number of chains: 33 Chain: "H" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 1 Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1620 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "I" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 1 Chain: "M" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1620 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "J" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 1 Chain: "N" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1620 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "C" Number of atoms: 7979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7979 Classifications: {'peptide': 1019} Link IDs: {'PTRANS': 57, 'TRANS': 961} Chain breaks: 7 Chain: "B" Number of atoms: 7998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7998 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 58, 'TRANS': 963} Chain breaks: 7 Chain: "A" Number of atoms: 7980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7980 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 58, 'TRANS': 961} Chain breaks: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "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: "b" 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: "c" 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: "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: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 9.18, per 1000 atoms: 0.27 Number of scatterers: 34509 At special positions: 0 Unit cell: (137.004, 206.904, 219.02, 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 141 16.00 O 6812 8.00 N 5657 7.00 C 21899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 155 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 155 " - pdb=" SG CYS M 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 155 " - pdb=" SG CYS N 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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 A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 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 b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 343 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 125 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C1074 " " NAG D 1 " - " ASN C 61 " " NAG E 1 " - " ASN C 234 " " NAG F 1 " - " ASN C 331 " " NAG G 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN B 61 " " NAG V 1 " - " ASN B 122 " " NAG W 1 " - " ASN B 165 " " NAG X 1 " - " ASN B 331 " " NAG Y 1 " - " ASN A 122 " " NAG Z 1 " - " ASN A 165 " " NAG a 1 " - " ASN A 717 " " NAG b 1 " - " ASN A 801 " " NAG c 1 " - " ASN A1098 " " NAG d 1 " - " ASN A1134 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8132 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 80 sheets defined 19.9% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'H' and resid 68 through 72 removed outlier: 3.584A pdb=" N LYS H 72 " --> pdb=" O PRO H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.655A pdb=" N THR H 99 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 205 removed outlier: 4.354A pdb=" N GLY H 205 " --> pdb=" O SER H 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 202 through 205' Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 142 through 148 Processing helix chain 'L' and resid 202 through 208 Processing helix chain 'I' and resid 68 through 72 removed outlier: 3.896A pdb=" N LYS I 72 " --> pdb=" O PRO I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'I' and resid 169 through 173 Processing helix chain 'I' and resid 202 through 205 removed outlier: 4.148A pdb=" N GLY I 205 " --> pdb=" O SER I 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 202 through 205' Processing helix chain 'M' and resid 29 through 37 removed outlier: 3.577A pdb=" N ASN M 37 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'M' and resid 142 through 147 Processing helix chain 'M' and resid 202 through 208 Processing helix chain 'J' and resid 69 through 72 removed outlier: 3.540A pdb=" N LYS J 72 " --> pdb=" O PRO J 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 69 through 72' Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.633A pdb=" N THR J 99 " --> pdb=" O ALA J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 173 No H-bonds generated for 'chain 'J' and resid 171 through 173' Processing helix chain 'J' and resid 202 through 205 removed outlier: 4.199A pdb=" N GLY J 205 " --> pdb=" O SER J 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 202 through 205' Processing helix chain 'N' and resid 29 through 37 removed outlier: 3.833A pdb=" N ASN N 37 " --> pdb=" O ILE N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 99 Processing helix chain 'N' and resid 142 through 147 Processing helix chain 'N' and resid 202 through 208 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.983A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.644A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.554A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.917A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.982A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.580A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 7.138A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.699A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.538A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.615A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.916A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 754 removed outlier: 3.956A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.536A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.654A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.157A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.545A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.829A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.119A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.705A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 removed outlier: 3.552A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' 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 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.615A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.809A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.232A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.517A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.844A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.536A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 12 through 13 removed outlier: 3.669A pdb=" N ALA H 100 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP H 39 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR H 55 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 135 through 139 removed outlier: 3.818A pdb=" N SER H 195 " --> pdb=" O CYS H 155 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 139 removed outlier: 3.818A pdb=" N SER H 195 " --> pdb=" O CYS H 155 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL H 184 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 168 through 169 removed outlier: 3.596A pdb=" N LYS H 224 " --> pdb=" O CYS H 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.250A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR L 102 " --> pdb=" O THR L 122 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP L 41 " --> pdb=" O VAL L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.250A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR L 102 " --> pdb=" O THR L 122 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL L 115 " --> pdb=" O ASP L 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 137 through 139 removed outlier: 3.832A pdb=" N SER L 200 " --> pdb=" O GLY L 179 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY L 179 " --> pdb=" O SER L 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 137 through 139 Processing sheet with id=AB2, first strand: chain 'L' and resid 166 through 170 removed outlier: 3.555A pdb=" N VAL L 223 " --> pdb=" O VAL L 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'I' and resid 51 through 56 removed outlier: 6.606A pdb=" N TRP I 41 " --> pdb=" O ILE I 53 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR I 55 " --> pdb=" O TRP I 39 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP I 39 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR I 38 " --> pdb=" O VAL I 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 135 through 139 removed outlier: 4.221A pdb=" N GLY I 154 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU I 153 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP I 159 " --> pdb=" O TYR I 191 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 135 through 139 removed outlier: 4.221A pdb=" N GLY I 154 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU I 153 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP I 159 " --> pdb=" O TYR I 191 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AB8, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.485A pdb=" N TRP M 41 " --> pdb=" O VAL M 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 9 through 13 Processing sheet with id=AC1, first strand: chain 'M' and resid 137 through 139 removed outlier: 6.126A pdb=" N TYR M 193 " --> pdb=" O ASP M 159 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR M 198 " --> pdb=" O GLU M 181 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER M 200 " --> pdb=" O GLY M 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY M 179 " --> pdb=" O SER M 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 137 through 139 removed outlier: 6.126A pdb=" N TYR M 193 " --> pdb=" O ASP M 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 167 through 170 removed outlier: 3.636A pdb=" N VAL M 223 " --> pdb=" O VAL M 216 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.544A pdb=" N PHE J 87 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN J 86 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 65 through 67 removed outlier: 6.507A pdb=" N TRP J 41 " --> pdb=" O ILE J 53 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR J 55 " --> pdb=" O TRP J 39 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP J 39 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA J 100 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 135 through 138 removed outlier: 5.950A pdb=" N TYR J 191 " --> pdb=" O ASP J 159 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 135 through 138 removed outlier: 5.950A pdb=" N TYR J 191 " --> pdb=" O ASP J 159 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL J 184 " --> pdb=" O SER J 192 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 165 through 169 removed outlier: 3.641A pdb=" N LYS J 224 " --> pdb=" O CYS J 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL J 213 " --> pdb=" O VAL J 222 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL J 222 " --> pdb=" O VAL J 213 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.516A pdb=" N ASP N 81 " --> pdb=" O SER N 86 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER N 77 " --> pdb=" O THR N 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.432A pdb=" N VAL N 11 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP N 41 " --> pdb=" O VAL N 53 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.432A pdb=" N VAL N 11 " --> pdb=" O THR N 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 135 through 139 Processing sheet with id=AD4, first strand: chain 'N' and resid 135 through 139 Processing sheet with id=AD5, first strand: chain 'N' and resid 166 through 170 Processing sheet with id=AD6, first strand: chain 'C' and resid 21 through 29 removed outlier: 3.930A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.724A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.189A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 166 through 170 removed outlier: 6.739A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.294A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.605A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C 435 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.535A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.638A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.234A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 702 through 704 removed outlier: 7.150A pdb=" N ASN C 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.771A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.771A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.398A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 787 through 789 removed outlier: 5.896A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.254A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 23 through 28 removed outlier: 3.641A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.188A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.556A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 141 through 142 removed outlier: 4.104A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 312 through 319 removed outlier: 5.651A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.509A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AG3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AG4, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.625A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.044A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.236A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS A 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN B 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.503A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.503A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.361A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.663A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.624A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AH4, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.851A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AH6, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.666A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.545A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.317A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.657A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AI2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AI3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AI4, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.990A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.522A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.522A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.384A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'A' and resid 1120 through 1122 1368 hydrogen bonds defined for protein. 3615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.90 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10940 1.34 - 1.46: 8668 1.46 - 1.58: 15533 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 35315 Sorted by residual: bond pdb=" C PHE J 161 " pdb=" N PRO J 162 " ideal model delta sigma weight residual 1.332 1.358 -0.026 1.12e-02 7.97e+03 5.23e+00 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 NAG Y 2 " pdb=" O5 NAG Y 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.87e+00 ... (remaining 35310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 47075 1.85 - 3.70: 1007 3.70 - 5.55: 46 5.55 - 7.40: 5 7.40 - 9.25: 1 Bond angle restraints: 48134 Sorted by residual: angle pdb=" N ASN B 137 " pdb=" CA ASN B 137 " pdb=" C ASN B 137 " ideal model delta sigma weight residual 113.18 108.44 4.74 1.33e+00 5.65e-01 1.27e+01 angle pdb=" N ILE I 30 " pdb=" CA ILE I 30 " pdb=" C ILE I 30 " ideal model delta sigma weight residual 106.21 109.50 -3.29 1.07e+00 8.73e-01 9.46e+00 angle pdb=" N ILE H 30 " pdb=" CA ILE H 30 " pdb=" C ILE H 30 " ideal model delta sigma weight residual 106.21 109.50 -3.29 1.07e+00 8.73e-01 9.43e+00 angle pdb=" C ALA N 171 " pdb=" N ASP N 172 " pdb=" CA ASP N 172 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.69e+00 angle pdb=" N VAL I 126 " pdb=" CA VAL I 126 " pdb=" C VAL I 126 " ideal model delta sigma weight residual 111.91 109.46 2.45 8.90e-01 1.26e+00 7.55e+00 ... (remaining 48129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 21341 21.71 - 43.43: 478 43.43 - 65.14: 59 65.14 - 86.86: 14 86.86 - 108.57: 4 Dihedral angle restraints: 21896 sinusoidal: 9240 harmonic: 12656 Sorted by residual: dihedral pdb=" CA HIS A 519 " pdb=" C HIS A 519 " pdb=" N ALA A 520 " pdb=" CA ALA A 520 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -125.71 39.71 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA PHE B 135 " pdb=" C PHE B 135 " pdb=" N CYS B 136 " pdb=" CA CYS B 136 " ideal model delta harmonic sigma weight residual 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 21893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4893 0.061 - 0.122: 749 0.122 - 0.184: 9 0.184 - 0.245: 0 0.245 - 0.306: 4 Chirality restraints: 5655 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5652 not shown) Planarity restraints: 6167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO B 986 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 174 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO N 175 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO N 175 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO N 175 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 898 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO C 899 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " 0.017 5.00e-02 4.00e+02 ... (remaining 6164 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5733 2.77 - 3.30: 32569 3.30 - 3.83: 56389 3.83 - 4.37: 64903 4.37 - 4.90: 115061 Nonbonded interactions: 274655 Sorted by model distance: nonbonded pdb=" O SER C 937 " pdb=" OG1 THR C 941 " model vdw 2.232 3.040 nonbonded pdb=" ND2 ASN A1125 " pdb=" OD1 ASP A1127 " model vdw 2.234 3.120 nonbonded pdb=" OD1 ASN I 34 " pdb=" OH TYR I 37 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 514 " pdb=" OE1 GLU B 516 " model vdw 2.240 3.040 nonbonded pdb=" O PHE H 115 " pdb=" OG1 THR L 52 " model vdw 2.241 3.040 ... (remaining 274650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 143 or resid 153 through 262 or resid 265 throu \ gh 620 or resid 640 through 1306)) selection = (chain 'B' and (resid 14 through 67 or resid 81 through 262 or resid 265 through \ 620 or resid 640 through 1306)) selection = (chain 'C' and (resid 14 through 67 or resid 81 through 143 or resid 153 through \ 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'K' 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' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.370 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.740 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.003 0.037 35431 Z= 0.158 Angle : 0.590 9.245 48428 Z= 0.335 Chirality : 0.042 0.306 5655 Planarity : 0.003 0.033 6127 Dihedral : 8.840 108.573 13602 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.37 % Allowed : 5.22 % Favored : 92.41 % 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: -1.98 (0.11), residues: 4282 helix: 0.05 (0.19), residues: 677 sheet: -0.59 (0.14), residues: 1158 loop : -2.17 (0.11), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.007 0.001 TYR A 91 PHE 0.009 0.001 PHE A 106 TRP 0.005 0.001 TRP A 886 HIS 0.002 0.000 HIS J 57 Details of bonding type rmsd covalent geometry : bond 0.00280 (35315) covalent geometry : angle 0.58437 (48134) SS BOND : bond 0.00122 ( 54) SS BOND : angle 0.57116 ( 108) hydrogen bonds : bond 0.23112 ( 1246) hydrogen bonds : angle 8.94328 ( 3615) link_BETA1-4 : bond 0.00426 ( 22) link_BETA1-4 : angle 1.01959 ( 66) link_NAG-ASN : bond 0.00263 ( 40) link_NAG-ASN : angle 1.61972 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1072 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 PRO cc_start: 0.7259 (Cg_exo) cc_final: 0.6842 (Cg_endo) REVERT: H 112 LEU cc_start: 0.7769 (mp) cc_final: 0.7195 (mp) REVERT: H 126 VAL cc_start: 0.6498 (OUTLIER) cc_final: 0.5631 (t) REVERT: H 200 PRO cc_start: 0.7954 (Cg_exo) cc_final: 0.7741 (Cg_endo) REVERT: H 216 LYS cc_start: 0.7905 (tppt) cc_final: 0.7392 (tppt) REVERT: I 44 GLN cc_start: 0.7479 (tt0) cc_final: 0.7139 (tt0) REVERT: I 53 ILE cc_start: 0.8271 (mt) cc_final: 0.7870 (mp) REVERT: I 55 TYR cc_start: 0.7087 (p90) cc_final: 0.6447 (p90) REVERT: I 95 THR cc_start: 0.6394 (p) cc_final: 0.6125 (p) REVERT: I 209 TYR cc_start: 0.2943 (OUTLIER) cc_final: 0.0911 (p90) REVERT: M 114 ASN cc_start: 0.6983 (t0) cc_final: 0.6762 (t0) REVERT: J 29 SER cc_start: 0.7398 (t) cc_final: 0.7121 (t) REVERT: J 39 TRP cc_start: 0.6230 (m100) cc_final: 0.5950 (m100) REVERT: C 101 ILE cc_start: 0.8570 (mt) cc_final: 0.8366 (tt) REVERT: C 205 SER cc_start: 0.8044 (p) cc_final: 0.7754 (t) REVERT: C 206 LYS cc_start: 0.8517 (tptt) cc_final: 0.8173 (tptm) REVERT: C 233 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7657 (pt) REVERT: C 273 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7389 (mmt90) REVERT: C 290 ASP cc_start: 0.7525 (t0) cc_final: 0.7257 (t0) REVERT: C 423 TYR cc_start: 0.6205 (t80) cc_final: 0.5894 (t80) REVERT: C 549 THR cc_start: 0.7877 (m) cc_final: 0.7597 (m) REVERT: C 776 LYS cc_start: 0.7890 (ttpp) cc_final: 0.7637 (ttpp) REVERT: C 808 ASP cc_start: 0.7975 (p0) cc_final: 0.7599 (p0) REVERT: C 936 ASP cc_start: 0.7173 (m-30) cc_final: 0.6900 (m-30) REVERT: C 950 ASP cc_start: 0.7008 (m-30) cc_final: 0.6649 (m-30) REVERT: C 963 VAL cc_start: 0.8742 (p) cc_final: 0.8481 (t) REVERT: C 1017 GLU cc_start: 0.6761 (tp30) cc_final: 0.6335 (tp30) REVERT: C 1103 PHE cc_start: 0.8139 (m-80) cc_final: 0.7794 (m-80) REVERT: C 1138 TYR cc_start: 0.7007 (t80) cc_final: 0.6761 (t80) REVERT: B 49 HIS cc_start: 0.6743 (t-90) cc_final: 0.6520 (t70) REVERT: B 106 PHE cc_start: 0.7163 (m-80) cc_final: 0.6962 (m-80) REVERT: B 266 TYR cc_start: 0.8128 (m-80) cc_final: 0.7665 (m-80) REVERT: B 418 ILE cc_start: 0.8385 (mm) cc_final: 0.7951 (mm) REVERT: B 421 TYR cc_start: 0.6506 (m-80) cc_final: 0.5904 (m-80) REVERT: B 428 ASP cc_start: 0.6108 (p0) cc_final: 0.5555 (p0) REVERT: B 591 SER cc_start: 0.6705 (t) cc_final: 0.6385 (p) REVERT: B 644 GLN cc_start: 0.8269 (tp40) cc_final: 0.8068 (tp40) REVERT: B 663 ASP cc_start: 0.7394 (t0) cc_final: 0.7147 (t0) REVERT: B 707 TYR cc_start: 0.8114 (t80) cc_final: 0.7820 (t80) REVERT: B 790 LYS cc_start: 0.7520 (tppp) cc_final: 0.7299 (tppp) REVERT: B 997 ILE cc_start: 0.8800 (mt) cc_final: 0.8576 (mt) REVERT: B 1031 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7290 (mt-10) REVERT: B 1108 ASN cc_start: 0.7645 (m-40) cc_final: 0.7371 (m-40) REVERT: A 19 ILE cc_start: 0.3217 (pt) cc_final: 0.2626 (pt) REVERT: A 54 LEU cc_start: 0.7847 (mt) cc_final: 0.7364 (mt) REVERT: A 129 LYS cc_start: 0.8215 (ptmt) cc_final: 0.7978 (ptmt) REVERT: A 290 ASP cc_start: 0.7452 (t0) cc_final: 0.7249 (t0) REVERT: A 304 LYS cc_start: 0.7564 (mmmm) cc_final: 0.7351 (mmmm) REVERT: A 357 ARG cc_start: 0.7869 (ttt90) cc_final: 0.7490 (ttt90) REVERT: A 374 PHE cc_start: 0.8180 (m-80) cc_final: 0.7965 (m-80) REVERT: A 378 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7605 (mmmt) REVERT: A 402 ILE cc_start: 0.7906 (pt) cc_final: 0.7600 (pp) REVERT: A 452 LEU cc_start: 0.8055 (mp) cc_final: 0.7850 (mp) REVERT: A 514 SER cc_start: 0.8284 (t) cc_final: 0.7873 (m) REVERT: A 556 ASN cc_start: 0.8121 (p0) cc_final: 0.7890 (p0) REVERT: A 567 ARG cc_start: 0.7785 (mtt-85) cc_final: 0.7559 (mtt-85) REVERT: A 751 ASN cc_start: 0.7749 (m-40) cc_final: 0.7526 (m-40) REVERT: A 776 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7833 (ttpp) REVERT: A 977 LEU cc_start: 0.7680 (mp) cc_final: 0.7440 (mt) REVERT: A 1103 PHE cc_start: 0.7950 (m-80) cc_final: 0.7527 (m-80) REVERT: A 1144 GLU cc_start: 0.6803 (mm-30) cc_final: 0.5978 (mm-30) outliers start: 90 outliers final: 26 residues processed: 1136 average time/residue: 0.5869 time to fit residues: 824.2230 Evaluate side-chains 854 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 825 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 160 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN I 3 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN I 212 ASN M 188 GLN J 3 GLN J 57 HIS J 92 ASN N 43 GLN N 188 GLN ** N 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 49 HIS C 360 ASN C 422 ASN C 439 ASN C 505 HIS C 777 ASN C 895 GLN C 955 ASN C1005 GLN C1011 GLN C1083 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 675 GLN B 703 ASN B 895 GLN B 957 GLN B 978 ASN B1048 HIS A 196 ASN A 207 HIS A 218 GLN A 245 HIS A 271 GLN A 317 ASN A 321 GLN A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 540 ASN A 603 ASN A 606 ASN A 644 GLN A 657 ASN A 675 GLN A 690 GLN A 762 GLN A 777 ASN A 856 ASN A 907 ASN A 913 GLN A 914 ASN A 965 GLN A1011 GLN A1142 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.177037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141141 restraints weight = 64721.598| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.76 r_work: 0.3661 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 35431 Z= 0.234 Angle : 0.699 10.767 48428 Z= 0.357 Chirality : 0.050 0.346 5655 Planarity : 0.005 0.072 6127 Dihedral : 6.601 65.147 6017 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.83 % Allowed : 14.29 % Favored : 80.88 % 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: -1.31 (0.12), residues: 4282 helix: 0.73 (0.20), residues: 691 sheet: -0.30 (0.15), residues: 1158 loop : -1.69 (0.11), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 403 TYR 0.034 0.002 TYR B 423 PHE 0.026 0.003 PHE C 565 TRP 0.032 0.002 TRP I 52 HIS 0.013 0.001 HIS L 218 Details of bonding type rmsd covalent geometry : bond 0.00531 (35315) covalent geometry : angle 0.68627 (48134) SS BOND : bond 0.00544 ( 54) SS BOND : angle 1.71518 ( 108) hydrogen bonds : bond 0.04986 ( 1246) hydrogen bonds : angle 6.38052 ( 3615) link_BETA1-4 : bond 0.00438 ( 22) link_BETA1-4 : angle 1.30484 ( 66) link_NAG-ASN : bond 0.00428 ( 40) link_NAG-ASN : angle 2.19601 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 901 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 PRO cc_start: 0.7840 (Cg_exo) cc_final: 0.7429 (Cg_endo) REVERT: H 40 SER cc_start: 0.7181 (t) cc_final: 0.6980 (m) REVERT: H 65 THR cc_start: 0.8156 (p) cc_final: 0.7926 (t) REVERT: H 126 VAL cc_start: 0.7190 (OUTLIER) cc_final: 0.6360 (t) REVERT: H 169 TRP cc_start: 0.6868 (m100) cc_final: 0.5457 (m100) REVERT: H 199 VAL cc_start: 0.7913 (m) cc_final: 0.7672 (p) REVERT: H 200 PRO cc_start: 0.8238 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: H 216 LYS cc_start: 0.8355 (tppt) cc_final: 0.7857 (tppt) REVERT: L 42 TYR cc_start: 0.5909 (m-80) cc_final: 0.5311 (m-80) REVERT: L 45 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.7599 (tpp-160) REVERT: L 107 TYR cc_start: 0.6798 (m-80) cc_final: 0.6553 (m-80) REVERT: L 150 LYS cc_start: 0.7486 (tmtm) cc_final: 0.7223 (tmtm) REVERT: I 39 TRP cc_start: 0.7884 (m100) cc_final: 0.7681 (m100) REVERT: I 43 ARG cc_start: 0.7540 (ptt180) cc_final: 0.7123 (ptt-90) REVERT: I 44 GLN cc_start: 0.8231 (tt0) cc_final: 0.7782 (tt0) REVERT: I 55 TYR cc_start: 0.7910 (p90) cc_final: 0.7591 (p90) REVERT: I 75 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7475 (mtm110) REVERT: I 95 THR cc_start: 0.7197 (p) cc_final: 0.6976 (p) REVERT: I 209 TYR cc_start: 0.3182 (OUTLIER) cc_final: 0.1142 (p90) REVERT: M 88 SER cc_start: 0.6756 (t) cc_final: 0.6498 (m) REVERT: M 114 ASN cc_start: 0.7342 (t0) cc_final: 0.6929 (t0) REVERT: J 39 TRP cc_start: 0.6867 (m100) cc_final: 0.6389 (m100) REVERT: N 2 PHE cc_start: 0.7917 (t80) cc_final: 0.7124 (t80) REVERT: N 17 MET cc_start: 0.4522 (pp-130) cc_final: 0.3692 (pp-130) REVERT: N 69 SER cc_start: 0.7982 (t) cc_final: 0.7676 (p) REVERT: C 28 TYR cc_start: 0.7650 (m-80) cc_final: 0.7243 (m-80) REVERT: C 29 THR cc_start: 0.7801 (m) cc_final: 0.7573 (m) REVERT: C 105 ILE cc_start: 0.8421 (mt) cc_final: 0.8118 (mm) REVERT: C 108 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7814 (m) REVERT: C 115 GLN cc_start: 0.6762 (mt0) cc_final: 0.6302 (tp-100) REVERT: C 168 PHE cc_start: 0.7932 (t80) cc_final: 0.7614 (t80) REVERT: C 173 GLN cc_start: 0.8318 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 205 SER cc_start: 0.8587 (p) cc_final: 0.8331 (t) REVERT: C 206 LYS cc_start: 0.8471 (tptt) cc_final: 0.8196 (tptt) REVERT: C 286 THR cc_start: 0.8687 (p) cc_final: 0.8462 (m) REVERT: C 335 LEU cc_start: 0.8559 (mt) cc_final: 0.8347 (mm) REVERT: C 423 TYR cc_start: 0.6756 (t80) cc_final: 0.6144 (t80) REVERT: C 578 ASP cc_start: 0.7134 (t0) cc_final: 0.6798 (p0) REVERT: C 654 GLU cc_start: 0.7801 (pt0) cc_final: 0.7564 (pt0) REVERT: C 675 GLN cc_start: 0.7238 (pp30) cc_final: 0.6753 (pp30) REVERT: C 773 GLU cc_start: 0.8003 (tt0) cc_final: 0.7725 (tt0) REVERT: C 882 ILE cc_start: 0.8522 (pt) cc_final: 0.8243 (mt) REVERT: C 900 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8106 (mtt) REVERT: C 936 ASP cc_start: 0.7593 (m-30) cc_final: 0.7265 (m-30) REVERT: C 950 ASP cc_start: 0.7675 (m-30) cc_final: 0.7230 (m-30) REVERT: C 1017 GLU cc_start: 0.7538 (tp30) cc_final: 0.7296 (tp30) REVERT: C 1103 PHE cc_start: 0.8522 (m-80) cc_final: 0.8221 (m-80) REVERT: C 1127 ASP cc_start: 0.7833 (p0) cc_final: 0.7516 (p0) REVERT: C 1138 TYR cc_start: 0.7872 (t80) cc_final: 0.7464 (t80) REVERT: B 164 ASN cc_start: 0.6303 (OUTLIER) cc_final: 0.5590 (t0) REVERT: B 345 THR cc_start: 0.8598 (p) cc_final: 0.8356 (m) REVERT: B 421 TYR cc_start: 0.7453 (m-80) cc_final: 0.6410 (m-80) REVERT: B 430 THR cc_start: 0.8194 (m) cc_final: 0.7714 (p) REVERT: B 456 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7628 (tm) REVERT: B 457 ARG cc_start: 0.7615 (ttp-170) cc_final: 0.7376 (ttp80) REVERT: B 591 SER cc_start: 0.7052 (t) cc_final: 0.6650 (m) REVERT: B 619 GLU cc_start: 0.7633 (pt0) cc_final: 0.7254 (pt0) REVERT: B 661 GLU cc_start: 0.7583 (mp0) cc_final: 0.7344 (mp0) REVERT: B 673 SER cc_start: 0.8701 (t) cc_final: 0.8330 (p) REVERT: B 705 VAL cc_start: 0.8445 (t) cc_final: 0.8167 (m) REVERT: B 710 ASN cc_start: 0.8073 (p0) cc_final: 0.7768 (p0) REVERT: B 776 LYS cc_start: 0.8390 (ttmt) cc_final: 0.8102 (tttp) REVERT: B 790 LYS cc_start: 0.7975 (tppp) cc_final: 0.7625 (tppp) REVERT: B 997 ILE cc_start: 0.8931 (mt) cc_final: 0.8726 (mt) REVERT: B 1084 ASP cc_start: 0.7206 (t0) cc_final: 0.6923 (t0) REVERT: B 1138 TYR cc_start: 0.7903 (t80) cc_final: 0.7304 (t80) REVERT: A 19 ILE cc_start: 0.3699 (pt) cc_final: 0.1950 (pp) REVERT: A 241 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7053 (pp) REVERT: A 305 SER cc_start: 0.8701 (t) cc_final: 0.8362 (p) REVERT: A 332 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 357 ARG cc_start: 0.8562 (ttt90) cc_final: 0.8227 (ttt180) REVERT: A 360 ASN cc_start: 0.8164 (m-40) cc_final: 0.7633 (m-40) REVERT: A 378 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7806 (mmmt) REVERT: A 402 ILE cc_start: 0.8255 (pt) cc_final: 0.7946 (pt) REVERT: A 438 SER cc_start: 0.8025 (p) cc_final: 0.7674 (p) REVERT: A 452 LEU cc_start: 0.8049 (mp) cc_final: 0.7649 (mp) REVERT: A 514 SER cc_start: 0.8597 (t) cc_final: 0.8158 (m) REVERT: A 529 LYS cc_start: 0.8773 (mptt) cc_final: 0.8360 (mmmm) REVERT: A 567 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7762 (mtt-85) REVERT: A 610 VAL cc_start: 0.8656 (m) cc_final: 0.8434 (t) REVERT: A 661 GLU cc_start: 0.7547 (mp0) cc_final: 0.7342 (mp0) REVERT: A 691 SER cc_start: 0.8634 (t) cc_final: 0.8433 (p) REVERT: A 725 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: A 747 THR cc_start: 0.8246 (m) cc_final: 0.7867 (t) REVERT: A 748 GLU cc_start: 0.8174 (pm20) cc_final: 0.7755 (mp0) REVERT: A 751 ASN cc_start: 0.8107 (m-40) cc_final: 0.7680 (m-40) REVERT: A 819 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7015 (mt-10) REVERT: A 964 LYS cc_start: 0.8637 (mtpm) cc_final: 0.8435 (mttm) REVERT: A 1031 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 1092 GLU cc_start: 0.7513 (tp30) cc_final: 0.7250 (tp30) REVERT: A 1103 PHE cc_start: 0.8455 (m-80) cc_final: 0.7776 (m-80) REVERT: A 1144 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6644 (mm-30) outliers start: 183 outliers final: 78 residues processed: 999 average time/residue: 0.5707 time to fit residues: 704.4479 Evaluate side-chains 890 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 802 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 160 TYR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1111 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 170 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 303 optimal weight: 0.8980 chunk 403 optimal weight: 1.9990 chunk 398 optimal weight: 0.6980 chunk 368 optimal weight: 5.9990 chunk 280 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 343 optimal weight: 0.7980 chunk 13 optimal weight: 20.0000 chunk 351 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN L 66 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 218 GLN C 532 ASN C 675 GLN C 755 GLN C 777 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 540 ASN A 563 GLN A 606 ASN A 657 ASN A 856 ASN A 919 ASN A 957 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.178323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142560 restraints weight = 65058.658| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.80 r_work: 0.3692 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35431 Z= 0.139 Angle : 0.636 13.175 48428 Z= 0.322 Chirality : 0.047 0.274 5655 Planarity : 0.004 0.070 6127 Dihedral : 6.126 97.814 5999 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.11 % Allowed : 17.17 % Favored : 78.72 % 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: -1.02 (0.12), residues: 4282 helix: 1.17 (0.20), residues: 685 sheet: -0.23 (0.15), residues: 1163 loop : -1.51 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 355 TYR 0.028 0.001 TYR B 423 PHE 0.034 0.002 PHE A 106 TRP 0.024 0.002 TRP I 52 HIS 0.010 0.001 HIS L 218 Details of bonding type rmsd covalent geometry : bond 0.00307 (35315) covalent geometry : angle 0.62384 (48134) SS BOND : bond 0.00382 ( 54) SS BOND : angle 1.52075 ( 108) hydrogen bonds : bond 0.04170 ( 1246) hydrogen bonds : angle 5.90856 ( 3615) link_BETA1-4 : bond 0.00420 ( 22) link_BETA1-4 : angle 1.22937 ( 66) link_NAG-ASN : bond 0.00329 ( 40) link_NAG-ASN : angle 2.10260 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 817 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 THR cc_start: 0.8134 (p) cc_final: 0.7895 (t) REVERT: H 81 ASP cc_start: 0.7884 (t0) cc_final: 0.7444 (t0) REVERT: H 126 VAL cc_start: 0.6827 (OUTLIER) cc_final: 0.5979 (t) REVERT: H 216 LYS cc_start: 0.8155 (tppt) cc_final: 0.7653 (tppt) REVERT: L 17 MET cc_start: 0.6089 (ptt) cc_final: 0.5824 (ppp) REVERT: L 45 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7781 (tpp-160) REVERT: L 135 SER cc_start: 0.7507 (t) cc_final: 0.6927 (m) REVERT: L 223 VAL cc_start: 0.7517 (t) cc_final: 0.7296 (m) REVERT: I 38 TYR cc_start: 0.6082 (m-10) cc_final: 0.5790 (m-10) REVERT: I 44 GLN cc_start: 0.7928 (tt0) cc_final: 0.7553 (tt0) REVERT: I 51 GLU cc_start: 0.7575 (tt0) cc_final: 0.7233 (tt0) REVERT: I 52 TRP cc_start: 0.7406 (t60) cc_final: 0.6854 (t60) REVERT: I 209 TYR cc_start: 0.3188 (OUTLIER) cc_final: 0.0986 (p90) REVERT: M 24 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7958 (p) REVERT: M 88 SER cc_start: 0.6671 (OUTLIER) cc_final: 0.6395 (m) REVERT: M 114 ASN cc_start: 0.7201 (t0) cc_final: 0.6629 (t0) REVERT: J 39 TRP cc_start: 0.6678 (m100) cc_final: 0.6368 (m100) REVERT: C 28 TYR cc_start: 0.7553 (m-80) cc_final: 0.7201 (m-80) REVERT: C 41 LYS cc_start: 0.8232 (mmmt) cc_final: 0.8026 (mmmt) REVERT: C 47 VAL cc_start: 0.8763 (m) cc_final: 0.8546 (t) REVERT: C 105 ILE cc_start: 0.8546 (mt) cc_final: 0.8275 (mm) REVERT: C 108 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7842 (m) REVERT: C 115 GLN cc_start: 0.6880 (mt0) cc_final: 0.6421 (tp-100) REVERT: C 173 GLN cc_start: 0.8262 (tm-30) cc_final: 0.8041 (tm-30) REVERT: C 191 GLU cc_start: 0.7622 (pt0) cc_final: 0.7199 (mt-10) REVERT: C 205 SER cc_start: 0.8575 (p) cc_final: 0.8333 (t) REVERT: C 213 GLU cc_start: 0.4190 (OUTLIER) cc_final: 0.3807 (tp30) REVERT: C 328 ARG cc_start: 0.7904 (mmm160) cc_final: 0.7683 (mmm-85) REVERT: C 335 LEU cc_start: 0.8510 (mt) cc_final: 0.8298 (mm) REVERT: C 353 TRP cc_start: 0.7187 (p90) cc_final: 0.6702 (p-90) REVERT: C 423 TYR cc_start: 0.6431 (t80) cc_final: 0.5922 (t80) REVERT: C 578 ASP cc_start: 0.6972 (t0) cc_final: 0.6739 (p0) REVERT: C 675 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6778 (pp30) REVERT: C 693 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8432 (pt) REVERT: C 740 MET cc_start: 0.8544 (tpp) cc_final: 0.8128 (ttp) REVERT: C 773 GLU cc_start: 0.7885 (tt0) cc_final: 0.7590 (tt0) REVERT: C 882 ILE cc_start: 0.8479 (pt) cc_final: 0.8266 (mt) REVERT: C 900 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8081 (mtt) REVERT: C 936 ASP cc_start: 0.7592 (m-30) cc_final: 0.7338 (m-30) REVERT: C 950 ASP cc_start: 0.7783 (m-30) cc_final: 0.7323 (m-30) REVERT: C 957 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7169 (tp-100) REVERT: C 1017 GLU cc_start: 0.7639 (tp30) cc_final: 0.7348 (tp30) REVERT: C 1103 PHE cc_start: 0.8579 (m-80) cc_final: 0.8241 (m-80) REVERT: C 1138 TYR cc_start: 0.7867 (t80) cc_final: 0.7460 (t80) REVERT: C 1139 ASP cc_start: 0.7836 (t0) cc_final: 0.7379 (t70) REVERT: B 171 VAL cc_start: 0.8432 (p) cc_final: 0.8211 (t) REVERT: B 345 THR cc_start: 0.8544 (p) cc_final: 0.8253 (m) REVERT: B 421 TYR cc_start: 0.7158 (m-80) cc_final: 0.6273 (m-80) REVERT: B 430 THR cc_start: 0.8058 (m) cc_final: 0.7651 (p) REVERT: B 456 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7472 (tm) REVERT: B 503 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (m) REVERT: B 528 LYS cc_start: 0.7769 (ptpp) cc_final: 0.7329 (ptmt) REVERT: B 591 SER cc_start: 0.6848 (t) cc_final: 0.6579 (m) REVERT: B 619 GLU cc_start: 0.7444 (pt0) cc_final: 0.7087 (pt0) REVERT: B 661 GLU cc_start: 0.7623 (mp0) cc_final: 0.7420 (mp0) REVERT: B 673 SER cc_start: 0.8759 (t) cc_final: 0.8448 (p) REVERT: B 705 VAL cc_start: 0.8444 (t) cc_final: 0.8170 (m) REVERT: B 710 ASN cc_start: 0.8008 (p0) cc_final: 0.7701 (p0) REVERT: B 776 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8177 (tttp) REVERT: B 790 LYS cc_start: 0.7938 (tppp) cc_final: 0.7601 (tppp) REVERT: B 895 GLN cc_start: 0.8423 (pt0) cc_final: 0.8066 (pt0) REVERT: B 997 ILE cc_start: 0.8938 (mt) cc_final: 0.8720 (mt) REVERT: B 1005 GLN cc_start: 0.7841 (mm110) cc_final: 0.7534 (mp10) REVERT: B 1138 TYR cc_start: 0.7826 (t80) cc_final: 0.7236 (t80) REVERT: A 19 ILE cc_start: 0.3827 (pt) cc_final: 0.1933 (OUTLIER) REVERT: A 21 ARG cc_start: 0.5743 (ptm-80) cc_final: 0.5327 (ppt170) REVERT: A 100 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8526 (mp) REVERT: A 153 MET cc_start: 0.6814 (mmt) cc_final: 0.6578 (mmp) REVERT: A 190 ARG cc_start: 0.5377 (ptm160) cc_final: 0.5162 (ptm160) REVERT: A 242 LEU cc_start: 0.7859 (mm) cc_final: 0.7298 (tm) REVERT: A 244 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6067 (pt) REVERT: A 305 SER cc_start: 0.8645 (t) cc_final: 0.8305 (p) REVERT: A 332 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 339 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.7230 (p90) REVERT: A 340 GLU cc_start: 0.7932 (mp0) cc_final: 0.7690 (mm-30) REVERT: A 357 ARG cc_start: 0.8525 (ttt90) cc_final: 0.8258 (ttt180) REVERT: A 360 ASN cc_start: 0.8099 (m-40) cc_final: 0.7889 (m-40) REVERT: A 378 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7796 (mmmt) REVERT: A 402 ILE cc_start: 0.8286 (pt) cc_final: 0.7887 (tp) REVERT: A 506 GLN cc_start: 0.8029 (mt0) cc_final: 0.7579 (mt0) REVERT: A 514 SER cc_start: 0.8591 (t) cc_final: 0.8188 (m) REVERT: A 529 LYS cc_start: 0.8856 (mptt) cc_final: 0.8425 (mmmm) REVERT: A 567 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7761 (mtt-85) REVERT: A 586 ASP cc_start: 0.7647 (m-30) cc_final: 0.7391 (m-30) REVERT: A 610 VAL cc_start: 0.8664 (m) cc_final: 0.8447 (t) REVERT: A 691 SER cc_start: 0.8654 (t) cc_final: 0.8450 (p) REVERT: A 747 THR cc_start: 0.8295 (m) cc_final: 0.7923 (t) REVERT: A 751 ASN cc_start: 0.8043 (m-40) cc_final: 0.7596 (m-40) REVERT: A 773 GLU cc_start: 0.7747 (tt0) cc_final: 0.7324 (tp30) REVERT: A 918 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7738 (mt-10) REVERT: A 949 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7864 (mm-40) REVERT: A 950 ASP cc_start: 0.7481 (m-30) cc_final: 0.7145 (p0) REVERT: A 964 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8471 (mttm) REVERT: A 990 GLU cc_start: 0.7610 (tt0) cc_final: 0.7297 (tm-30) REVERT: A 1055 SER cc_start: 0.8579 (t) cc_final: 0.8233 (p) REVERT: A 1092 GLU cc_start: 0.7562 (tp30) cc_final: 0.7190 (tp30) REVERT: A 1103 PHE cc_start: 0.8464 (m-80) cc_final: 0.7875 (m-80) REVERT: A 1111 GLU cc_start: 0.7768 (tp30) cc_final: 0.7544 (mt-10) outliers start: 156 outliers final: 73 residues processed: 897 average time/residue: 0.5752 time to fit residues: 635.5448 Evaluate side-chains 878 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 790 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 973 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 231 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 398 optimal weight: 0.4980 chunk 214 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 215 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 540 ASN C 580 GLN C 675 GLN C 777 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 804 GLN B 935 GLN B 955 ASN A 115 GLN A 196 ASN A 207 HIS A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 606 ASN A 657 ASN A 856 ASN A 919 ASN A 957 GLN A1106 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.174662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.138475 restraints weight = 63831.064| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.78 r_work: 0.3636 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35431 Z= 0.241 Angle : 0.691 12.592 48428 Z= 0.350 Chirality : 0.049 0.343 5655 Planarity : 0.005 0.079 6127 Dihedral : 5.995 59.076 5989 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.96 % Allowed : 17.27 % Favored : 77.77 % 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: -1.01 (0.12), residues: 4282 helix: 0.97 (0.20), residues: 685 sheet: -0.22 (0.15), residues: 1184 loop : -1.43 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 509 TYR 0.023 0.002 TYR C 674 PHE 0.027 0.002 PHE B 374 TRP 0.037 0.002 TRP A 64 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00546 (35315) covalent geometry : angle 0.67656 (48134) SS BOND : bond 0.00495 ( 54) SS BOND : angle 1.71054 ( 108) hydrogen bonds : bond 0.04524 ( 1246) hydrogen bonds : angle 5.91753 ( 3615) link_BETA1-4 : bond 0.00334 ( 22) link_BETA1-4 : angle 1.37546 ( 66) link_NAG-ASN : bond 0.00457 ( 40) link_NAG-ASN : angle 2.29328 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 828 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 LEU cc_start: 0.8195 (mt) cc_final: 0.7959 (mt) REVERT: H 65 THR cc_start: 0.8162 (p) cc_final: 0.7941 (t) REVERT: H 126 VAL cc_start: 0.6945 (OUTLIER) cc_final: 0.6034 (t) REVERT: H 216 LYS cc_start: 0.8331 (tppt) cc_final: 0.7852 (tppt) REVERT: L 17 MET cc_start: 0.6447 (ptt) cc_final: 0.6086 (ppp) REVERT: I 43 ARG cc_start: 0.7409 (ptt180) cc_final: 0.6976 (ptt-90) REVERT: I 44 GLN cc_start: 0.7951 (tt0) cc_final: 0.7593 (tt0) REVERT: I 52 TRP cc_start: 0.7418 (t60) cc_final: 0.7042 (t60) REVERT: I 67 TYR cc_start: 0.7759 (m-80) cc_final: 0.7445 (m-80) REVERT: I 75 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7172 (mtm110) REVERT: I 82 THR cc_start: 0.8504 (p) cc_final: 0.8055 (t) REVERT: I 117 TYR cc_start: 0.7892 (m-80) cc_final: 0.7625 (m-80) REVERT: I 125 THR cc_start: 0.6436 (m) cc_final: 0.6068 (p) REVERT: I 209 TYR cc_start: 0.3153 (OUTLIER) cc_final: 0.1108 (p90) REVERT: M 24 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8033 (p) REVERT: M 88 SER cc_start: 0.6977 (OUTLIER) cc_final: 0.6721 (m) REVERT: M 106 SER cc_start: 0.7474 (t) cc_final: 0.7074 (p) REVERT: M 114 ASN cc_start: 0.7322 (t0) cc_final: 0.6775 (t0) REVERT: J 39 TRP cc_start: 0.6777 (m100) cc_final: 0.6498 (m100) REVERT: C 32 PHE cc_start: 0.8238 (m-80) cc_final: 0.8013 (m-80) REVERT: C 108 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7902 (m) REVERT: C 115 GLN cc_start: 0.7160 (mt0) cc_final: 0.6777 (tp40) REVERT: C 173 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7913 (tm-30) REVERT: C 196 ASN cc_start: 0.8576 (t0) cc_final: 0.8360 (t0) REVERT: C 213 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.4264 (tp30) REVERT: C 218 GLN cc_start: 0.8138 (tp40) cc_final: 0.7911 (tp40) REVERT: C 335 LEU cc_start: 0.8622 (mt) cc_final: 0.8399 (mm) REVERT: C 423 TYR cc_start: 0.6566 (t80) cc_final: 0.6076 (t80) REVERT: C 528 LYS cc_start: 0.7270 (mmmm) cc_final: 0.7028 (mmmm) REVERT: C 539 VAL cc_start: 0.8283 (p) cc_final: 0.8046 (m) REVERT: C 740 MET cc_start: 0.8540 (tpp) cc_final: 0.8195 (ttp) REVERT: C 773 GLU cc_start: 0.7914 (tt0) cc_final: 0.7714 (tt0) REVERT: C 779 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: C 900 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8085 (mtp) REVERT: C 950 ASP cc_start: 0.7841 (m-30) cc_final: 0.7325 (m-30) REVERT: C 957 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7274 (tm-30) REVERT: C 995 ARG cc_start: 0.8215 (mtm-85) cc_final: 0.7972 (mtt180) REVERT: C 1017 GLU cc_start: 0.7735 (tp30) cc_final: 0.7428 (tp30) REVERT: C 1138 TYR cc_start: 0.7856 (t80) cc_final: 0.7439 (t80) REVERT: C 1139 ASP cc_start: 0.7929 (t0) cc_final: 0.7374 (t70) REVERT: B 153 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7961 (mpm) REVERT: B 216 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6865 (mp) REVERT: B 236 THR cc_start: 0.8277 (p) cc_final: 0.8033 (m) REVERT: B 345 THR cc_start: 0.8538 (p) cc_final: 0.8282 (m) REVERT: B 351 TYR cc_start: 0.7504 (p90) cc_final: 0.5453 (p90) REVERT: B 421 TYR cc_start: 0.7375 (m-80) cc_final: 0.7086 (m-80) REVERT: B 430 THR cc_start: 0.8120 (m) cc_final: 0.7711 (p) REVERT: B 452 LEU cc_start: 0.8150 (mm) cc_final: 0.6617 (mm) REVERT: B 456 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7448 (pp) REVERT: B 457 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7409 (ttp80) REVERT: B 503 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8304 (m) REVERT: B 591 SER cc_start: 0.7214 (t) cc_final: 0.6800 (m) REVERT: B 619 GLU cc_start: 0.7549 (pt0) cc_final: 0.7165 (pt0) REVERT: B 673 SER cc_start: 0.8753 (t) cc_final: 0.8472 (p) REVERT: B 705 VAL cc_start: 0.8470 (t) cc_final: 0.8235 (m) REVERT: B 731 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8439 (ptm) REVERT: B 776 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8241 (tttp) REVERT: B 804 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8201 (mm-40) REVERT: B 895 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: B 935 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6826 (mt0) REVERT: B 950 ASP cc_start: 0.7779 (m-30) cc_final: 0.7167 (t0) REVERT: B 1003 SER cc_start: 0.8505 (t) cc_final: 0.8068 (m) REVERT: B 1138 TYR cc_start: 0.7875 (t80) cc_final: 0.7330 (t80) REVERT: A 19 ILE cc_start: 0.3955 (OUTLIER) cc_final: 0.2332 (tt) REVERT: A 46 SER cc_start: 0.8466 (m) cc_final: 0.8231 (p) REVERT: A 63 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7154 (t) REVERT: A 100 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8319 (mp) REVERT: A 102 ARG cc_start: 0.7432 (mmm-85) cc_final: 0.7183 (mmt90) REVERT: A 242 LEU cc_start: 0.7936 (mm) cc_final: 0.7433 (tm) REVERT: A 278 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8199 (ttmt) REVERT: A 305 SER cc_start: 0.8574 (t) cc_final: 0.8230 (p) REVERT: A 318 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8427 (t80) REVERT: A 332 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8042 (tt) REVERT: A 378 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7765 (mmmt) REVERT: A 394 ASN cc_start: 0.7852 (m110) cc_final: 0.7502 (m-40) REVERT: A 402 ILE cc_start: 0.8341 (pt) cc_final: 0.7987 (tp) REVERT: A 444 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7718 (mptt) REVERT: A 452 LEU cc_start: 0.8106 (mp) cc_final: 0.7800 (mp) REVERT: A 514 SER cc_start: 0.8592 (t) cc_final: 0.8191 (m) REVERT: A 529 LYS cc_start: 0.8865 (mptt) cc_final: 0.8446 (mmmm) REVERT: A 546 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7812 (pp) REVERT: A 586 ASP cc_start: 0.7710 (m-30) cc_final: 0.7429 (m-30) REVERT: A 691 SER cc_start: 0.8720 (t) cc_final: 0.8440 (p) REVERT: A 747 THR cc_start: 0.8408 (m) cc_final: 0.7979 (t) REVERT: A 748 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: A 751 ASN cc_start: 0.8112 (m-40) cc_final: 0.7619 (m-40) REVERT: A 918 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7839 (mt-10) REVERT: A 949 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8113 (mm-40) REVERT: A 950 ASP cc_start: 0.7666 (m-30) cc_final: 0.7292 (p0) REVERT: A 964 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8470 (mtmm) REVERT: A 990 GLU cc_start: 0.7590 (tt0) cc_final: 0.7276 (tm-30) REVERT: A 995 ARG cc_start: 0.7946 (ptp-110) cc_final: 0.7649 (ptp-110) REVERT: A 1055 SER cc_start: 0.8579 (t) cc_final: 0.8294 (p) REVERT: A 1092 GLU cc_start: 0.7467 (tp30) cc_final: 0.7091 (tp30) outliers start: 188 outliers final: 88 residues processed: 924 average time/residue: 0.6065 time to fit residues: 690.1274 Evaluate side-chains 904 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 792 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 111 ARG Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 106 optimal weight: 30.0000 chunk 345 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 chunk 304 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN C 30 ASN C 87 ASN C 245 HIS C 540 ASN C 675 GLN C 777 ASN C 955 ASN C 965 GLN B 52 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 777 ASN B 804 GLN B 935 GLN B1048 HIS A 207 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 606 ASN A 657 ASN A 856 ASN A 914 ASN A 957 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.168962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132622 restraints weight = 64083.191| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.77 r_work: 0.3607 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 35431 Z= 0.341 Angle : 0.767 13.779 48428 Z= 0.392 Chirality : 0.053 0.394 5655 Planarity : 0.005 0.089 6127 Dihedral : 6.213 59.496 5984 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.59 % Allowed : 18.12 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.17 (0.12), residues: 4282 helix: 0.65 (0.19), residues: 688 sheet: -0.21 (0.15), residues: 1152 loop : -1.52 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 328 TYR 0.026 0.002 TYR A 508 PHE 0.033 0.003 PHE A 541 TRP 0.043 0.003 TRP A 64 HIS 0.011 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00771 (35315) covalent geometry : angle 0.74893 (48134) SS BOND : bond 0.00728 ( 54) SS BOND : angle 2.09115 ( 108) hydrogen bonds : bond 0.04945 ( 1246) hydrogen bonds : angle 6.00748 ( 3615) link_BETA1-4 : bond 0.00315 ( 22) link_BETA1-4 : angle 1.40266 ( 66) link_NAG-ASN : bond 0.00632 ( 40) link_NAG-ASN : angle 2.73145 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 828 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 LEU cc_start: 0.8157 (mt) cc_final: 0.7933 (mt) REVERT: H 25 VAL cc_start: 0.8340 (t) cc_final: 0.8086 (m) REVERT: H 31 ARG cc_start: 0.7465 (mtm180) cc_final: 0.7092 (mtm180) REVERT: H 55 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.7050 (p90) REVERT: H 65 THR cc_start: 0.8177 (p) cc_final: 0.7959 (t) REVERT: H 126 VAL cc_start: 0.6835 (OUTLIER) cc_final: 0.6359 (p) REVERT: H 216 LYS cc_start: 0.8243 (tppt) cc_final: 0.7783 (tppt) REVERT: L 17 MET cc_start: 0.6294 (ptt) cc_final: 0.6081 (ppp) REVERT: L 38 TYR cc_start: 0.6193 (m-80) cc_final: 0.5442 (m-10) REVERT: L 45 ARG cc_start: 0.8339 (tpp-160) cc_final: 0.7671 (tpp-160) REVERT: L 150 LYS cc_start: 0.7415 (tmtm) cc_final: 0.7178 (tmtm) REVERT: I 38 TYR cc_start: 0.6545 (m-10) cc_final: 0.6236 (m-10) REVERT: I 43 ARG cc_start: 0.7523 (ptt180) cc_final: 0.7198 (ptt-90) REVERT: I 44 GLN cc_start: 0.8005 (tt0) cc_final: 0.7663 (tt0) REVERT: I 52 TRP cc_start: 0.7525 (t60) cc_final: 0.7262 (t60) REVERT: I 67 TYR cc_start: 0.7773 (m-80) cc_final: 0.7472 (m-80) REVERT: I 75 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7274 (mtm110) REVERT: I 82 THR cc_start: 0.8443 (p) cc_final: 0.8067 (t) REVERT: I 117 TYR cc_start: 0.7921 (m-80) cc_final: 0.7145 (m-80) REVERT: I 125 THR cc_start: 0.6509 (m) cc_final: 0.6135 (p) REVERT: I 209 TYR cc_start: 0.3314 (OUTLIER) cc_final: 0.1374 (p90) REVERT: M 88 SER cc_start: 0.7074 (OUTLIER) cc_final: 0.6746 (m) REVERT: M 106 SER cc_start: 0.7689 (t) cc_final: 0.7284 (p) REVERT: M 114 ASN cc_start: 0.7331 (t0) cc_final: 0.6813 (t0) REVERT: J 39 TRP cc_start: 0.6820 (m100) cc_final: 0.6553 (m100) REVERT: J 68 ASN cc_start: 0.7747 (p0) cc_final: 0.5842 (m-40) REVERT: C 84 LEU cc_start: 0.8103 (mt) cc_final: 0.7853 (mm) REVERT: C 108 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7933 (m) REVERT: C 115 GLN cc_start: 0.7187 (mt0) cc_final: 0.6881 (tp40) REVERT: C 129 LYS cc_start: 0.7543 (mttt) cc_final: 0.7104 (mttm) REVERT: C 196 ASN cc_start: 0.8600 (t0) cc_final: 0.8398 (t0) REVERT: C 388 ASN cc_start: 0.7722 (p0) cc_final: 0.7356 (t0) REVERT: C 423 TYR cc_start: 0.6704 (t80) cc_final: 0.6293 (t80) REVERT: C 539 VAL cc_start: 0.8320 (p) cc_final: 0.8047 (m) REVERT: C 599 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8343 (p) REVERT: C 740 MET cc_start: 0.8442 (tpp) cc_final: 0.8094 (ttp) REVERT: C 779 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: C 950 ASP cc_start: 0.7904 (m-30) cc_final: 0.7387 (m-30) REVERT: C 957 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7184 (tm-30) REVERT: C 1017 GLU cc_start: 0.7679 (tp30) cc_final: 0.7339 (tp30) REVERT: C 1138 TYR cc_start: 0.7802 (t80) cc_final: 0.7432 (t80) REVERT: C 1139 ASP cc_start: 0.7992 (t0) cc_final: 0.7588 (t70) REVERT: B 236 THR cc_start: 0.8305 (p) cc_final: 0.8072 (m) REVERT: B 345 THR cc_start: 0.8554 (p) cc_final: 0.8288 (m) REVERT: B 351 TYR cc_start: 0.7788 (p90) cc_final: 0.5604 (p90) REVERT: B 421 TYR cc_start: 0.7478 (m-80) cc_final: 0.7189 (m-80) REVERT: B 430 THR cc_start: 0.8071 (m) cc_final: 0.7662 (p) REVERT: B 452 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.6854 (mm) REVERT: B 456 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7544 (pp) REVERT: B 503 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8315 (m) REVERT: B 554 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: B 577 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6610 (mtm-85) REVERT: B 591 SER cc_start: 0.7300 (t) cc_final: 0.6806 (m) REVERT: B 619 GLU cc_start: 0.7683 (pt0) cc_final: 0.7330 (pt0) REVERT: B 673 SER cc_start: 0.8753 (t) cc_final: 0.8501 (p) REVERT: B 776 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8237 (tttp) REVERT: B 895 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7986 (pt0) REVERT: B 918 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 950 ASP cc_start: 0.7838 (m-30) cc_final: 0.7261 (t0) REVERT: B 1003 SER cc_start: 0.8573 (t) cc_final: 0.8160 (m) REVERT: B 1094 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8384 (m) REVERT: B 1138 TYR cc_start: 0.7944 (t80) cc_final: 0.7462 (t80) REVERT: A 19 ILE cc_start: 0.3998 (OUTLIER) cc_final: 0.2396 (tt) REVERT: A 46 SER cc_start: 0.8560 (m) cc_final: 0.8289 (p) REVERT: A 100 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8411 (mp) REVERT: A 190 ARG cc_start: 0.5309 (OUTLIER) cc_final: 0.4859 (ptm160) REVERT: A 195 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8276 (mtpt) REVERT: A 242 LEU cc_start: 0.7849 (mm) cc_final: 0.7420 (tm) REVERT: A 278 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8202 (ttmt) REVERT: A 305 SER cc_start: 0.8462 (t) cc_final: 0.8109 (p) REVERT: A 318 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8423 (t80) REVERT: A 332 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8124 (tt) REVERT: A 359 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8383 (m) REVERT: A 367 VAL cc_start: 0.8355 (p) cc_final: 0.8137 (t) REVERT: A 378 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7863 (mmmt) REVERT: A 402 ILE cc_start: 0.8345 (pt) cc_final: 0.8018 (tp) REVERT: A 506 GLN cc_start: 0.8203 (mt0) cc_final: 0.7842 (mt0) REVERT: A 514 SER cc_start: 0.8583 (t) cc_final: 0.8228 (m) REVERT: A 529 LYS cc_start: 0.8897 (mptt) cc_final: 0.8488 (mmmm) REVERT: A 546 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7957 (pp) REVERT: A 586 ASP cc_start: 0.7701 (m-30) cc_final: 0.7462 (m-30) REVERT: A 747 THR cc_start: 0.8401 (m) cc_final: 0.8024 (t) REVERT: A 748 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: A 751 ASN cc_start: 0.8142 (m-40) cc_final: 0.7633 (m110) REVERT: A 790 LYS cc_start: 0.8595 (mttm) cc_final: 0.8322 (mttm) REVERT: A 819 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7433 (mt-10) REVERT: A 949 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8251 (mm-40) REVERT: A 950 ASP cc_start: 0.7725 (m-30) cc_final: 0.7389 (m-30) REVERT: A 964 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8508 (mtmm) REVERT: A 973 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8239 (pt) REVERT: A 1002 GLN cc_start: 0.7774 (tp40) cc_final: 0.7400 (tp-100) REVERT: A 1029 MET cc_start: 0.8709 (tpp) cc_final: 0.8483 (tpp) REVERT: A 1050 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7873 (ptt) REVERT: A 1055 SER cc_start: 0.8529 (t) cc_final: 0.8288 (p) REVERT: A 1092 GLU cc_start: 0.7539 (tp30) cc_final: 0.7123 (tp30) REVERT: A 1144 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7387 (mm-30) outliers start: 212 outliers final: 112 residues processed: 935 average time/residue: 0.6243 time to fit residues: 716.5763 Evaluate side-chains 942 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 803 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 111 ARG Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain I residue 212 ASN Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 354 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 403 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 337 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 342 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 212 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN M 123 GLN C 30 ASN C 87 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 580 GLN C 955 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 218 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1048 HIS A 115 GLN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 606 ASN A 657 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.174196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138171 restraints weight = 63955.612| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.78 r_work: 0.3631 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.004 0.107 35431 Z= 0.168 Angle : 0.701 12.934 48428 Z= 0.352 Chirality : 0.048 0.311 5655 Planarity : 0.005 0.094 6127 Dihedral : 5.936 59.694 5983 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.67 % Allowed : 20.07 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.98 (0.12), residues: 4282 helix: 1.04 (0.20), residues: 679 sheet: -0.12 (0.15), residues: 1148 loop : -1.45 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 983 TYR 0.027 0.002 TYR C 28 PHE 0.030 0.002 PHE C 168 TRP 0.041 0.002 TRP I 39 HIS 0.007 0.001 HIS L 218 Details of bonding type rmsd covalent geometry : bond 0.00381 (35315) covalent geometry : angle 0.68359 (48134) SS BOND : bond 0.00467 ( 54) SS BOND : angle 1.66548 ( 108) hydrogen bonds : bond 0.04113 ( 1246) hydrogen bonds : angle 5.74707 ( 3615) link_BETA1-4 : bond 0.00331 ( 22) link_BETA1-4 : angle 1.26147 ( 66) link_NAG-ASN : bond 0.00407 ( 40) link_NAG-ASN : angle 2.75914 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 823 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 LEU cc_start: 0.8156 (mt) cc_final: 0.7901 (mt) REVERT: H 31 ARG cc_start: 0.7336 (mtm180) cc_final: 0.6893 (mtm180) REVERT: H 55 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.6951 (p90) REVERT: H 65 THR cc_start: 0.8199 (p) cc_final: 0.7950 (t) REVERT: H 126 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6321 (p) REVERT: H 216 LYS cc_start: 0.8281 (tppt) cc_final: 0.7745 (tppt) REVERT: L 17 MET cc_start: 0.6618 (ptt) cc_final: 0.6113 (ppp) REVERT: L 38 TYR cc_start: 0.6244 (m-80) cc_final: 0.5377 (m-10) REVERT: L 45 ARG cc_start: 0.8357 (tpp-160) cc_final: 0.7585 (tpp-160) REVERT: I 30 ILE cc_start: 0.8581 (mm) cc_final: 0.8332 (mm) REVERT: I 43 ARG cc_start: 0.7487 (ptt180) cc_final: 0.7059 (ptt-90) REVERT: I 44 GLN cc_start: 0.8040 (tt0) cc_final: 0.7678 (tt0) REVERT: I 67 TYR cc_start: 0.7852 (m-80) cc_final: 0.7554 (m-80) REVERT: I 75 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7243 (mtm110) REVERT: I 117 TYR cc_start: 0.7748 (m-80) cc_final: 0.7108 (m-80) REVERT: I 125 THR cc_start: 0.6406 (m) cc_final: 0.6072 (p) REVERT: I 209 TYR cc_start: 0.3331 (OUTLIER) cc_final: 0.1349 (p90) REVERT: M 88 SER cc_start: 0.7173 (OUTLIER) cc_final: 0.6826 (m) REVERT: M 106 SER cc_start: 0.7595 (t) cc_final: 0.7134 (p) REVERT: M 114 ASN cc_start: 0.7264 (t0) cc_final: 0.6705 (t0) REVERT: J 39 TRP cc_start: 0.6802 (m100) cc_final: 0.6359 (m100) REVERT: J 52 TRP cc_start: 0.7675 (t60) cc_final: 0.7386 (t60) REVERT: J 68 ASN cc_start: 0.7651 (p0) cc_final: 0.6004 (m-40) REVERT: N 114 ASN cc_start: 0.8114 (t0) cc_final: 0.6621 (t0) REVERT: C 32 PHE cc_start: 0.8274 (m-80) cc_final: 0.8047 (m-80) REVERT: C 84 LEU cc_start: 0.7994 (mt) cc_final: 0.7735 (mm) REVERT: C 108 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7826 (m) REVERT: C 115 GLN cc_start: 0.7233 (mt0) cc_final: 0.6591 (tp-100) REVERT: C 173 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 196 ASN cc_start: 0.8592 (t0) cc_final: 0.8365 (t0) REVERT: C 239 GLN cc_start: 0.7738 (tp40) cc_final: 0.7510 (mt0) REVERT: C 329 PHE cc_start: 0.7523 (m-10) cc_final: 0.7298 (m-10) REVERT: C 388 ASN cc_start: 0.7883 (p0) cc_final: 0.7335 (t0) REVERT: C 423 TYR cc_start: 0.6692 (t80) cc_final: 0.6169 (t80) REVERT: C 539 VAL cc_start: 0.8254 (p) cc_final: 0.7994 (m) REVERT: C 599 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8308 (p) REVERT: C 602 THR cc_start: 0.8531 (m) cc_final: 0.8261 (p) REVERT: C 740 MET cc_start: 0.8381 (tpp) cc_final: 0.8024 (ttp) REVERT: C 779 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: C 950 ASP cc_start: 0.7916 (m-30) cc_final: 0.7389 (m-30) REVERT: C 957 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7098 (tm-30) REVERT: C 1017 GLU cc_start: 0.7714 (tp30) cc_final: 0.7306 (tp30) REVERT: C 1138 TYR cc_start: 0.7877 (t80) cc_final: 0.7449 (t80) REVERT: C 1139 ASP cc_start: 0.7982 (t0) cc_final: 0.7469 (t70) REVERT: B 153 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7974 (mpm) REVERT: B 220 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7356 (t80) REVERT: B 320 VAL cc_start: 0.8585 (t) cc_final: 0.8205 (p) REVERT: B 345 THR cc_start: 0.8433 (p) cc_final: 0.8179 (m) REVERT: B 351 TYR cc_start: 0.7840 (p90) cc_final: 0.5617 (p90) REVERT: B 421 TYR cc_start: 0.7343 (m-80) cc_final: 0.7099 (m-80) REVERT: B 430 THR cc_start: 0.8096 (m) cc_final: 0.7673 (p) REVERT: B 452 LEU cc_start: 0.8290 (mm) cc_final: 0.6812 (mm) REVERT: B 456 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7518 (pp) REVERT: B 500 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8812 (m) REVERT: B 554 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: B 577 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6566 (mtm-85) REVERT: B 591 SER cc_start: 0.7143 (t) cc_final: 0.6595 (m) REVERT: B 619 GLU cc_start: 0.7511 (pt0) cc_final: 0.7157 (pt0) REVERT: B 673 SER cc_start: 0.8740 (t) cc_final: 0.8472 (p) REVERT: B 736 VAL cc_start: 0.9063 (m) cc_final: 0.8862 (p) REVERT: B 776 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8215 (tttp) REVERT: B 895 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: B 950 ASP cc_start: 0.7820 (m-30) cc_final: 0.7171 (t0) REVERT: B 1003 SER cc_start: 0.8501 (t) cc_final: 0.8082 (m) REVERT: B 1005 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7914 (mp10) REVERT: B 1094 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8184 (m) REVERT: B 1138 TYR cc_start: 0.7875 (t80) cc_final: 0.7323 (t80) REVERT: A 19 ILE cc_start: 0.3858 (OUTLIER) cc_final: 0.2289 (tt) REVERT: A 46 SER cc_start: 0.8490 (m) cc_final: 0.8255 (p) REVERT: A 129 LYS cc_start: 0.8615 (ptmt) cc_final: 0.8344 (ptmt) REVERT: A 278 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8196 (ttmt) REVERT: A 305 SER cc_start: 0.8457 (t) cc_final: 0.8117 (p) REVERT: A 318 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8460 (t80) REVERT: A 357 ARG cc_start: 0.8630 (ttt-90) cc_final: 0.8414 (ttt90) REVERT: A 359 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8393 (m) REVERT: A 378 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7767 (mmmt) REVERT: A 402 ILE cc_start: 0.8352 (pt) cc_final: 0.7966 (tp) REVERT: A 452 LEU cc_start: 0.8108 (mt) cc_final: 0.7895 (mm) REVERT: A 514 SER cc_start: 0.8621 (t) cc_final: 0.8241 (m) REVERT: A 529 LYS cc_start: 0.8815 (mptt) cc_final: 0.8351 (mmmm) REVERT: A 546 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7757 (pp) REVERT: A 586 ASP cc_start: 0.7716 (m-30) cc_final: 0.7486 (m-30) REVERT: A 747 THR cc_start: 0.8423 (m) cc_final: 0.8104 (t) REVERT: A 751 ASN cc_start: 0.8116 (m-40) cc_final: 0.7587 (m-40) REVERT: A 790 LYS cc_start: 0.8554 (mttm) cc_final: 0.8285 (mttp) REVERT: A 819 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 825 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8391 (mttt) REVERT: A 949 GLN cc_start: 0.8500 (tp-100) cc_final: 0.8184 (mm-40) REVERT: A 950 ASP cc_start: 0.7693 (m-30) cc_final: 0.7363 (m-30) REVERT: A 954 HIS cc_start: 0.8018 (m90) cc_final: 0.7807 (m90) REVERT: A 990 GLU cc_start: 0.7530 (tp30) cc_final: 0.7318 (tp30) REVERT: A 1002 GLN cc_start: 0.7815 (tp40) cc_final: 0.7503 (tp-100) REVERT: A 1055 SER cc_start: 0.8534 (t) cc_final: 0.8251 (p) REVERT: A 1092 GLU cc_start: 0.7503 (tp30) cc_final: 0.7121 (tp30) REVERT: A 1144 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7719 (mm-30) outliers start: 177 outliers final: 100 residues processed: 914 average time/residue: 0.6149 time to fit residues: 688.6609 Evaluate side-chains 902 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 781 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 219 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 55 optimal weight: 40.0000 chunk 377 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 396 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 403 optimal weight: 0.2980 chunk 314 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 212 ASN L 43 GLN L 215 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN I 212 ASN M 6 GLN M 123 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 580 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1071 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 777 ASN A 121 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 603 ASN A 657 ASN A 856 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A 960 ASN A1125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.174800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139027 restraints weight = 63792.995| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.77 r_work: 0.3655 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 35431 Z= 0.156 Angle : 0.695 15.337 48428 Z= 0.348 Chirality : 0.047 0.305 5655 Planarity : 0.005 0.065 6127 Dihedral : 5.856 59.866 5983 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.25 % Allowed : 21.23 % Favored : 74.53 % 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: -0.86 (0.12), residues: 4282 helix: 1.18 (0.20), residues: 679 sheet: -0.00 (0.15), residues: 1148 loop : -1.41 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 328 TYR 0.040 0.002 TYR B 501 PHE 0.031 0.002 PHE H 137 TRP 0.036 0.002 TRP A 64 HIS 0.007 0.001 HIS L 218 Details of bonding type rmsd covalent geometry : bond 0.00358 (35315) covalent geometry : angle 0.67885 (48134) SS BOND : bond 0.00442 ( 54) SS BOND : angle 1.70256 ( 108) hydrogen bonds : bond 0.03996 ( 1246) hydrogen bonds : angle 5.61034 ( 3615) link_BETA1-4 : bond 0.00367 ( 22) link_BETA1-4 : angle 1.23027 ( 66) link_NAG-ASN : bond 0.00347 ( 40) link_NAG-ASN : angle 2.60379 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 785 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 LEU cc_start: 0.8213 (mt) cc_final: 0.7965 (mt) REVERT: H 31 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7077 (mtm180) REVERT: H 55 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6964 (p90) REVERT: H 65 THR cc_start: 0.8147 (p) cc_final: 0.7912 (t) REVERT: H 107 VAL cc_start: 0.7394 (OUTLIER) cc_final: 0.7174 (t) REVERT: H 126 VAL cc_start: 0.6743 (OUTLIER) cc_final: 0.6244 (p) REVERT: H 216 LYS cc_start: 0.8213 (tppt) cc_final: 0.7699 (tppt) REVERT: L 17 MET cc_start: 0.6339 (ptt) cc_final: 0.6067 (ppp) REVERT: L 38 TYR cc_start: 0.6224 (m-80) cc_final: 0.5465 (m-10) REVERT: L 45 ARG cc_start: 0.8322 (tpp-160) cc_final: 0.7174 (tpp-160) REVERT: L 101 ASP cc_start: 0.7256 (m-30) cc_final: 0.7054 (m-30) REVERT: L 150 LYS cc_start: 0.7469 (tmtm) cc_final: 0.7244 (tptt) REVERT: I 30 ILE cc_start: 0.8647 (mm) cc_final: 0.8439 (mm) REVERT: I 43 ARG cc_start: 0.7394 (ptt180) cc_final: 0.6958 (ptt-90) REVERT: I 44 GLN cc_start: 0.7939 (tt0) cc_final: 0.7596 (tt0) REVERT: I 67 TYR cc_start: 0.7813 (m-80) cc_final: 0.7527 (m-80) REVERT: I 117 TYR cc_start: 0.7758 (m-80) cc_final: 0.7164 (m-80) REVERT: I 125 THR cc_start: 0.6354 (m) cc_final: 0.6014 (p) REVERT: I 209 TYR cc_start: 0.3241 (OUTLIER) cc_final: 0.1267 (p90) REVERT: M 106 SER cc_start: 0.7499 (t) cc_final: 0.7057 (p) REVERT: M 114 ASN cc_start: 0.7205 (t0) cc_final: 0.6636 (t0) REVERT: J 39 TRP cc_start: 0.6755 (m100) cc_final: 0.6403 (m100) REVERT: J 52 TRP cc_start: 0.7545 (t60) cc_final: 0.7182 (t60) REVERT: N 79 SER cc_start: 0.1822 (OUTLIER) cc_final: 0.1589 (m) REVERT: C 84 LEU cc_start: 0.7970 (mt) cc_final: 0.7707 (mm) REVERT: C 108 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7871 (m) REVERT: C 115 GLN cc_start: 0.7212 (mt0) cc_final: 0.6823 (tp40) REVERT: C 173 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7601 (tm-30) REVERT: C 196 ASN cc_start: 0.8568 (t0) cc_final: 0.8342 (t0) REVERT: C 388 ASN cc_start: 0.7732 (p0) cc_final: 0.7298 (t0) REVERT: C 423 TYR cc_start: 0.6585 (t80) cc_final: 0.6108 (t80) REVERT: C 539 VAL cc_start: 0.8250 (p) cc_final: 0.8006 (m) REVERT: C 599 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8308 (p) REVERT: C 602 THR cc_start: 0.8526 (m) cc_final: 0.8269 (p) REVERT: C 740 MET cc_start: 0.8253 (tpp) cc_final: 0.8033 (ttp) REVERT: C 779 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: C 950 ASP cc_start: 0.7920 (m-30) cc_final: 0.7379 (m-30) REVERT: C 957 GLN cc_start: 0.7423 (tm-30) cc_final: 0.6832 (tp-100) REVERT: C 1017 GLU cc_start: 0.7687 (tp30) cc_final: 0.7326 (tp30) REVERT: C 1138 TYR cc_start: 0.7767 (t80) cc_final: 0.7354 (t80) REVERT: C 1139 ASP cc_start: 0.7992 (t0) cc_final: 0.7558 (t70) REVERT: B 153 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7966 (mpm) REVERT: B 320 VAL cc_start: 0.8572 (t) cc_final: 0.8191 (p) REVERT: B 345 THR cc_start: 0.8455 (p) cc_final: 0.8203 (m) REVERT: B 430 THR cc_start: 0.8034 (m) cc_final: 0.7685 (p) REVERT: B 456 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7486 (pp) REVERT: B 500 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8840 (m) REVERT: B 554 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: B 577 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6532 (mtm-85) REVERT: B 591 SER cc_start: 0.7054 (t) cc_final: 0.6526 (m) REVERT: B 619 GLU cc_start: 0.7438 (pt0) cc_final: 0.7097 (pt0) REVERT: B 673 SER cc_start: 0.8708 (t) cc_final: 0.8482 (p) REVERT: B 776 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8204 (tttp) REVERT: B 895 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: B 950 ASP cc_start: 0.7787 (m-30) cc_final: 0.7139 (t0) REVERT: B 1003 SER cc_start: 0.8500 (t) cc_final: 0.8070 (m) REVERT: B 1094 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8152 (m) REVERT: B 1138 TYR cc_start: 0.7784 (t80) cc_final: 0.7231 (t80) REVERT: A 19 ILE cc_start: 0.3793 (OUTLIER) cc_final: 0.2232 (tt) REVERT: A 46 SER cc_start: 0.8454 (m) cc_final: 0.8242 (p) REVERT: A 129 LYS cc_start: 0.8574 (ptmt) cc_final: 0.8338 (ptmt) REVERT: A 305 SER cc_start: 0.8441 (t) cc_final: 0.8089 (p) REVERT: A 332 ILE cc_start: 0.8593 (mp) cc_final: 0.8163 (tt) REVERT: A 359 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8361 (m) REVERT: A 378 LYS cc_start: 0.8009 (mmmt) cc_final: 0.7752 (mmmt) REVERT: A 402 ILE cc_start: 0.8357 (pt) cc_final: 0.7970 (tp) REVERT: A 444 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7656 (mptt) REVERT: A 514 SER cc_start: 0.8587 (t) cc_final: 0.8217 (m) REVERT: A 529 LYS cc_start: 0.8863 (mptt) cc_final: 0.8440 (mmmm) REVERT: A 546 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7688 (pp) REVERT: A 646 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7613 (ttp-110) REVERT: A 747 THR cc_start: 0.8470 (m) cc_final: 0.8035 (t) REVERT: A 751 ASN cc_start: 0.8136 (m-40) cc_final: 0.7615 (m-40) REVERT: A 790 LYS cc_start: 0.8572 (mttm) cc_final: 0.8318 (mttp) REVERT: A 819 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 914 ASN cc_start: 0.8006 (m110) cc_final: 0.7713 (m-40) REVERT: A 949 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8145 (mm-40) REVERT: A 950 ASP cc_start: 0.7678 (m-30) cc_final: 0.7349 (m-30) REVERT: A 954 HIS cc_start: 0.7994 (m90) cc_final: 0.7679 (m90) REVERT: A 990 GLU cc_start: 0.7501 (tp30) cc_final: 0.7290 (tp30) REVERT: A 1055 SER cc_start: 0.8530 (t) cc_final: 0.8258 (p) REVERT: A 1092 GLU cc_start: 0.7496 (tp30) cc_final: 0.7103 (tp30) REVERT: A 1144 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7701 (mm-30) outliers start: 161 outliers final: 108 residues processed: 872 average time/residue: 0.6286 time to fit residues: 674.9511 Evaluate side-chains 897 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 771 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain I residue 212 ASN Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 390 optimal weight: 4.9990 chunk 419 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 251 optimal weight: 3.9990 chunk 280 optimal weight: 0.0370 chunk 63 optimal weight: 0.0060 chunk 332 optimal weight: 2.9990 chunk 365 optimal weight: 0.3980 chunk 227 optimal weight: 4.9990 chunk 381 optimal weight: 5.9990 overall best weight: 1.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 215 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN I 212 ASN M 123 GLN C 30 ASN C 87 ASN C 218 GLN C 439 ASN C 580 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 804 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 606 ASN A 657 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 957 GLN A 960 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.174354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138340 restraints weight = 63963.980| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.79 r_work: 0.3649 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35431 Z= 0.174 Angle : 0.705 13.463 48428 Z= 0.354 Chirality : 0.048 0.315 5655 Planarity : 0.005 0.077 6127 Dihedral : 5.884 59.403 5983 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.06 % Allowed : 21.89 % Favored : 74.05 % 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: -0.84 (0.13), residues: 4282 helix: 1.17 (0.20), residues: 679 sheet: 0.03 (0.15), residues: 1155 loop : -1.40 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 403 TYR 0.051 0.002 TYR B 421 PHE 0.041 0.002 PHE H 137 TRP 0.047 0.002 TRP I 39 HIS 0.006 0.001 HIS L 218 Details of bonding type rmsd covalent geometry : bond 0.00396 (35315) covalent geometry : angle 0.68863 (48134) SS BOND : bond 0.00481 ( 54) SS BOND : angle 1.58166 ( 108) hydrogen bonds : bond 0.03964 ( 1246) hydrogen bonds : angle 5.60265 ( 3615) link_BETA1-4 : bond 0.00340 ( 22) link_BETA1-4 : angle 1.22522 ( 66) link_NAG-ASN : bond 0.00350 ( 40) link_NAG-ASN : angle 2.65952 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 798 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 VAL cc_start: 0.7695 (t) cc_final: 0.7459 (p) REVERT: H 21 LEU cc_start: 0.8220 (mt) cc_final: 0.7969 (mt) REVERT: H 31 ARG cc_start: 0.7310 (mtm180) cc_final: 0.6944 (mtm180) REVERT: H 55 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6884 (p90) REVERT: H 65 THR cc_start: 0.8135 (p) cc_final: 0.7907 (t) REVERT: H 126 VAL cc_start: 0.6750 (OUTLIER) cc_final: 0.6249 (p) REVERT: H 216 LYS cc_start: 0.8113 (tppt) cc_final: 0.7625 (tppt) REVERT: L 17 MET cc_start: 0.6332 (ptt) cc_final: 0.6084 (ppp) REVERT: L 38 TYR cc_start: 0.6148 (m-80) cc_final: 0.5419 (m-10) REVERT: L 45 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7561 (tpp-160) REVERT: L 101 ASP cc_start: 0.7358 (m-30) cc_final: 0.7125 (m-30) REVERT: L 150 LYS cc_start: 0.7495 (tmtm) cc_final: 0.7264 (tptt) REVERT: I 30 ILE cc_start: 0.8614 (mm) cc_final: 0.8410 (mm) REVERT: I 43 ARG cc_start: 0.7355 (ptt180) cc_final: 0.6916 (ptt-90) REVERT: I 44 GLN cc_start: 0.8018 (tt0) cc_final: 0.7677 (tt0) REVERT: I 67 TYR cc_start: 0.7741 (m-80) cc_final: 0.7472 (m-80) REVERT: I 117 TYR cc_start: 0.7727 (m-80) cc_final: 0.7107 (m-80) REVERT: I 125 THR cc_start: 0.6388 (m) cc_final: 0.6090 (p) REVERT: I 209 TYR cc_start: 0.3294 (OUTLIER) cc_final: 0.1302 (p90) REVERT: M 88 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6768 (m) REVERT: M 106 SER cc_start: 0.7509 (t) cc_final: 0.7076 (p) REVERT: M 114 ASN cc_start: 0.7234 (t0) cc_final: 0.6688 (t0) REVERT: J 39 TRP cc_start: 0.6711 (m100) cc_final: 0.6387 (m100) REVERT: J 68 ASN cc_start: 0.7782 (p0) cc_final: 0.6383 (m-40) REVERT: C 108 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7900 (m) REVERT: C 115 GLN cc_start: 0.7167 (mt0) cc_final: 0.6766 (tp40) REVERT: C 196 ASN cc_start: 0.8556 (t0) cc_final: 0.8326 (t0) REVERT: C 388 ASN cc_start: 0.7730 (p0) cc_final: 0.7342 (t0) REVERT: C 423 TYR cc_start: 0.6637 (t80) cc_final: 0.6180 (t80) REVERT: C 539 VAL cc_start: 0.8237 (p) cc_final: 0.7979 (m) REVERT: C 580 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7183 (mp10) REVERT: C 599 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8300 (p) REVERT: C 602 THR cc_start: 0.8534 (m) cc_final: 0.8305 (p) REVERT: C 740 MET cc_start: 0.8213 (tpp) cc_final: 0.7920 (ttp) REVERT: C 748 GLU cc_start: 0.7487 (mp0) cc_final: 0.7186 (pm20) REVERT: C 950 ASP cc_start: 0.7940 (m-30) cc_final: 0.7404 (m-30) REVERT: C 957 GLN cc_start: 0.7434 (tm-30) cc_final: 0.6825 (tp-100) REVERT: C 1017 GLU cc_start: 0.7687 (tp30) cc_final: 0.7350 (tp30) REVERT: C 1138 TYR cc_start: 0.7799 (t80) cc_final: 0.7415 (t80) REVERT: C 1139 ASP cc_start: 0.7971 (t0) cc_final: 0.7574 (t70) REVERT: B 153 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7929 (mpm) REVERT: B 171 VAL cc_start: 0.8439 (p) cc_final: 0.8225 (t) REVERT: B 320 VAL cc_start: 0.8577 (t) cc_final: 0.8173 (p) REVERT: B 345 THR cc_start: 0.8425 (p) cc_final: 0.8162 (m) REVERT: B 354 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 386 LYS cc_start: 0.8080 (pmtt) cc_final: 0.7868 (pmtt) REVERT: B 430 THR cc_start: 0.8060 (m) cc_final: 0.7707 (p) REVERT: B 452 LEU cc_start: 0.8235 (mm) cc_final: 0.7983 (tp) REVERT: B 500 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8832 (m) REVERT: B 554 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: B 577 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6527 (mtm-85) REVERT: B 673 SER cc_start: 0.8721 (t) cc_final: 0.8491 (p) REVERT: B 697 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7304 (mtp) REVERT: B 776 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8305 (tttm) REVERT: B 895 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8024 (pt0) REVERT: B 950 ASP cc_start: 0.7842 (m-30) cc_final: 0.7212 (t0) REVERT: B 1003 SER cc_start: 0.8528 (t) cc_final: 0.8086 (m) REVERT: B 1138 TYR cc_start: 0.7860 (t80) cc_final: 0.7280 (t80) REVERT: A 19 ILE cc_start: 0.3836 (OUTLIER) cc_final: 0.2218 (tt) REVERT: A 46 SER cc_start: 0.8471 (m) cc_final: 0.8258 (p) REVERT: A 129 LYS cc_start: 0.8553 (ptmt) cc_final: 0.8341 (ptmt) REVERT: A 305 SER cc_start: 0.8436 (t) cc_final: 0.8080 (p) REVERT: A 332 ILE cc_start: 0.8604 (mp) cc_final: 0.8178 (tt) REVERT: A 359 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8349 (m) REVERT: A 378 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7803 (mmmt) REVERT: A 402 ILE cc_start: 0.8345 (pt) cc_final: 0.7985 (tp) REVERT: A 444 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7619 (mptt) REVERT: A 514 SER cc_start: 0.8584 (t) cc_final: 0.8231 (m) REVERT: A 529 LYS cc_start: 0.8795 (mptt) cc_final: 0.8383 (mmmm) REVERT: A 546 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7698 (pp) REVERT: A 565 PHE cc_start: 0.8527 (p90) cc_final: 0.8178 (p90) REVERT: A 646 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7617 (ttp-110) REVERT: A 747 THR cc_start: 0.8473 (m) cc_final: 0.8076 (t) REVERT: A 751 ASN cc_start: 0.8143 (m-40) cc_final: 0.7646 (m-40) REVERT: A 790 LYS cc_start: 0.8557 (mttm) cc_final: 0.8308 (mttp) REVERT: A 819 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7490 (mt-10) REVERT: A 914 ASN cc_start: 0.7988 (m110) cc_final: 0.7696 (m-40) REVERT: A 949 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8169 (mm-40) REVERT: A 950 ASP cc_start: 0.7720 (m-30) cc_final: 0.7373 (m-30) REVERT: A 954 HIS cc_start: 0.8046 (m90) cc_final: 0.7835 (m90) REVERT: A 990 GLU cc_start: 0.7514 (tp30) cc_final: 0.7306 (tp30) REVERT: A 1055 SER cc_start: 0.8539 (t) cc_final: 0.8254 (p) REVERT: A 1092 GLU cc_start: 0.7539 (tp30) cc_final: 0.7170 (tp30) outliers start: 154 outliers final: 105 residues processed: 884 average time/residue: 0.6153 time to fit residues: 671.3279 Evaluate side-chains 902 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 781 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 41 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 211 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 344 optimal weight: 0.9990 chunk 388 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN M 123 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN B 121 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 580 GLN A 657 ASN A 856 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A 960 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.174386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138602 restraints weight = 63444.813| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.79 r_work: 0.3647 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 35431 Z= 0.177 Angle : 0.721 13.334 48428 Z= 0.363 Chirality : 0.048 0.312 5655 Planarity : 0.005 0.073 6127 Dihedral : 5.925 58.785 5983 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.72 % Allowed : 22.60 % Favored : 73.68 % 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: -0.85 (0.13), residues: 4282 helix: 1.15 (0.20), residues: 679 sheet: 0.06 (0.15), residues: 1148 loop : -1.42 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 319 TYR 0.039 0.002 TYR B 421 PHE 0.030 0.002 PHE C 759 TRP 0.042 0.002 TRP I 39 HIS 0.006 0.001 HIS L 218 Details of bonding type rmsd covalent geometry : bond 0.00408 (35315) covalent geometry : angle 0.70500 (48134) SS BOND : bond 0.00473 ( 54) SS BOND : angle 1.73212 ( 108) hydrogen bonds : bond 0.04045 ( 1246) hydrogen bonds : angle 5.58021 ( 3615) link_BETA1-4 : bond 0.00350 ( 22) link_BETA1-4 : angle 1.21578 ( 66) link_NAG-ASN : bond 0.00360 ( 40) link_NAG-ASN : angle 2.59733 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 798 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 VAL cc_start: 0.7812 (t) cc_final: 0.7545 (p) REVERT: H 21 LEU cc_start: 0.8204 (mt) cc_final: 0.7945 (mt) REVERT: H 31 ARG cc_start: 0.7129 (mtm180) cc_final: 0.6851 (mtm180) REVERT: H 55 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6904 (p90) REVERT: H 65 THR cc_start: 0.8188 (p) cc_final: 0.7947 (t) REVERT: H 81 ASP cc_start: 0.7871 (t70) cc_final: 0.7358 (t0) REVERT: H 113 SER cc_start: 0.6444 (p) cc_final: 0.6160 (t) REVERT: H 126 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6667 (m) REVERT: H 216 LYS cc_start: 0.8118 (tppt) cc_final: 0.7615 (tppt) REVERT: L 17 MET cc_start: 0.6429 (ptt) cc_final: 0.6143 (ppp) REVERT: L 38 TYR cc_start: 0.6178 (m-80) cc_final: 0.5417 (m-10) REVERT: L 45 ARG cc_start: 0.8219 (tpp-160) cc_final: 0.7864 (tpp-160) REVERT: L 101 ASP cc_start: 0.7331 (m-30) cc_final: 0.7061 (m-30) REVERT: L 150 LYS cc_start: 0.7456 (tmtm) cc_final: 0.7255 (tmtm) REVERT: I 43 ARG cc_start: 0.7365 (ptt180) cc_final: 0.6893 (ptt-90) REVERT: I 44 GLN cc_start: 0.8093 (tt0) cc_final: 0.7752 (tt0) REVERT: I 67 TYR cc_start: 0.7743 (m-80) cc_final: 0.7477 (m-80) REVERT: I 117 TYR cc_start: 0.7749 (m-80) cc_final: 0.7024 (m-80) REVERT: I 125 THR cc_start: 0.6498 (m) cc_final: 0.6192 (p) REVERT: I 209 TYR cc_start: 0.3451 (OUTLIER) cc_final: 0.1349 (p90) REVERT: M 88 SER cc_start: 0.7271 (OUTLIER) cc_final: 0.6899 (m) REVERT: M 106 SER cc_start: 0.7515 (t) cc_final: 0.7061 (p) REVERT: M 114 ASN cc_start: 0.7201 (t0) cc_final: 0.6673 (t0) REVERT: J 39 TRP cc_start: 0.6774 (m100) cc_final: 0.6352 (m100) REVERT: J 68 ASN cc_start: 0.7782 (p0) cc_final: 0.6466 (m-40) REVERT: N 17 MET cc_start: 0.4579 (pp-130) cc_final: 0.4069 (pp-130) REVERT: N 114 ASN cc_start: 0.8129 (t0) cc_final: 0.6803 (t0) REVERT: C 41 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7766 (mmmt) REVERT: C 108 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7871 (m) REVERT: C 115 GLN cc_start: 0.7185 (mt0) cc_final: 0.6782 (tp40) REVERT: C 196 ASN cc_start: 0.8572 (t0) cc_final: 0.8339 (t0) REVERT: C 388 ASN cc_start: 0.7758 (p0) cc_final: 0.7327 (t0) REVERT: C 423 TYR cc_start: 0.6600 (t80) cc_final: 0.6134 (t80) REVERT: C 539 VAL cc_start: 0.8260 (p) cc_final: 0.8000 (m) REVERT: C 580 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7369 (mm110) REVERT: C 599 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8292 (p) REVERT: C 602 THR cc_start: 0.8531 (m) cc_final: 0.8308 (p) REVERT: C 675 GLN cc_start: 0.7345 (pp30) cc_final: 0.6757 (pp30) REVERT: C 748 GLU cc_start: 0.7507 (mp0) cc_final: 0.7178 (pm20) REVERT: C 950 ASP cc_start: 0.7897 (m-30) cc_final: 0.7353 (m-30) REVERT: C 957 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6760 (tp-100) REVERT: C 1017 GLU cc_start: 0.7702 (tp30) cc_final: 0.7427 (tp30) REVERT: C 1138 TYR cc_start: 0.7728 (t80) cc_final: 0.7342 (t80) REVERT: C 1139 ASP cc_start: 0.7997 (t0) cc_final: 0.7584 (t70) REVERT: B 153 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7915 (mpm) REVERT: B 171 VAL cc_start: 0.8458 (p) cc_final: 0.8257 (t) REVERT: B 320 VAL cc_start: 0.8583 (t) cc_final: 0.8172 (p) REVERT: B 345 THR cc_start: 0.8445 (p) cc_final: 0.8174 (m) REVERT: B 354 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7842 (p0) REVERT: B 430 THR cc_start: 0.8106 (m) cc_final: 0.7676 (p) REVERT: B 452 LEU cc_start: 0.8236 (mm) cc_final: 0.7976 (tp) REVERT: B 455 LEU cc_start: 0.8608 (tp) cc_final: 0.8277 (tt) REVERT: B 456 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7994 (pt) REVERT: B 500 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8682 (m) REVERT: B 554 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: B 577 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6509 (mtm-85) REVERT: B 619 GLU cc_start: 0.7419 (pt0) cc_final: 0.7162 (pt0) REVERT: B 673 SER cc_start: 0.8723 (t) cc_final: 0.8461 (p) REVERT: B 697 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7324 (mtp) REVERT: B 804 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8083 (mm110) REVERT: B 895 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: B 950 ASP cc_start: 0.7753 (m-30) cc_final: 0.7159 (t0) REVERT: B 1003 SER cc_start: 0.8514 (t) cc_final: 0.8054 (m) REVERT: B 1005 GLN cc_start: 0.7900 (mp10) cc_final: 0.7630 (mp10) REVERT: B 1138 TYR cc_start: 0.7804 (t80) cc_final: 0.7234 (t80) REVERT: A 19 ILE cc_start: 0.3656 (OUTLIER) cc_final: 0.2073 (tt) REVERT: A 46 SER cc_start: 0.8479 (m) cc_final: 0.8257 (p) REVERT: A 129 LYS cc_start: 0.8519 (ptmt) cc_final: 0.8216 (ptmt) REVERT: A 332 ILE cc_start: 0.8628 (mp) cc_final: 0.8214 (tt) REVERT: A 339 HIS cc_start: 0.7354 (OUTLIER) cc_final: 0.6906 (p90) REVERT: A 340 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 359 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8311 (m) REVERT: A 378 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7826 (mmmt) REVERT: A 402 ILE cc_start: 0.8352 (pt) cc_final: 0.7989 (tp) REVERT: A 444 LYS cc_start: 0.7888 (mtmt) cc_final: 0.7626 (mptt) REVERT: A 514 SER cc_start: 0.8591 (t) cc_final: 0.8225 (m) REVERT: A 529 LYS cc_start: 0.8805 (mptt) cc_final: 0.8370 (mmmm) REVERT: A 546 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7688 (pp) REVERT: A 565 PHE cc_start: 0.8526 (p90) cc_final: 0.8178 (p90) REVERT: A 583 GLU cc_start: 0.7934 (tp30) cc_final: 0.7647 (tp30) REVERT: A 646 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7571 (ttp-110) REVERT: A 751 ASN cc_start: 0.8126 (m-40) cc_final: 0.7588 (m-40) REVERT: A 790 LYS cc_start: 0.8571 (mttm) cc_final: 0.8316 (mttp) REVERT: A 825 LYS cc_start: 0.8645 (mttm) cc_final: 0.8404 (mttt) REVERT: A 914 ASN cc_start: 0.8025 (m110) cc_final: 0.7643 (m-40) REVERT: A 918 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 949 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8149 (mm-40) REVERT: A 950 ASP cc_start: 0.7642 (m-30) cc_final: 0.7287 (m-30) REVERT: A 954 HIS cc_start: 0.7975 (m90) cc_final: 0.7757 (m90) REVERT: A 990 GLU cc_start: 0.7512 (tp30) cc_final: 0.7262 (tp30) REVERT: A 1055 SER cc_start: 0.8556 (t) cc_final: 0.8263 (p) REVERT: A 1092 GLU cc_start: 0.7479 (tp30) cc_final: 0.7116 (tp30) outliers start: 141 outliers final: 96 residues processed: 875 average time/residue: 0.6150 time to fit residues: 664.2609 Evaluate side-chains 895 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 781 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 148 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 162 optimal weight: 8.9990 chunk 402 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 307 optimal weight: 0.9980 chunk 260 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 340 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 212 ASN I 64 ASN I 85 ASN ** M 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1071 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 580 GLN A 606 ASN A 657 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A 960 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.175344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139592 restraints weight = 64034.125| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.78 r_work: 0.3665 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 35431 Z= 0.149 Angle : 0.723 13.075 48428 Z= 0.364 Chirality : 0.048 0.294 5655 Planarity : 0.005 0.085 6127 Dihedral : 5.876 57.640 5979 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.45 % Allowed : 23.23 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.79 (0.13), residues: 4282 helix: 1.25 (0.20), residues: 685 sheet: 0.06 (0.15), residues: 1166 loop : -1.39 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 403 TYR 0.029 0.002 TYR B 501 PHE 0.038 0.002 PHE A 168 TRP 0.060 0.002 TRP I 41 HIS 0.006 0.001 HIS L 218 Details of bonding type rmsd covalent geometry : bond 0.00344 (35315) covalent geometry : angle 0.70423 (48134) SS BOND : bond 0.00499 ( 54) SS BOND : angle 2.12958 ( 108) hydrogen bonds : bond 0.03857 ( 1246) hydrogen bonds : angle 5.51356 ( 3615) link_BETA1-4 : bond 0.00364 ( 22) link_BETA1-4 : angle 1.18891 ( 66) link_NAG-ASN : bond 0.00414 ( 40) link_NAG-ASN : angle 2.68348 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 786 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 VAL cc_start: 0.7522 (t) cc_final: 0.7301 (p) REVERT: H 21 LEU cc_start: 0.8193 (mt) cc_final: 0.7941 (mt) REVERT: H 31 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7105 (mtm180) REVERT: H 55 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6955 (p90) REVERT: H 65 THR cc_start: 0.8148 (p) cc_final: 0.7913 (t) REVERT: H 81 ASP cc_start: 0.7882 (t70) cc_final: 0.7415 (t0) REVERT: H 113 SER cc_start: 0.6376 (p) cc_final: 0.6107 (t) REVERT: H 126 VAL cc_start: 0.6648 (OUTLIER) cc_final: 0.6440 (m) REVERT: H 216 LYS cc_start: 0.8270 (tppt) cc_final: 0.7691 (tppt) REVERT: L 17 MET cc_start: 0.6464 (ptt) cc_final: 0.6125 (ppp) REVERT: L 38 TYR cc_start: 0.6308 (m-80) cc_final: 0.5495 (m-10) REVERT: L 45 ARG cc_start: 0.8245 (tpp-160) cc_final: 0.7819 (tpp-160) REVERT: L 101 ASP cc_start: 0.7521 (m-30) cc_final: 0.7104 (m-30) REVERT: I 43 ARG cc_start: 0.7361 (ptt180) cc_final: 0.6881 (ptt-90) REVERT: I 44 GLN cc_start: 0.7980 (tt0) cc_final: 0.7666 (tt0) REVERT: I 67 TYR cc_start: 0.7821 (m-80) cc_final: 0.7556 (m-80) REVERT: I 82 THR cc_start: 0.8673 (p) cc_final: 0.8306 (t) REVERT: I 117 TYR cc_start: 0.7704 (m-80) cc_final: 0.7072 (m-80) REVERT: I 125 THR cc_start: 0.6536 (m) cc_final: 0.6238 (p) REVERT: I 209 TYR cc_start: 0.3375 (OUTLIER) cc_final: 0.2607 (p90) REVERT: M 106 SER cc_start: 0.7470 (t) cc_final: 0.7029 (p) REVERT: M 114 ASN cc_start: 0.7183 (t0) cc_final: 0.6646 (t0) REVERT: J 39 TRP cc_start: 0.6736 (m100) cc_final: 0.6383 (m100) REVERT: N 17 MET cc_start: 0.4596 (pp-130) cc_final: 0.4104 (pp-130) REVERT: N 114 ASN cc_start: 0.8199 (t0) cc_final: 0.6914 (t0) REVERT: C 41 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7750 (mmmt) REVERT: C 108 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7840 (m) REVERT: C 115 GLN cc_start: 0.7196 (mt0) cc_final: 0.6736 (tp40) REVERT: C 196 ASN cc_start: 0.8556 (t0) cc_final: 0.8336 (t0) REVERT: C 388 ASN cc_start: 0.7826 (p0) cc_final: 0.7337 (t0) REVERT: C 423 TYR cc_start: 0.6492 (t80) cc_final: 0.6045 (t80) REVERT: C 539 VAL cc_start: 0.8219 (p) cc_final: 0.7936 (m) REVERT: C 583 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6775 (tm-30) REVERT: C 599 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8277 (p) REVERT: C 602 THR cc_start: 0.8531 (m) cc_final: 0.8310 (p) REVERT: C 950 ASP cc_start: 0.7878 (m-30) cc_final: 0.7344 (m-30) REVERT: C 957 GLN cc_start: 0.7314 (tm-30) cc_final: 0.6797 (tp-100) REVERT: C 1017 GLU cc_start: 0.7721 (tp30) cc_final: 0.7357 (tp30) REVERT: C 1138 TYR cc_start: 0.7817 (t80) cc_final: 0.7427 (t80) REVERT: C 1139 ASP cc_start: 0.7988 (t0) cc_final: 0.7522 (t70) REVERT: B 320 VAL cc_start: 0.8576 (t) cc_final: 0.8151 (p) REVERT: B 345 THR cc_start: 0.8460 (p) cc_final: 0.8220 (m) REVERT: B 354 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7756 (p0) REVERT: B 421 TYR cc_start: 0.7060 (m-10) cc_final: 0.6834 (m-10) REVERT: B 430 THR cc_start: 0.8073 (m) cc_final: 0.7648 (p) REVERT: B 452 LEU cc_start: 0.8257 (mm) cc_final: 0.7989 (tp) REVERT: B 455 LEU cc_start: 0.8657 (tp) cc_final: 0.8249 (tt) REVERT: B 554 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: B 576 VAL cc_start: 0.8818 (p) cc_final: 0.8548 (m) REVERT: B 619 GLU cc_start: 0.7329 (pt0) cc_final: 0.7094 (pt0) REVERT: B 673 SER cc_start: 0.8760 (t) cc_final: 0.8504 (p) REVERT: B 697 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7348 (mtp) REVERT: B 804 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8137 (mm110) REVERT: B 895 GLN cc_start: 0.8341 (pt0) cc_final: 0.8034 (pt0) REVERT: B 914 ASN cc_start: 0.7587 (t0) cc_final: 0.7380 (t0) REVERT: B 950 ASP cc_start: 0.7797 (m-30) cc_final: 0.7150 (t0) REVERT: B 1005 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: B 1138 TYR cc_start: 0.7784 (t80) cc_final: 0.7202 (t80) REVERT: A 19 ILE cc_start: 0.3794 (OUTLIER) cc_final: 0.2202 (tt) REVERT: A 46 SER cc_start: 0.8457 (m) cc_final: 0.8237 (p) REVERT: A 129 LYS cc_start: 0.8520 (ptmt) cc_final: 0.8192 (ptmt) REVERT: A 305 SER cc_start: 0.8403 (m) cc_final: 0.8072 (p) REVERT: A 332 ILE cc_start: 0.8625 (mp) cc_final: 0.8203 (tt) REVERT: A 339 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.6956 (p90) REVERT: A 340 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 359 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8259 (m) REVERT: A 378 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7808 (mmmt) REVERT: A 402 ILE cc_start: 0.8356 (pt) cc_final: 0.7974 (tp) REVERT: A 514 SER cc_start: 0.8571 (t) cc_final: 0.8237 (m) REVERT: A 529 LYS cc_start: 0.8812 (mptt) cc_final: 0.8385 (mmmm) REVERT: A 546 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7578 (pp) REVERT: A 565 PHE cc_start: 0.8512 (p90) cc_final: 0.8133 (p90) REVERT: A 646 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7616 (ttp-110) REVERT: A 748 GLU cc_start: 0.8099 (pm20) cc_final: 0.7857 (pm20) REVERT: A 751 ASN cc_start: 0.8132 (m-40) cc_final: 0.7669 (m-40) REVERT: A 790 LYS cc_start: 0.8557 (mttm) cc_final: 0.8320 (mttp) REVERT: A 819 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 825 LYS cc_start: 0.8650 (mttm) cc_final: 0.8416 (mttt) REVERT: A 914 ASN cc_start: 0.7984 (m110) cc_final: 0.7672 (m-40) REVERT: A 949 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8153 (mm-40) REVERT: A 950 ASP cc_start: 0.7675 (m-30) cc_final: 0.7342 (m-30) REVERT: A 954 HIS cc_start: 0.8014 (m90) cc_final: 0.7689 (m90) REVERT: A 973 ILE cc_start: 0.8686 (mt) cc_final: 0.8431 (pp) REVERT: A 990 GLU cc_start: 0.7494 (tp30) cc_final: 0.7253 (tp30) REVERT: A 1055 SER cc_start: 0.8546 (t) cc_final: 0.8254 (p) REVERT: A 1092 GLU cc_start: 0.7522 (tp30) cc_final: 0.7155 (tp30) outliers start: 131 outliers final: 97 residues processed: 854 average time/residue: 0.5795 time to fit residues: 611.9571 Evaluate side-chains 866 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 756 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 90 LYS Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 209 TYR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 257 optimal weight: 0.7980 chunk 361 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 415 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 335 optimal weight: 0.7980 chunk 289 optimal weight: 0.9990 chunk 310 optimal weight: 5.9990 chunk 304 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 212 ASN I 85 ASN ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1071 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN A 121 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 580 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 957 GLN A 960 ASN A1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.175789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140251 restraints weight = 63730.449| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.76 r_work: 0.3677 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35431 Z= 0.152 Angle : 0.728 13.037 48428 Z= 0.366 Chirality : 0.048 0.298 5655 Planarity : 0.005 0.074 6127 Dihedral : 5.845 58.322 5979 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.35 % Allowed : 23.68 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.13), residues: 4282 helix: 1.34 (0.20), residues: 685 sheet: 0.06 (0.15), residues: 1177 loop : -1.35 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 355 TYR 0.031 0.001 TYR J 55 PHE 0.031 0.002 PHE A 192 TRP 0.081 0.002 TRP I 41 HIS 0.005 0.001 HIS L 218 Details of bonding type rmsd covalent geometry : bond 0.00356 (35315) covalent geometry : angle 0.71157 (48134) SS BOND : bond 0.00457 ( 54) SS BOND : angle 1.86490 ( 108) hydrogen bonds : bond 0.03845 ( 1246) hydrogen bonds : angle 5.48689 ( 3615) link_BETA1-4 : bond 0.00386 ( 22) link_BETA1-4 : angle 1.19956 ( 66) link_NAG-ASN : bond 0.00386 ( 40) link_NAG-ASN : angle 2.63366 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15842.84 seconds wall clock time: 270 minutes 12.34 seconds (16212.34 seconds total)