Starting phenix.real_space_refine on Fri Mar 6 11:05:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ntc_12587/03_2026/7ntc_12587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ntc_12587/03_2026/7ntc_12587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ntc_12587/03_2026/7ntc_12587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ntc_12587/03_2026/7ntc_12587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ntc_12587/03_2026/7ntc_12587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ntc_12587/03_2026/7ntc_12587.map" } resolution = 3.6 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= 0.002 sd= 0.063 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 129 5.16 5 C 19031 2.51 5 N 4907 2.21 5 O 5938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30005 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8496 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 3 Chain: "B" Number of atoms: 8496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8496 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 3 Chain: "C" Number of atoms: 8496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8496 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 3 Chain: "H" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1691 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "L" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1634 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLA': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLA': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.93, per 1000 atoms: 0.23 Number of scatterers: 30005 At special positions: 0 Unit cell: (222.18, 160.08, 204.24, 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 129 16.00 O 5938 8.00 N 4907 7.00 C 19031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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=2.02 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=2.04 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=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 169 " - pdb=" SG CYS H 225 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.04 Simple disulfide: pdb=" SG CYS L 153 " - pdb=" SG CYS L 213 " 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 603 " " NAG B1302 " - " ASN B 149 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 603 " " NAG C1301 " - " ASN C 149 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 17 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 17 " " NAG O 1 " - " ASN B 122 " " NAG P 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 616 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN A 17 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 122 " " NAG Y 1 " - " ASN C 165 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6906 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 57 sheets defined 21.1% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.744A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.866A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.719A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.599A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.855A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.864A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.571A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.621A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 939 removed outlier: 4.251A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.573A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.955A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.157A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.844A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.678A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.508A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 423 removed outlier: 3.506A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.930A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.657A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 881 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.680A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 938 removed outlier: 3.699A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.323A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (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 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.361A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.103A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.956A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.526A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.604A pdb=" N VAL C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 408' Processing helix chain 'C' and resid 417 through 423 removed outlier: 4.156A pdb=" N TYR C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.550A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.586A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.694A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.579A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C 917 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.632A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.052A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.547A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.996A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.582A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.723A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 218 removed outlier: 3.597A pdb=" N SER H 217 " --> pdb=" O PRO H 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 147 Processing helix chain 'L' and resid 201 through 206 removed outlier: 3.799A pdb=" N GLU L 206 " --> pdb=" O LYS L 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.185A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.670A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.286A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 143 removed outlier: 8.750A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.483A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.643A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 587 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.318A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.529A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 714 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.659A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.750A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.500A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.882A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 14.041A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 13.637A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.871A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.504A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.243A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.566A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 355 through 358 removed outlier: 5.397A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.817A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.531A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.511A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.636A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.724A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.478A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.711A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.929A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.738A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.184A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.672A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.087A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.961A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.664A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.849A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.744A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.657A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.467A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.621A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AF6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.186A pdb=" N GLY H 29 " --> pdb=" O THR H 139 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N MET H 53 " --> pdb=" O SER H 69 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 149 through 153 removed outlier: 6.212A pdb=" N TYR H 205 " --> pdb=" O ASP H 173 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 180 through 182 removed outlier: 4.259A pdb=" N TYR H 223 " --> pdb=" O VAL H 240 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 23 through 26 removed outlier: 3.626A pdb=" N ASP L 89 " --> pdb=" O SER L 86 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 72 through 73 removed outlier: 6.751A pdb=" N TRP L 54 " --> pdb=" O LEU L 66 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TYR L 68 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU L 52 " --> pdb=" O TYR L 68 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 133 through 137 removed outlier: 5.460A pdb=" N SER L 150 " --> pdb=" O LEU L 200 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU L 200 " --> pdb=" O SER L 150 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL L 152 " --> pdb=" O LEU L 198 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU L 198 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU L 154 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER L 196 " --> pdb=" O LEU L 154 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ASN L 156 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU L 194 " --> pdb=" O ASN L 156 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 172 through 173 1008 hydrogen bonds defined for protein. 2700 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: 8.18 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9352 1.34 - 1.46: 7525 1.46 - 1.58: 13645 1.58 - 1.71: 0 1.71 - 1.83: 163 Bond restraints: 30685 Sorted by residual: bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" CGA BLA B1301 " pdb=" O2A BLA B1301 " ideal model delta sigma weight residual 1.246 1.308 -0.062 2.00e-02 2.50e+03 9.51e+00 bond pdb=" CGA BLA A1301 " pdb=" O2A BLA A1301 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.346 0.060 2.00e-02 2.50e+03 8.96e+00 ... (remaining 30680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 41043 2.17 - 4.33: 667 4.33 - 6.50: 48 6.50 - 8.67: 8 8.67 - 10.83: 1 Bond angle restraints: 41767 Sorted by residual: angle pdb=" C ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " ideal model delta sigma weight residual 116.54 110.38 6.16 1.15e+00 7.56e-01 2.87e+01 angle pdb=" N ILE A 468 " pdb=" CA ILE A 468 " pdb=" C ILE A 468 " ideal model delta sigma weight residual 113.20 108.20 5.00 9.60e-01 1.09e+00 2.72e+01 angle pdb=" C GLN C 183 " pdb=" CA GLN C 183 " pdb=" CB GLN C 183 " ideal model delta sigma weight residual 116.54 111.14 5.40 1.15e+00 7.56e-01 2.21e+01 angle pdb=" C ASP L 111 " pdb=" CA ASP L 111 " pdb=" CB ASP L 111 " ideal model delta sigma weight residual 112.31 106.87 5.44 1.53e+00 4.27e-01 1.27e+01 angle pdb=" C GLY C 184 " pdb=" N ASN C 185 " pdb=" CA ASN C 185 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 ... (remaining 41762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.75: 18234 24.75 - 49.49: 828 49.49 - 74.24: 166 74.24 - 98.99: 65 98.99 - 123.73: 6 Dihedral angle restraints: 19299 sinusoidal: 8542 harmonic: 10757 Sorted by residual: dihedral pdb=" CB CYS H 41 " pdb=" SG CYS H 41 " pdb=" SG CYS H 115 " pdb=" CB CYS H 115 " ideal model delta sinusoidal sigma weight residual 93.00 165.35 -72.35 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -147.14 61.14 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -31.04 -54.96 1 1.00e+01 1.00e-02 4.09e+01 ... (remaining 19296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 4900 0.155 - 0.309: 22 0.309 - 0.464: 1 0.464 - 0.618: 0 0.618 - 0.773: 1 Chirality restraints: 4924 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4921 not shown) Planarity restraints: 5354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1301 " -0.018 2.00e-02 2.50e+03 3.82e-02 3.65e+01 pdb=" C1A BLA A1301 " 0.085 2.00e-02 2.50e+03 pdb=" C1D BLA A1301 " -0.000 2.00e-02 2.50e+03 pdb=" C2D BLA A1301 " 0.009 2.00e-02 2.50e+03 pdb=" C3D BLA A1301 " -0.008 2.00e-02 2.50e+03 pdb=" C4D BLA A1301 " -0.027 2.00e-02 2.50e+03 pdb=" CAD BLA A1301 " 0.001 2.00e-02 2.50e+03 pdb=" CHA BLA A1301 " -0.068 2.00e-02 2.50e+03 pdb=" CHD BLA A1301 " -0.010 2.00e-02 2.50e+03 pdb=" CMD BLA A1301 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA B1301 " 0.026 2.00e-02 2.50e+03 3.49e-02 3.05e+01 pdb=" OB BLA B1301 " 0.007 2.00e-02 2.50e+03 pdb=" C1B BLA B1301 " 0.028 2.00e-02 2.50e+03 pdb=" C2B BLA B1301 " 0.013 2.00e-02 2.50e+03 pdb=" C3B BLA B1301 " -0.004 2.00e-02 2.50e+03 pdb=" C4A BLA B1301 " -0.076 2.00e-02 2.50e+03 pdb=" C4B BLA B1301 " 0.010 2.00e-02 2.50e+03 pdb=" CAB BLA B1301 " -0.055 2.00e-02 2.50e+03 pdb=" CHB BLA B1301 " 0.039 2.00e-02 2.50e+03 pdb=" CMB BLA B1301 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1301 " -0.016 2.00e-02 2.50e+03 3.38e-02 2.86e+01 pdb=" C1A BLA B1301 " 0.073 2.00e-02 2.50e+03 pdb=" C1D BLA B1301 " 0.001 2.00e-02 2.50e+03 pdb=" C2D BLA B1301 " 0.014 2.00e-02 2.50e+03 pdb=" C3D BLA B1301 " -0.004 2.00e-02 2.50e+03 pdb=" C4D BLA B1301 " -0.022 2.00e-02 2.50e+03 pdb=" CAD BLA B1301 " -0.012 2.00e-02 2.50e+03 pdb=" CHA BLA B1301 " -0.055 2.00e-02 2.50e+03 pdb=" CHD BLA B1301 " -0.019 2.00e-02 2.50e+03 pdb=" CMD BLA B1301 " 0.040 2.00e-02 2.50e+03 ... (remaining 5351 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1126 2.71 - 3.26: 29299 3.26 - 3.81: 46131 3.81 - 4.35: 54017 4.35 - 4.90: 93668 Nonbonded interactions: 224241 Sorted by model distance: nonbonded pdb=" OD1 ASN C1135 " pdb=" N THR C1136 " model vdw 2.165 3.120 nonbonded pdb=" NH1 ARG H 38 " pdb=" OG SER H 40 " model vdw 2.166 3.120 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.169 3.040 nonbonded pdb=" O MET A 731 " pdb=" NE2 GLN A 774 " model vdw 2.196 3.120 nonbonded pdb=" O PRO C 57 " pdb=" OG SER C 60 " model vdw 2.200 3.040 ... (remaining 224236 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 1146 or resid 1302 through 1310)) selection = (chain 'B' and (resid 14 through 1146 or resid 1302 through 1310)) selection = (chain 'C' and (resid 14 through 1146 or resid 1302 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.390 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 30810 Z= 0.216 Angle : 0.716 21.117 42094 Z= 0.353 Chirality : 0.048 0.773 4924 Planarity : 0.004 0.056 5300 Dihedral : 15.093 123.734 12258 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.70 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3670 helix: 1.19 (0.22), residues: 651 sheet: 0.16 (0.17), residues: 921 loop : -1.70 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 239 TYR 0.023 0.001 TYR H 114 PHE 0.037 0.001 PHE A 906 TRP 0.021 0.001 TRP A 64 HIS 0.010 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00452 (30685) covalent geometry : angle 0.64661 (41767) SS BOND : bond 0.00401 ( 45) SS BOND : angle 1.36537 ( 90) hydrogen bonds : bond 0.16681 ( 1001) hydrogen bonds : angle 6.81788 ( 2700) Misc. bond : bond 0.00138 ( 1) link_BETA1-4 : bond 0.00445 ( 25) link_BETA1-4 : angle 2.51657 ( 75) link_NAG-ASN : bond 0.00634 ( 54) link_NAG-ASN : angle 4.63859 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7829 (mm) cc_final: 0.7538 (mm) REVERT: A 1029 MET cc_start: 0.9251 (tpp) cc_final: 0.9046 (tpp) REVERT: B 173 GLN cc_start: 0.7297 (pm20) cc_final: 0.7057 (pm20) REVERT: B 242 LEU cc_start: 0.7882 (mm) cc_final: 0.7413 (tp) REVERT: C 1029 MET cc_start: 0.9199 (tpp) cc_final: 0.8907 (tpp) REVERT: H 53 MET cc_start: 0.7936 (mmp) cc_final: 0.7735 (mmp) REVERT: H 92 ASP cc_start: 0.8420 (t70) cc_final: 0.8142 (t0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1694 time to fit residues: 34.4968 Evaluate side-chains 81 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 360 ASN A 774 GLN B 207 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.098026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062526 restraints weight = 109151.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.064739 restraints weight = 51524.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.066185 restraints weight = 33065.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.067107 restraints weight = 25082.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.067663 restraints weight = 21168.097| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30810 Z= 0.128 Angle : 0.621 18.754 42094 Z= 0.302 Chirality : 0.045 0.437 4924 Planarity : 0.004 0.055 5300 Dihedral : 9.546 113.445 5689 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 0.25 % Allowed : 4.34 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.79 (0.14), residues: 3670 helix: 1.49 (0.21), residues: 671 sheet: 0.30 (0.17), residues: 916 loop : -1.68 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 37 TYR 0.028 0.001 TYR A 365 PHE 0.018 0.001 PHE A 906 TRP 0.014 0.001 TRP B 633 HIS 0.007 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00282 (30685) covalent geometry : angle 0.57210 (41767) SS BOND : bond 0.00395 ( 45) SS BOND : angle 1.18852 ( 90) hydrogen bonds : bond 0.04835 ( 1001) hydrogen bonds : angle 5.44598 ( 2700) Misc. bond : bond 0.00120 ( 1) link_BETA1-4 : bond 0.00434 ( 25) link_BETA1-4 : angle 1.96744 ( 75) link_NAG-ASN : bond 0.00578 ( 54) link_NAG-ASN : angle 3.62853 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7879 (mm) cc_final: 0.7562 (mm) REVERT: B 173 GLN cc_start: 0.7277 (pm20) cc_final: 0.7066 (pm20) REVERT: C 1029 MET cc_start: 0.9217 (tpp) cc_final: 0.8996 (tpp) REVERT: H 92 ASP cc_start: 0.8404 (t70) cc_final: 0.8120 (t0) REVERT: L 23 MET cc_start: 0.8460 (mmm) cc_final: 0.8035 (mmm) REVERT: L 161 ARG cc_start: 0.5620 (mpt180) cc_final: 0.5384 (mpt180) REVERT: L 214 GLU cc_start: 0.7205 (mp0) cc_final: 0.6912 (mp0) outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.1843 time to fit residues: 29.2066 Evaluate side-chains 79 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain L residue 192 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 104 optimal weight: 0.9990 chunk 329 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 305 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.098000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062782 restraints weight = 109477.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065000 restraints weight = 51581.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.066434 restraints weight = 32929.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.067346 restraints weight = 25008.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.067897 restraints weight = 21040.619| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30810 Z= 0.114 Angle : 0.579 17.611 42094 Z= 0.280 Chirality : 0.044 0.416 4924 Planarity : 0.004 0.052 5300 Dihedral : 8.338 108.337 5689 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 0.37 % Allowed : 6.91 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.72 (0.14), residues: 3670 helix: 1.74 (0.22), residues: 665 sheet: 0.23 (0.17), residues: 902 loop : -1.62 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 22 TYR 0.016 0.001 TYR C 380 PHE 0.013 0.001 PHE B1121 TRP 0.017 0.001 TRP C 258 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00251 (30685) covalent geometry : angle 0.53418 (41767) SS BOND : bond 0.00310 ( 45) SS BOND : angle 0.99811 ( 90) hydrogen bonds : bond 0.04347 ( 1001) hydrogen bonds : angle 5.12967 ( 2700) Misc. bond : bond 0.00061 ( 1) link_BETA1-4 : bond 0.00400 ( 25) link_BETA1-4 : angle 1.97628 ( 75) link_NAG-ASN : bond 0.00551 ( 54) link_NAG-ASN : angle 3.34624 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7976 (mm) cc_final: 0.7605 (mm) REVERT: B 79 PHE cc_start: 0.6786 (t80) cc_final: 0.6501 (t80) REVERT: B 904 TYR cc_start: 0.8109 (m-10) cc_final: 0.7833 (m-80) REVERT: C 1029 MET cc_start: 0.9236 (tpp) cc_final: 0.9031 (tpp) REVERT: H 92 ASP cc_start: 0.8426 (t70) cc_final: 0.8150 (t0) REVERT: L 214 GLU cc_start: 0.7179 (mp0) cc_final: 0.6864 (mp0) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.1974 time to fit residues: 31.8397 Evaluate side-chains 88 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain L residue 192 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 183 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 318 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 267 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1054 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.093510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059499 restraints weight = 109085.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.061827 restraints weight = 50707.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 77)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063331 restraints weight = 32540.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064254 restraints weight = 24816.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064845 restraints weight = 20985.978| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30810 Z= 0.120 Angle : 0.573 16.414 42094 Z= 0.277 Chirality : 0.044 0.406 4924 Planarity : 0.004 0.051 5300 Dihedral : 7.674 105.179 5689 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 0.53 % Allowed : 8.78 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.65 (0.14), residues: 3670 helix: 1.80 (0.22), residues: 666 sheet: 0.27 (0.17), residues: 909 loop : -1.59 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.015 0.001 TYR A 145 PHE 0.013 0.001 PHE B1121 TRP 0.013 0.001 TRP C 258 HIS 0.007 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00270 (30685) covalent geometry : angle 0.53126 (41767) SS BOND : bond 0.00308 ( 45) SS BOND : angle 1.04997 ( 90) hydrogen bonds : bond 0.04206 ( 1001) hydrogen bonds : angle 5.01448 ( 2700) Misc. bond : bond 0.00089 ( 1) link_BETA1-4 : bond 0.00410 ( 25) link_BETA1-4 : angle 1.95089 ( 75) link_NAG-ASN : bond 0.00523 ( 54) link_NAG-ASN : angle 3.20676 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7975 (mm) cc_final: 0.7643 (mm) REVERT: A 338 PHE cc_start: 0.7128 (m-80) cc_final: 0.6776 (m-80) REVERT: A 985 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: B 904 TYR cc_start: 0.8154 (m-10) cc_final: 0.7824 (m-10) REVERT: C 228 ASP cc_start: 0.7586 (p0) cc_final: 0.7175 (p0) REVERT: C 1029 MET cc_start: 0.9212 (tpp) cc_final: 0.9010 (tpp) REVERT: H 92 ASP cc_start: 0.8501 (t70) cc_final: 0.8238 (t0) REVERT: L 161 ARG cc_start: 0.5428 (mpt180) cc_final: 0.5113 (mpt180) REVERT: L 214 GLU cc_start: 0.7178 (mp0) cc_final: 0.6871 (mp0) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.1899 time to fit residues: 31.4025 Evaluate side-chains 88 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain L residue 192 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 292 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.092123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.057905 restraints weight = 110122.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060154 restraints weight = 52512.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.061595 restraints weight = 34020.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062508 restraints weight = 26196.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.063054 restraints weight = 22285.669| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30810 Z= 0.180 Angle : 0.610 15.510 42094 Z= 0.297 Chirality : 0.045 0.450 4924 Planarity : 0.004 0.055 5300 Dihedral : 7.118 87.818 5689 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.87 % Favored : 93.00 % Rotamer: Outliers : 0.71 % Allowed : 10.23 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.79 (0.14), residues: 3670 helix: 1.62 (0.21), residues: 674 sheet: 0.14 (0.17), residues: 922 loop : -1.65 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 22 TYR 0.018 0.001 TYR A 145 PHE 0.020 0.001 PHE B1121 TRP 0.011 0.001 TRP A 64 HIS 0.008 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00418 (30685) covalent geometry : angle 0.56995 (41767) SS BOND : bond 0.00359 ( 45) SS BOND : angle 1.21032 ( 90) hydrogen bonds : bond 0.04884 ( 1001) hydrogen bonds : angle 5.15282 ( 2700) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00382 ( 25) link_BETA1-4 : angle 2.24524 ( 75) link_NAG-ASN : bond 0.00498 ( 54) link_NAG-ASN : angle 3.10597 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7854 (t0) REVERT: C 1029 MET cc_start: 0.9243 (tpp) cc_final: 0.9038 (tpp) REVERT: H 83 MET cc_start: 0.5922 (mpp) cc_final: 0.5708 (mpp) REVERT: H 92 ASP cc_start: 0.8545 (t70) cc_final: 0.8298 (t0) REVERT: L 161 ARG cc_start: 0.5338 (mpt180) cc_final: 0.5096 (mpt180) REVERT: L 214 GLU cc_start: 0.6735 (mp0) cc_final: 0.6392 (mp0) outliers start: 23 outliers final: 15 residues processed: 97 average time/residue: 0.1982 time to fit residues: 32.4322 Evaluate side-chains 89 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain L residue 192 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 347 optimal weight: 0.0470 chunk 250 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 335 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.092337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058189 restraints weight = 109459.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060425 restraints weight = 52157.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061884 restraints weight = 33901.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.062805 restraints weight = 26071.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.063356 restraints weight = 22172.052| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30810 Z= 0.151 Angle : 0.599 14.300 42094 Z= 0.290 Chirality : 0.044 0.326 4924 Planarity : 0.004 0.055 5300 Dihedral : 7.238 121.373 5689 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.16 % Favored : 93.68 % Rotamer: Outliers : 0.90 % Allowed : 11.35 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.77 (0.14), residues: 3670 helix: 1.65 (0.21), residues: 674 sheet: 0.20 (0.17), residues: 909 loop : -1.66 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 22 TYR 0.021 0.001 TYR A 145 PHE 0.017 0.001 PHE B1121 TRP 0.011 0.001 TRP A 64 HIS 0.008 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00348 (30685) covalent geometry : angle 0.56200 (41767) SS BOND : bond 0.00330 ( 45) SS BOND : angle 1.10712 ( 90) hydrogen bonds : bond 0.04624 ( 1001) hydrogen bonds : angle 5.07056 ( 2700) Misc. bond : bond 0.00084 ( 1) link_BETA1-4 : bond 0.00453 ( 25) link_BETA1-4 : angle 1.92047 ( 75) link_NAG-ASN : bond 0.00461 ( 54) link_NAG-ASN : angle 3.08168 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7876 (mt) cc_final: 0.7450 (mm) REVERT: A 434 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8581 (tp) REVERT: A 495 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.5760 (m-80) REVERT: A 985 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7859 (t0) REVERT: C 902 MET cc_start: 0.9113 (tpp) cc_final: 0.8867 (tpp) REVERT: C 1029 MET cc_start: 0.9234 (tpp) cc_final: 0.9033 (tpp) REVERT: H 83 MET cc_start: 0.5763 (mpp) cc_final: 0.5546 (mpp) REVERT: H 92 ASP cc_start: 0.8576 (t70) cc_final: 0.8341 (t0) REVERT: L 214 GLU cc_start: 0.6906 (mp0) cc_final: 0.6576 (mp0) outliers start: 29 outliers final: 19 residues processed: 104 average time/residue: 0.2002 time to fit residues: 34.4409 Evaluate side-chains 96 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain L residue 192 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 12 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 285 optimal weight: 0.7980 chunk 325 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 268 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 ASN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.091964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.057842 restraints weight = 109126.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060103 restraints weight = 50891.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.061578 restraints weight = 32883.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062492 restraints weight = 25181.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.063037 restraints weight = 21364.770| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30810 Z= 0.155 Angle : 0.591 13.586 42094 Z= 0.288 Chirality : 0.044 0.312 4924 Planarity : 0.004 0.055 5300 Dihedral : 7.023 120.012 5689 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.87 % Favored : 93.00 % Rotamer: Outliers : 1.02 % Allowed : 11.88 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.77 (0.14), residues: 3670 helix: 1.61 (0.21), residues: 678 sheet: 0.20 (0.17), residues: 921 loop : -1.67 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 22 TYR 0.018 0.001 TYR A 145 PHE 0.017 0.001 PHE B1121 TRP 0.014 0.001 TRP A 64 HIS 0.008 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00360 (30685) covalent geometry : angle 0.55464 (41767) SS BOND : bond 0.00331 ( 45) SS BOND : angle 1.12900 ( 90) hydrogen bonds : bond 0.04652 ( 1001) hydrogen bonds : angle 5.04582 ( 2700) Misc. bond : bond 0.00181 ( 1) link_BETA1-4 : bond 0.00401 ( 25) link_BETA1-4 : angle 1.94030 ( 75) link_NAG-ASN : bond 0.00443 ( 54) link_NAG-ASN : angle 2.97599 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8462 (tp) REVERT: A 495 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.5842 (m-80) REVERT: A 985 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7864 (t0) REVERT: B 904 TYR cc_start: 0.8275 (m-10) cc_final: 0.7856 (m-80) REVERT: C 258 TRP cc_start: 0.3636 (p-90) cc_final: 0.2891 (p90) REVERT: C 408 ARG cc_start: 0.8987 (ppt170) cc_final: 0.8645 (tmm160) REVERT: C 1029 MET cc_start: 0.9235 (tpp) cc_final: 0.9024 (tpp) REVERT: H 92 ASP cc_start: 0.8625 (t70) cc_final: 0.8408 (t0) REVERT: L 214 GLU cc_start: 0.6753 (mp0) cc_final: 0.6405 (mp0) outliers start: 33 outliers final: 23 residues processed: 107 average time/residue: 0.1943 time to fit residues: 34.6459 Evaluate side-chains 100 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain L residue 192 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 16 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.091060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056892 restraints weight = 110368.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059100 restraints weight = 52847.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060530 restraints weight = 34487.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061415 restraints weight = 26579.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061944 restraints weight = 22673.890| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30810 Z= 0.201 Angle : 0.623 13.181 42094 Z= 0.307 Chirality : 0.045 0.307 4924 Planarity : 0.004 0.055 5300 Dihedral : 6.970 107.383 5689 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.00 % Favored : 92.83 % Rotamer: Outliers : 1.18 % Allowed : 12.28 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.88 (0.14), residues: 3670 helix: 1.47 (0.21), residues: 677 sheet: 0.10 (0.17), residues: 929 loop : -1.71 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 22 TYR 0.019 0.001 TYR B1067 PHE 0.017 0.001 PHE B1121 TRP 0.017 0.001 TRP A 64 HIS 0.008 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00471 (30685) covalent geometry : angle 0.59007 (41767) SS BOND : bond 0.00413 ( 45) SS BOND : angle 1.33458 ( 90) hydrogen bonds : bond 0.05179 ( 1001) hydrogen bonds : angle 5.20022 ( 2700) Misc. bond : bond 0.00115 ( 1) link_BETA1-4 : bond 0.00367 ( 25) link_BETA1-4 : angle 1.63548 ( 75) link_NAG-ASN : bond 0.00468 ( 54) link_NAG-ASN : angle 2.97273 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8596 (tp) REVERT: A 451 TYR cc_start: 0.6799 (t80) cc_final: 0.6525 (m-80) REVERT: A 495 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.5928 (m-80) REVERT: A 985 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7909 (t0) REVERT: B 229 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8125 (tt) REVERT: B 904 TYR cc_start: 0.8233 (m-10) cc_final: 0.8009 (m-10) REVERT: C 258 TRP cc_start: 0.4013 (p-90) cc_final: 0.3162 (p90) REVERT: C 1029 MET cc_start: 0.9226 (tpp) cc_final: 0.8976 (tpp) REVERT: L 214 GLU cc_start: 0.6760 (mp0) cc_final: 0.6414 (mp0) outliers start: 38 outliers final: 28 residues processed: 108 average time/residue: 0.2000 time to fit residues: 35.6342 Evaluate side-chains 102 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain L residue 192 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 246 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 141 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 chunk 336 optimal weight: 0.9980 chunk 294 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 348 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.096019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.060370 restraints weight = 108759.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.062532 restraints weight = 51717.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063919 restraints weight = 33394.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064813 restraints weight = 25588.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.065353 restraints weight = 21621.926| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30810 Z= 0.128 Angle : 0.572 12.234 42094 Z= 0.280 Chirality : 0.044 0.308 4924 Planarity : 0.004 0.055 5300 Dihedral : 6.761 103.174 5689 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.99 % Favored : 93.84 % Rotamer: Outliers : 0.93 % Allowed : 12.90 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.75 (0.14), residues: 3670 helix: 1.69 (0.22), residues: 673 sheet: 0.23 (0.17), residues: 911 loop : -1.67 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 22 TYR 0.019 0.001 TYR A 145 PHE 0.015 0.001 PHE B1121 TRP 0.013 0.001 TRP A 64 HIS 0.006 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00293 (30685) covalent geometry : angle 0.53993 (41767) SS BOND : bond 0.00298 ( 45) SS BOND : angle 1.07206 ( 90) hydrogen bonds : bond 0.04491 ( 1001) hydrogen bonds : angle 4.99811 ( 2700) Misc. bond : bond 0.00093 ( 1) link_BETA1-4 : bond 0.00428 ( 25) link_BETA1-4 : angle 1.57361 ( 75) link_NAG-ASN : bond 0.00445 ( 54) link_NAG-ASN : angle 2.82029 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8575 (tp) REVERT: A 451 TYR cc_start: 0.6979 (t80) cc_final: 0.6445 (m-80) REVERT: A 495 TYR cc_start: 0.6289 (OUTLIER) cc_final: 0.5863 (m-80) REVERT: A 985 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7891 (t0) REVERT: B 229 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8083 (tt) REVERT: C 258 TRP cc_start: 0.3817 (p-90) cc_final: 0.3322 (p90) REVERT: C 902 MET cc_start: 0.9103 (tpp) cc_final: 0.8898 (tpp) REVERT: C 1029 MET cc_start: 0.9206 (tpp) cc_final: 0.8961 (tpp) REVERT: L 214 GLU cc_start: 0.6751 (mp0) cc_final: 0.6182 (mp0) outliers start: 30 outliers final: 24 residues processed: 103 average time/residue: 0.2071 time to fit residues: 35.2293 Evaluate side-chains 102 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain L residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 105 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 366 optimal weight: 1.9990 chunk 337 optimal weight: 30.0000 chunk 340 optimal weight: 9.9990 chunk 334 optimal weight: 7.9990 chunk 307 optimal weight: 6.9990 chunk 363 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 270 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.089382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055216 restraints weight = 109731.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057348 restraints weight = 53336.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058710 restraints weight = 35189.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059586 restraints weight = 27357.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.060069 restraints weight = 23396.527| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 30810 Z= 0.315 Angle : 0.736 13.416 42094 Z= 0.367 Chirality : 0.047 0.302 4924 Planarity : 0.005 0.055 5300 Dihedral : 7.149 96.401 5689 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.09 % Favored : 91.69 % Rotamer: Outliers : 1.09 % Allowed : 12.99 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.19 (0.14), residues: 3670 helix: 1.09 (0.21), residues: 679 sheet: -0.12 (0.17), residues: 929 loop : -1.84 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 22 TYR 0.040 0.002 TYR B 904 PHE 0.027 0.002 PHE B1121 TRP 0.024 0.002 TRP A 64 HIS 0.010 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00744 (30685) covalent geometry : angle 0.70485 (41767) SS BOND : bond 0.00518 ( 45) SS BOND : angle 1.65291 ( 90) hydrogen bonds : bond 0.06122 ( 1001) hydrogen bonds : angle 5.54750 ( 2700) Misc. bond : bond 0.00123 ( 1) link_BETA1-4 : bond 0.00332 ( 25) link_BETA1-4 : angle 1.71672 ( 75) link_NAG-ASN : bond 0.00544 ( 54) link_NAG-ASN : angle 3.11813 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7340 Ramachandran restraints generated. 3670 Oldfield, 0 Emsley, 3670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8829 (mt) cc_final: 0.8470 (mt) REVERT: A 434 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8546 (tp) REVERT: A 495 TYR cc_start: 0.6408 (OUTLIER) cc_final: 0.5329 (m-80) REVERT: A 985 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7949 (t0) REVERT: B 229 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8009 (tt) REVERT: C 258 TRP cc_start: 0.3672 (p-90) cc_final: 0.2912 (p90) REVERT: C 1029 MET cc_start: 0.9242 (tpp) cc_final: 0.8871 (tpp) REVERT: H 102 MET cc_start: 0.8709 (ppp) cc_final: 0.7973 (ppp) REVERT: L 214 GLU cc_start: 0.6843 (mp0) cc_final: 0.6507 (mp0) outliers start: 35 outliers final: 27 residues processed: 107 average time/residue: 0.1974 time to fit residues: 35.1486 Evaluate side-chains 103 residues out of total 3225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 99 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 264 optimal weight: 0.3980 chunk 366 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 279 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN C 30 ASN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.095716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.060248 restraints weight = 108827.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062392 restraints weight = 51260.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063792 restraints weight = 32916.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064667 restraints weight = 25082.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.065194 restraints weight = 21189.536| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30810 Z= 0.112 Angle : 0.578 11.892 42094 Z= 0.285 Chirality : 0.044 0.303 4924 Planarity : 0.004 0.055 5300 Dihedral : 6.812 96.468 5689 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.64 % Favored : 94.20 % Rotamer: Outliers : 0.96 % Allowed : 13.33 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.83 (0.14), residues: 3670 helix: 1.60 (0.21), residues: 670 sheet: 0.14 (0.17), residues: 923 loop : -1.70 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 22 TYR 0.019 0.001 TYR A 145 PHE 0.014 0.001 PHE A 275 TRP 0.015 0.001 TRP A 64 HIS 0.006 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00247 (30685) covalent geometry : angle 0.54618 (41767) SS BOND : bond 0.00292 ( 45) SS BOND : angle 1.10972 ( 90) hydrogen bonds : bond 0.04623 ( 1001) hydrogen bonds : angle 5.04780 ( 2700) Misc. bond : bond 0.00080 ( 1) link_BETA1-4 : bond 0.00458 ( 25) link_BETA1-4 : angle 1.54973 ( 75) link_NAG-ASN : bond 0.00468 ( 54) link_NAG-ASN : angle 2.83700 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7146.95 seconds wall clock time: 123 minutes 29.22 seconds (7409.22 seconds total)