Starting phenix.real_space_refine on Mon Jul 6 13:16:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kml_22926/07_2026/7kml_22926.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kml_22926/07_2026/7kml_22926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7kml_22926/07_2026/7kml_22926.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kml_22926/07_2026/7kml_22926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kml_22926/07_2026/7kml_22926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kml_22926/07_2026/7kml_22926.map" model { file = "/net/cci-nas-00/data/ceres_data/7kml_22926/07_2026/7kml_22926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kml_22926/07_2026/7kml_22926.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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 156 5.16 5 C 22239 2.51 5 N 5757 2.21 5 O 6984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 207 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35136 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8078 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 55, 'TRANS': 978} Chain breaks: 7 Chain: "B" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8078 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 55, 'TRANS': 978} Chain breaks: 7 Chain: "C" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8078 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 55, 'TRANS': 978} Chain breaks: 7 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "M" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "I" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "N" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "J" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 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 chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.97, per 1000 atoms: 0.23 Number of scatterers: 35136 At special positions: 0 Unit cell: (147.29, 148.32, 224.54, 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 156 16.00 O 6984 8.00 N 5757 7.00 C 22239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.08 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.22 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.08 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=2.07 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=2.02 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.08 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.22 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.08 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=2.07 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.08 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.22 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.08 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=2.07 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=2.02 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=2.02 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 L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 154 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 234 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.02 Simple disulfide: pdb=" SG CYS M 154 " - pdb=" SG CYS M 214 " distance=2.03 Simple disulfide: pdb=" SG CYS M 234 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 154 " - pdb=" SG CYS N 214 " distance=2.03 Simple disulfide: pdb=" SG CYS N 234 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C1134 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 709 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1074 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 331 " " NAG V 1 " - " ASN B 343 " " NAG W 1 " - " ASN B 709 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 331 " " NAG e 1 " - " ASN C 343 " " NAG f 1 " - " ASN C 709 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 78 sheets defined 20.0% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.774A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.675A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 4.172A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.775A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.675A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 4.172A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.775A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.675A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 4.172A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 143 through 147 Processing helix chain 'L' and resid 203 through 207 Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 206 Processing helix chain 'H' and resid 216 through 219 Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'M' and resid 143 through 147 Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'I' and resid 69 through 72 Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 216 through 219 Processing helix chain 'N' and resid 95 through 99 Processing helix chain 'N' and resid 143 through 147 Processing helix chain 'N' and resid 203 through 207 Processing helix chain 'J' and resid 69 through 72 Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 171 through 173 No H-bonds generated for 'chain 'J' and resid 171 through 173' Processing helix chain 'J' and resid 202 through 206 Processing helix chain 'J' and resid 216 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.336A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.491A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.034A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.479A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.863A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.411A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 7.471A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR A 495 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.705A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.653A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.125A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.241A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.336A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.491A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.034A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.478A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.863A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.411A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 448 through 454 removed outlier: 7.471A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR B 495 " --> pdb=" O TYR B 451 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.705A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.653A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.125A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 787 through 789 removed outlier: 6.241A 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 1125 removed outlier: 4.602A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.336A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.491A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.034A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.479A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.863A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.411A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 7.471A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.705A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.652A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.125A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR L 55 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 134 through 138 removed outlier: 5.427A pdb=" N TYR L 193 " --> pdb=" O ASN L 158 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 173 through 174 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 13 removed outlier: 7.217A pdb=" N TYR H 37 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR H 57 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET H 39 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AG5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU M 11 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL M 39 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR M 55 " --> pdb=" O VAL M 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU M 11 " --> pdb=" O GLU M 125 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 134 through 138 removed outlier: 5.427A pdb=" N TYR M 193 " --> pdb=" O ASN M 158 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 173 through 174 Processing sheet with id=AH1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'I' and resid 11 through 13 removed outlier: 7.217A pdb=" N TYR I 37 " --> pdb=" O TYR I 57 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR I 57 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET I 39 " --> pdb=" O GLY I 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY I 55 " --> pdb=" O MET I 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP I 41 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 166 through 169 Processing sheet with id=AH6, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AH7, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.542A pdb=" N LEU N 11 " --> pdb=" O GLU N 125 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL N 39 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR N 55 " --> pdb=" O VAL N 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.542A pdb=" N LEU N 11 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 134 through 138 removed outlier: 5.427A pdb=" N TYR N 193 " --> pdb=" O ASN N 158 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 173 through 174 Processing sheet with id=AI2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AI3, first strand: chain 'J' and resid 11 through 13 removed outlier: 7.217A pdb=" N TYR J 37 " --> pdb=" O TYR J 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR J 57 " --> pdb=" O TYR J 37 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET J 39 " --> pdb=" O GLY J 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY J 55 " --> pdb=" O MET J 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP J 41 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR J 191 " --> pdb=" O ASP J 159 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR J 191 " --> pdb=" O ASP J 159 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 166 through 169 1481 hydrogen bonds defined for protein. 3897 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: 11.19 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 7113 1.32 - 1.47: 12747 1.47 - 1.61: 15822 1.61 - 1.75: 48 1.75 - 1.89: 186 Bond restraints: 35916 Sorted by residual: bond pdb=" NE ARG B 78 " pdb=" CZ ARG B 78 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.54e+01 bond pdb=" NE ARG C 78 " pdb=" CZ ARG C 78 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.50e+01 bond pdb=" NE ARG A 78 " pdb=" CZ ARG A 78 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.50e+01 bond pdb=" CB HIS H 215 " pdb=" CG HIS H 215 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" CB HIS J 215 " pdb=" CG HIS J 215 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.04e+01 ... (remaining 35911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 41004 2.40 - 4.80: 6513 4.80 - 7.20: 1160 7.20 - 9.60: 161 9.60 - 12.00: 29 Bond angle restraints: 48867 Sorted by residual: angle pdb=" N LYS A 97 " pdb=" CA LYS A 97 " pdb=" C LYS A 97 " ideal model delta sigma weight residual 114.04 102.04 12.00 1.24e+00 6.50e-01 9.37e+01 angle pdb=" N LYS C 97 " pdb=" CA LYS C 97 " pdb=" C LYS C 97 " ideal model delta sigma weight residual 114.04 102.04 12.00 1.24e+00 6.50e-01 9.36e+01 angle pdb=" N LYS B 97 " pdb=" CA LYS B 97 " pdb=" C LYS B 97 " ideal model delta sigma weight residual 114.04 102.06 11.98 1.24e+00 6.50e-01 9.34e+01 angle pdb=" C CYS A 336 " pdb=" N PRO A 337 " pdb=" CA PRO A 337 " ideal model delta sigma weight residual 119.82 128.42 -8.60 9.80e-01 1.04e+00 7.71e+01 angle pdb=" C CYS C 336 " pdb=" N PRO C 337 " pdb=" CA PRO C 337 " ideal model delta sigma weight residual 119.82 128.41 -8.59 9.80e-01 1.04e+00 7.69e+01 ... (remaining 48862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20068 17.98 - 35.96: 497 35.96 - 53.94: 162 53.94 - 71.93: 57 71.93 - 89.91: 42 Dihedral angle restraints: 20826 sinusoidal: 8034 harmonic: 12792 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual 93.00 -177.09 -89.91 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 -177.10 -89.90 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 -177.11 -89.89 1 1.00e+01 1.00e-02 9.58e+01 ... (remaining 20823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4375 0.110 - 0.219: 1202 0.219 - 0.329: 171 0.329 - 0.438: 11 0.438 - 0.548: 7 Chirality restraints: 5766 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.76e+01 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.64e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.53e+01 ... (remaining 5763 not shown) Planarity restraints: 6249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 42 " 0.073 2.00e-02 2.50e+03 4.11e-02 3.38e+01 pdb=" CG TYR L 42 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR L 42 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR L 42 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR L 42 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR L 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR L 42 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 42 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 42 " 0.073 2.00e-02 2.50e+03 4.11e-02 3.37e+01 pdb=" CG TYR M 42 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR M 42 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR M 42 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR M 42 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR M 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR M 42 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR M 42 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 42 " 0.073 2.00e-02 2.50e+03 4.11e-02 3.37e+01 pdb=" CG TYR N 42 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR N 42 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR N 42 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR N 42 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR N 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR N 42 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR N 42 " 0.065 2.00e-02 2.50e+03 ... (remaining 6246 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 14504 2.91 - 3.41: 31878 3.41 - 3.91: 61921 3.91 - 4.40: 70570 4.40 - 4.90: 112736 Nonbonded interactions: 291609 Sorted by model distance: nonbonded pdb=" C4 NAG h 1 " pdb=" O5 NAG h 2 " model vdw 2.415 2.776 nonbonded pdb=" C4 NAG P 1 " pdb=" O5 NAG P 2 " model vdw 2.415 2.776 nonbonded pdb=" C4 NAG Y 1 " pdb=" O5 NAG Y 2 " model vdw 2.415 2.776 nonbonded pdb=" NZ LYS J 221 " pdb=" OD2 ASP J 223 " model vdw 2.416 3.120 nonbonded pdb=" NZ LYS I 221 " pdb=" OD2 ASP I 223 " model vdw 2.416 3.120 ... (remaining 291604 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'U' selection = chain 'V' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.910 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.220 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.018 0.188 36051 Z= 0.941 Angle : 1.879 12.002 49215 Z= 1.264 Chirality : 0.099 0.548 5766 Planarity : 0.009 0.042 6204 Dihedral : 10.572 89.657 12447 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.39 % Allowed : 0.76 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.45 (0.12), residues: 4353 helix: -0.37 (0.17), residues: 690 sheet: 0.74 (0.14), residues: 1269 loop : 0.40 (0.13), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1000 TYR 0.074 0.011 TYR B 204 PHE 0.039 0.007 PHE B 140 TRP 0.067 0.013 TRP A 353 HIS 0.009 0.002 HIS L 108 Details of bonding type rmsd/Z covalent geometry : bond 0.01798 / 0.94 (35916) covalent geometry : angle 1.87487 / 1.27 (48867) SS BOND : bond 0.04722 / 3.34 ( 57) SS BOND : angle 3.04255 / 2.05 ( 114) hydrogen bonds : bond 0.18008 / 11.44 ( 1430) hydrogen bonds : angle 8.80310 / 6.08 ( 3897) link_BETA1-4 : bond 0.00348 / 0.22 ( 33) link_BETA1-4 : angle 1.36828 / 0.94 ( 99) link_NAG-ASN : bond 0.00436 / 0.26 ( 45) link_NAG-ASN : angle 2.34110 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 667 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.9546 (m-10) cc_final: 0.8998 (m-80) REVERT: A 369 TYR cc_start: 0.9016 (t80) cc_final: 0.8729 (t80) REVERT: A 727 LEU cc_start: 0.9356 (mp) cc_final: 0.9081 (mt) REVERT: A 759 PHE cc_start: 0.8526 (t80) cc_final: 0.7968 (t80) REVERT: A 763 LEU cc_start: 0.9549 (mt) cc_final: 0.8941 (mp) REVERT: A 781 VAL cc_start: 0.9559 (t) cc_final: 0.9282 (m) REVERT: A 826 VAL cc_start: 0.8347 (t) cc_final: 0.8125 (t) REVERT: A 878 LEU cc_start: 0.9490 (mt) cc_final: 0.9264 (mt) REVERT: A 886 TRP cc_start: 0.6804 (p-90) cc_final: 0.6521 (p-90) REVERT: A 919 ASN cc_start: 0.8948 (m-40) cc_final: 0.8538 (t0) REVERT: A 936 ASP cc_start: 0.9241 (m-30) cc_final: 0.8678 (t0) REVERT: A 1014 ARG cc_start: 0.9056 (mtt180) cc_final: 0.8662 (ttm170) REVERT: A 1021 SER cc_start: 0.9672 (m) cc_final: 0.9093 (t) REVERT: A 1052 PHE cc_start: 0.9070 (m-80) cc_final: 0.8768 (m-10) REVERT: A 1125 ASN cc_start: 0.7713 (t0) cc_final: 0.7491 (t0) REVERT: B 175 PHE cc_start: 0.9515 (m-10) cc_final: 0.8978 (m-80) REVERT: B 318 PHE cc_start: 0.8339 (t80) cc_final: 0.8074 (t80) REVERT: B 369 TYR cc_start: 0.9057 (t80) cc_final: 0.8797 (t80) REVERT: B 610 VAL cc_start: 0.9387 (t) cc_final: 0.9098 (p) REVERT: B 727 LEU cc_start: 0.9388 (mp) cc_final: 0.8893 (mt) REVERT: B 759 PHE cc_start: 0.8612 (t80) cc_final: 0.7825 (t80) REVERT: B 763 LEU cc_start: 0.9598 (mt) cc_final: 0.8984 (mp) REVERT: B 781 VAL cc_start: 0.9512 (t) cc_final: 0.9230 (m) REVERT: B 878 LEU cc_start: 0.9513 (mt) cc_final: 0.9250 (mt) REVERT: B 886 TRP cc_start: 0.6832 (p-90) cc_final: 0.6398 (p-90) REVERT: B 919 ASN cc_start: 0.8906 (m-40) cc_final: 0.8519 (t0) REVERT: B 936 ASP cc_start: 0.9228 (m-30) cc_final: 0.8691 (t0) REVERT: B 1014 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8741 (mtm-85) REVERT: B 1040 VAL cc_start: 0.8769 (t) cc_final: 0.8536 (t) REVERT: B 1125 ASN cc_start: 0.7746 (t0) cc_final: 0.7526 (t0) REVERT: C 175 PHE cc_start: 0.9566 (m-10) cc_final: 0.9175 (m-80) REVERT: C 318 PHE cc_start: 0.8307 (t80) cc_final: 0.8005 (t80) REVERT: C 369 TYR cc_start: 0.9055 (t80) cc_final: 0.8801 (t80) REVERT: C 610 VAL cc_start: 0.9336 (t) cc_final: 0.9025 (p) REVERT: C 727 LEU cc_start: 0.9353 (mp) cc_final: 0.8847 (mt) REVERT: C 759 PHE cc_start: 0.8527 (t80) cc_final: 0.7577 (t80) REVERT: C 763 LEU cc_start: 0.9632 (mt) cc_final: 0.9008 (mp) REVERT: C 780 GLU cc_start: 0.8830 (tp30) cc_final: 0.8503 (tp30) REVERT: C 781 VAL cc_start: 0.9501 (t) cc_final: 0.9231 (m) REVERT: C 826 VAL cc_start: 0.8091 (t) cc_final: 0.7841 (t) REVERT: C 919 ASN cc_start: 0.8846 (m-40) cc_final: 0.8481 (t0) REVERT: C 922 LEU cc_start: 0.9475 (mp) cc_final: 0.9267 (mm) REVERT: C 936 ASP cc_start: 0.9213 (m-30) cc_final: 0.8689 (t0) REVERT: C 1014 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8869 (ttm170) REVERT: C 1021 SER cc_start: 0.9670 (m) cc_final: 0.9083 (t) REVERT: C 1031 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7985 (mt-10) REVERT: C 1125 ASN cc_start: 0.7675 (t0) cc_final: 0.7454 (t0) REVERT: L 4 MET cc_start: 0.7687 (mmm) cc_final: 0.4264 (tpp) REVERT: H 39 MET cc_start: 0.5272 (mmp) cc_final: 0.4908 (mpp) REVERT: M 4 MET cc_start: 0.7317 (mmm) cc_final: 0.3736 (tpp) REVERT: I 39 MET cc_start: 0.5240 (mmp) cc_final: 0.4889 (mpp) REVERT: N 4 MET cc_start: 0.7524 (mmm) cc_final: 0.4431 (tpp) outliers start: 15 outliers final: 10 residues processed: 682 average time/residue: 0.2488 time to fit residues: 262.5502 Evaluate side-chains 335 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 325 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 440 ASN A 501 ASN A 544 ASN B 49 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B 501 ASN B 544 ASN B 762 GLN B 965 GLN C 49 HIS C 440 ASN C 501 ASN C 544 ASN C 690 GLN C 762 GLN C 907 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.064404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.052996 restraints weight = 352854.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.054262 restraints weight = 179781.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.055031 restraints weight = 111892.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.055535 restraints weight = 79919.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.055825 restraints weight = 63436.149| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 36051 Z= 0.250 Angle : 0.858 17.806 49215 Z= 0.453 Chirality : 0.049 0.294 5766 Planarity : 0.005 0.048 6204 Dihedral : 5.982 50.475 4748 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.83 % Allowed : 6.94 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.40 (0.12), residues: 4353 helix: 0.94 (0.19), residues: 696 sheet: 0.45 (0.14), residues: 1323 loop : 0.06 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.026 0.002 TYR A1067 PHE 0.025 0.003 PHE B 377 TRP 0.022 0.003 TRP B 353 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.25 (35916) covalent geometry : angle 0.83076 / 0.45 (48867) SS BOND : bond 0.00412 / 0.28 ( 57) SS BOND : angle 1.27190 / 0.88 ( 114) hydrogen bonds : bond 0.06332 / 4.04 ( 1430) hydrogen bonds : angle 7.29254 / 5.03 ( 3897) link_BETA1-4 : bond 0.00569 / 0.36 ( 33) link_BETA1-4 : angle 1.57064 / 1.07 ( 99) link_NAG-ASN : bond 0.00474 / 0.29 ( 45) link_NAG-ASN : angle 3.94375 / 3.09 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 348 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 LEU cc_start: 0.8862 (tp) cc_final: 0.8571 (pp) REVERT: A 740 MET cc_start: 0.8424 (mmt) cc_final: 0.7878 (mmt) REVERT: A 919 ASN cc_start: 0.9003 (m-40) cc_final: 0.8483 (t0) REVERT: A 936 ASP cc_start: 0.9078 (m-30) cc_final: 0.8708 (t0) REVERT: A 1002 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8159 (tm-30) REVERT: A 1021 SER cc_start: 0.9694 (m) cc_final: 0.9126 (t) REVERT: A 1029 MET cc_start: 0.7267 (tmm) cc_final: 0.6750 (tmm) REVERT: A 1047 TYR cc_start: 0.4326 (OUTLIER) cc_final: 0.3030 (m-80) REVERT: A 1123 SER cc_start: 0.7719 (t) cc_final: 0.7379 (t) REVERT: A 1125 ASN cc_start: 0.7943 (t0) cc_final: 0.7711 (t0) REVERT: B 513 LEU cc_start: 0.8875 (tp) cc_final: 0.8596 (pp) REVERT: B 759 PHE cc_start: 0.8292 (t80) cc_final: 0.7100 (t80) REVERT: B 776 LYS cc_start: 0.9476 (tmtt) cc_final: 0.9207 (tptp) REVERT: B 780 GLU cc_start: 0.9183 (tp30) cc_final: 0.8798 (tp30) REVERT: B 796 ASP cc_start: 0.8848 (m-30) cc_final: 0.8594 (p0) REVERT: B 886 TRP cc_start: 0.6976 (p-90) cc_final: 0.6585 (p-90) REVERT: B 902 MET cc_start: 0.9007 (tpp) cc_final: 0.8446 (tpp) REVERT: B 916 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8196 (pp) REVERT: B 919 ASN cc_start: 0.8966 (m-40) cc_final: 0.8464 (t0) REVERT: B 936 ASP cc_start: 0.9114 (m-30) cc_final: 0.8721 (t0) REVERT: B 1001 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9432 (pp) REVERT: B 1052 PHE cc_start: 0.9349 (m-10) cc_final: 0.9054 (m-10) REVERT: B 1125 ASN cc_start: 0.7997 (t0) cc_final: 0.7766 (t0) REVERT: C 513 LEU cc_start: 0.8966 (tp) cc_final: 0.8617 (pp) REVERT: C 709 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8103 (p0) REVERT: C 740 MET cc_start: 0.8478 (mmt) cc_final: 0.8040 (mmt) REVERT: C 796 ASP cc_start: 0.8854 (m-30) cc_final: 0.8514 (p0) REVERT: C 869 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8838 (ptp) REVERT: C 902 MET cc_start: 0.9332 (mmm) cc_final: 0.8768 (mmm) REVERT: C 919 ASN cc_start: 0.8983 (m-40) cc_final: 0.8434 (t0) REVERT: C 936 ASP cc_start: 0.9079 (m-30) cc_final: 0.8695 (t0) REVERT: C 1021 SER cc_start: 0.9650 (m) cc_final: 0.9314 (p) REVERT: C 1029 MET cc_start: 0.7401 (tmm) cc_final: 0.7003 (tmm) REVERT: C 1040 VAL cc_start: 0.9094 (t) cc_final: 0.8882 (m) REVERT: C 1101 HIS cc_start: 0.8624 (m90) cc_final: 0.8418 (m90) REVERT: C 1125 ASN cc_start: 0.7892 (t0) cc_final: 0.7634 (t0) REVERT: L 1 ASP cc_start: 0.8038 (m-30) cc_final: 0.7702 (t0) REVERT: L 4 MET cc_start: 0.5161 (mmm) cc_final: 0.3904 (tpp) REVERT: L 162 ARG cc_start: 0.8992 (tpt90) cc_final: 0.8432 (tpp80) REVERT: H 39 MET cc_start: 0.5143 (mmp) cc_final: 0.4847 (mpp) REVERT: M 4 MET cc_start: 0.5060 (mmm) cc_final: 0.3697 (tpp) REVERT: M 162 ARG cc_start: 0.8968 (tpt90) cc_final: 0.8357 (tpp80) REVERT: I 81 ASP cc_start: 0.7081 (p0) cc_final: 0.6821 (p0) REVERT: I 115 MET cc_start: 0.8277 (tpp) cc_final: 0.7922 (tpp) REVERT: N 4 MET cc_start: 0.5863 (mmm) cc_final: 0.4416 (tpp) REVERT: N 162 ARG cc_start: 0.9025 (tpt90) cc_final: 0.8434 (tpp80) REVERT: J 81 ASP cc_start: 0.7323 (p0) cc_final: 0.7036 (p0) REVERT: J 115 MET cc_start: 0.8093 (mmm) cc_final: 0.7781 (mmt) outliers start: 70 outliers final: 45 residues processed: 404 average time/residue: 0.2395 time to fit residues: 150.8127 Evaluate side-chains 306 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 82 optimal weight: 3.9990 chunk 409 optimal weight: 0.6980 chunk 316 optimal weight: 8.9990 chunk 424 optimal weight: 9.9990 chunk 177 optimal weight: 0.6980 chunk 318 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 365 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 218 GLN A 901 GLN A 926 GLN A 955 ASN A1011 GLN A1083 HIS B 173 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN L 3 GLN M 3 GLN N 3 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.062445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.050874 restraints weight = 355741.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.052139 restraints weight = 180038.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.052902 restraints weight = 111073.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.053373 restraints weight = 79275.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.053663 restraints weight = 63016.013| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 36051 Z= 0.198 Angle : 0.744 13.501 49215 Z= 0.384 Chirality : 0.047 0.255 5766 Planarity : 0.005 0.053 6204 Dihedral : 5.441 25.923 4730 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.88 % Allowed : 7.15 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.28 (0.12), residues: 4353 helix: 1.05 (0.19), residues: 681 sheet: 0.32 (0.13), residues: 1335 loop : -0.06 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 34 TYR 0.049 0.002 TYR A1067 PHE 0.032 0.002 PHE C 782 TRP 0.021 0.002 TRP A 152 HIS 0.010 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (35916) covalent geometry : angle 0.72539 / 0.38 (48867) SS BOND : bond 0.00369 / 0.26 ( 57) SS BOND : angle 0.95738 / 0.64 ( 114) hydrogen bonds : bond 0.05268 / 3.37 ( 1430) hydrogen bonds : angle 6.88370 / 4.74 ( 3897) link_BETA1-4 : bond 0.00516 / 0.32 ( 33) link_BETA1-4 : angle 1.67313 / 1.14 ( 99) link_NAG-ASN : bond 0.00554 / 0.30 ( 45) link_NAG-ASN : angle 2.94950 / 2.26 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 272 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.7970 (mmtm) cc_final: 0.7755 (mmtm) REVERT: A 513 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8585 (pp) REVERT: A 759 PHE cc_start: 0.8845 (t80) cc_final: 0.8555 (t80) REVERT: A 775 ASP cc_start: 0.8843 (m-30) cc_final: 0.8633 (m-30) REVERT: A 902 MET cc_start: 0.9249 (mmm) cc_final: 0.9046 (tpp) REVERT: A 922 LEU cc_start: 0.9535 (mm) cc_final: 0.9290 (mp) REVERT: A 936 ASP cc_start: 0.9087 (m-30) cc_final: 0.8725 (t0) REVERT: A 945 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8976 (pp) REVERT: A 1002 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8316 (tm-30) REVERT: A 1021 SER cc_start: 0.9746 (m) cc_final: 0.9442 (p) REVERT: A 1047 TYR cc_start: 0.4590 (OUTLIER) cc_final: 0.3273 (m-80) REVERT: A 1123 SER cc_start: 0.7844 (t) cc_final: 0.7512 (t) REVERT: A 1125 ASN cc_start: 0.8055 (t0) cc_final: 0.7820 (t0) REVERT: B 513 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8549 (pp) REVERT: B 775 ASP cc_start: 0.8877 (m-30) cc_final: 0.8628 (m-30) REVERT: B 902 MET cc_start: 0.8918 (tpp) cc_final: 0.8523 (tpp) REVERT: B 916 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8249 (pp) REVERT: B 936 ASP cc_start: 0.9099 (m-30) cc_final: 0.8714 (t0) REVERT: B 1001 LEU cc_start: 0.9723 (tt) cc_final: 0.9466 (pp) REVERT: B 1052 PHE cc_start: 0.9556 (m-80) cc_final: 0.9304 (m-10) REVERT: B 1123 SER cc_start: 0.7756 (t) cc_final: 0.7417 (t) REVERT: B 1125 ASN cc_start: 0.8071 (t0) cc_final: 0.7820 (t0) REVERT: C 513 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8683 (pp) REVERT: C 775 ASP cc_start: 0.8853 (m-30) cc_final: 0.8532 (m-30) REVERT: C 936 ASP cc_start: 0.9050 (m-30) cc_final: 0.8709 (t0) REVERT: C 1005 GLN cc_start: 0.9442 (mm-40) cc_final: 0.9202 (mm-40) REVERT: C 1021 SER cc_start: 0.9697 (m) cc_final: 0.9393 (p) REVERT: C 1038 LYS cc_start: 0.9550 (mttp) cc_final: 0.9232 (mmmt) REVERT: C 1123 SER cc_start: 0.7886 (t) cc_final: 0.7600 (t) REVERT: C 1125 ASN cc_start: 0.8085 (t0) cc_final: 0.7815 (t0) REVERT: L 4 MET cc_start: 0.5740 (mmm) cc_final: 0.5186 (tpp) REVERT: H 91 MET cc_start: 0.7028 (mpp) cc_final: 0.6623 (mpp) REVERT: H 115 MET cc_start: 0.7976 (mmm) cc_final: 0.7484 (tpp) REVERT: H 159 ASP cc_start: 0.9550 (m-30) cc_final: 0.9209 (p0) REVERT: M 4 MET cc_start: 0.5628 (mmm) cc_final: 0.4876 (tpp) REVERT: I 39 MET cc_start: 0.5576 (mpp) cc_final: 0.4479 (mmm) REVERT: I 91 MET cc_start: 0.7126 (mpp) cc_final: 0.6744 (mpp) REVERT: I 159 ASP cc_start: 0.9567 (m-30) cc_final: 0.9233 (p0) REVERT: N 4 MET cc_start: 0.5998 (mmm) cc_final: 0.4938 (tpp) REVERT: J 91 MET cc_start: 0.7283 (mpp) cc_final: 0.6951 (mpp) REVERT: J 115 MET cc_start: 0.8355 (mmm) cc_final: 0.7924 (mmt) REVERT: J 159 ASP cc_start: 0.9550 (m-30) cc_final: 0.9135 (p0) outliers start: 110 outliers final: 63 residues processed: 362 average time/residue: 0.2227 time to fit residues: 127.7123 Evaluate side-chains 318 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 249 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 229 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain I residue 229 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 221 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 378 optimal weight: 0.0060 chunk 136 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 398 optimal weight: 6.9990 chunk 373 optimal weight: 30.0000 chunk 349 optimal weight: 0.0980 chunk 357 optimal weight: 0.8980 chunk 421 optimal weight: 9.9990 chunk 307 optimal weight: 7.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 239 GLN B 239 GLN B 762 GLN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 239 GLN C 901 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 108 HIS M 3 GLN M 108 HIS N 3 GLN N 108 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.056558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.041090 restraints weight = 284585.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.042387 restraints weight = 164836.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.043261 restraints weight = 111484.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.043858 restraints weight = 83709.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.044265 restraints weight = 67870.750| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 36051 Z= 0.146 Angle : 0.674 12.693 49215 Z= 0.344 Chirality : 0.045 0.237 5766 Planarity : 0.004 0.053 6204 Dihedral : 5.109 23.343 4730 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.36 % Allowed : 8.75 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.22 (0.13), residues: 4353 helix: 1.13 (0.20), residues: 684 sheet: 0.21 (0.13), residues: 1335 loop : -0.09 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1039 TYR 0.043 0.002 TYR A1067 PHE 0.025 0.002 PHE B 759 TRP 0.016 0.002 TRP A 152 HIS 0.007 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (35916) covalent geometry : angle 0.65540 / 0.34 (48867) SS BOND : bond 0.00330 / 0.24 ( 57) SS BOND : angle 0.92836 / 0.63 ( 114) hydrogen bonds : bond 0.04702 / 3.00 ( 1430) hydrogen bonds : angle 6.52951 / 4.49 ( 3897) link_BETA1-4 : bond 0.00542 / 0.34 ( 33) link_BETA1-4 : angle 1.60149 / 1.09 ( 99) link_NAG-ASN : bond 0.00446 / 0.23 ( 45) link_NAG-ASN : angle 2.70189 / 2.08 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 260 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8069 (t80) cc_final: 0.7776 (t80) REVERT: A 226 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8746 (mt) REVERT: A 513 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8745 (pp) REVERT: A 725 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 775 ASP cc_start: 0.8890 (m-30) cc_final: 0.8645 (m-30) REVERT: A 780 GLU cc_start: 0.9153 (tp30) cc_final: 0.8820 (mm-30) REVERT: A 869 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8589 (ptp) REVERT: A 936 ASP cc_start: 0.9164 (m-30) cc_final: 0.8782 (t0) REVERT: A 945 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8968 (pp) REVERT: A 1021 SER cc_start: 0.9732 (m) cc_final: 0.9470 (p) REVERT: A 1047 TYR cc_start: 0.4088 (OUTLIER) cc_final: 0.3296 (m-80) REVERT: A 1050 MET cc_start: 0.8598 (mtp) cc_final: 0.8190 (mtp) REVERT: A 1123 SER cc_start: 0.7710 (t) cc_final: 0.7363 (t) REVERT: A 1125 ASN cc_start: 0.8143 (t0) cc_final: 0.7893 (t0) REVERT: B 513 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8772 (pp) REVERT: B 725 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8069 (tm-30) REVERT: B 775 ASP cc_start: 0.8935 (m-30) cc_final: 0.8695 (m-30) REVERT: B 902 MET cc_start: 0.8998 (tpp) cc_final: 0.8581 (tpp) REVERT: B 916 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8357 (pp) REVERT: B 936 ASP cc_start: 0.9160 (m-30) cc_final: 0.8764 (t0) REVERT: B 1001 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9488 (pp) REVERT: B 1021 SER cc_start: 0.9674 (m) cc_final: 0.9278 (t) REVERT: B 1050 MET cc_start: 0.8643 (mtp) cc_final: 0.7944 (mtp) REVERT: B 1052 PHE cc_start: 0.9529 (m-80) cc_final: 0.9247 (m-10) REVERT: B 1123 SER cc_start: 0.7839 (t) cc_final: 0.7483 (t) REVERT: B 1125 ASN cc_start: 0.8106 (t0) cc_final: 0.7808 (t0) REVERT: C 513 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8815 (pp) REVERT: C 775 ASP cc_start: 0.8867 (m-30) cc_final: 0.8452 (m-30) REVERT: C 776 LYS cc_start: 0.9352 (tmtt) cc_final: 0.9096 (tptp) REVERT: C 780 GLU cc_start: 0.9044 (tp30) cc_final: 0.8777 (tp30) REVERT: C 869 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8794 (ptp) REVERT: C 936 ASP cc_start: 0.9147 (m-30) cc_final: 0.8768 (t0) REVERT: C 1001 LEU cc_start: 0.9832 (tp) cc_final: 0.9353 (pp) REVERT: C 1005 GLN cc_start: 0.9473 (mm-40) cc_final: 0.9247 (mm-40) REVERT: C 1021 SER cc_start: 0.9675 (m) cc_final: 0.9381 (p) REVERT: C 1038 LYS cc_start: 0.9549 (mttp) cc_final: 0.8851 (mttt) REVERT: C 1040 VAL cc_start: 0.9247 (m) cc_final: 0.8961 (p) REVERT: C 1123 SER cc_start: 0.7750 (t) cc_final: 0.7468 (t) REVERT: C 1125 ASN cc_start: 0.8128 (t0) cc_final: 0.7863 (t0) REVERT: L 4 MET cc_start: 0.6382 (mmm) cc_final: 0.6039 (tpp) REVERT: H 39 MET cc_start: 0.5674 (mpp) cc_final: 0.5289 (mmm) REVERT: H 91 MET cc_start: 0.7175 (mpp) cc_final: 0.6760 (mpp) REVERT: H 115 MET cc_start: 0.7826 (mmm) cc_final: 0.7312 (tpp) REVERT: H 159 ASP cc_start: 0.9457 (m-30) cc_final: 0.9008 (p0) REVERT: M 4 MET cc_start: 0.5765 (mmm) cc_final: 0.5149 (tpp) REVERT: I 39 MET cc_start: 0.5656 (mpp) cc_final: 0.4487 (mmm) REVERT: I 91 MET cc_start: 0.7010 (mpp) cc_final: 0.6591 (mpp) REVERT: I 159 ASP cc_start: 0.9458 (m-30) cc_final: 0.9027 (p0) REVERT: N 4 MET cc_start: 0.6380 (mmm) cc_final: 0.5682 (tpp) REVERT: J 81 ASP cc_start: 0.7077 (p0) cc_final: 0.6822 (p0) REVERT: J 91 MET cc_start: 0.7226 (mpp) cc_final: 0.6910 (mpp) REVERT: J 115 MET cc_start: 0.8384 (mmm) cc_final: 0.7912 (mmt) REVERT: J 159 ASP cc_start: 0.9452 (m-30) cc_final: 0.8994 (p0) outliers start: 90 outliers final: 57 residues processed: 334 average time/residue: 0.2445 time to fit residues: 130.3908 Evaluate side-chains 287 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 221 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 314 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 257 optimal weight: 0.4980 chunk 315 optimal weight: 8.9990 chunk 376 optimal weight: 20.0000 chunk 413 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 380 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN A 935 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.055910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.040619 restraints weight = 294335.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.041913 restraints weight = 166985.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.042769 restraints weight = 111848.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.043359 restraints weight = 83659.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.043731 restraints weight = 67654.334| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 36051 Z= 0.152 Angle : 0.660 12.072 49215 Z= 0.334 Chirality : 0.045 0.301 5766 Planarity : 0.004 0.052 6204 Dihedral : 4.970 21.635 4730 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % Rotamer: Outliers : 2.57 % Allowed : 9.45 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4353 helix: 1.36 (0.20), residues: 666 sheet: 0.20 (0.14), residues: 1290 loop : -0.01 (0.13), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1107 TYR 0.039 0.001 TYR A1067 PHE 0.019 0.002 PHE B 759 TRP 0.011 0.001 TRP C 436 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (35916) covalent geometry : angle 0.64208 / 0.33 (48867) SS BOND : bond 0.00325 / 0.23 ( 57) SS BOND : angle 0.88080 / 0.60 ( 114) hydrogen bonds : bond 0.04417 / 2.84 ( 1430) hydrogen bonds : angle 6.35338 / 4.36 ( 3897) link_BETA1-4 : bond 0.00502 / 0.32 ( 33) link_BETA1-4 : angle 1.64147 / 1.11 ( 99) link_NAG-ASN : bond 0.00445 / 0.23 ( 45) link_NAG-ASN : angle 2.61524 / 2.00 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 245 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8116 (t80) cc_final: 0.7846 (t80) REVERT: A 226 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8903 (mt) REVERT: A 513 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8747 (pp) REVERT: A 725 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 775 ASP cc_start: 0.8860 (m-30) cc_final: 0.8484 (m-30) REVERT: A 904 TYR cc_start: 0.9008 (m-10) cc_final: 0.8764 (m-10) REVERT: A 936 ASP cc_start: 0.9167 (m-30) cc_final: 0.8800 (t0) REVERT: A 945 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8903 (pp) REVERT: A 1017 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8910 (pp20) REVERT: A 1021 SER cc_start: 0.9743 (m) cc_final: 0.9505 (p) REVERT: A 1038 LYS cc_start: 0.9554 (mttt) cc_final: 0.9076 (mmmt) REVERT: A 1047 TYR cc_start: 0.4508 (OUTLIER) cc_final: 0.3841 (m-80) REVERT: A 1123 SER cc_start: 0.7703 (t) cc_final: 0.7353 (t) REVERT: A 1125 ASN cc_start: 0.8267 (t0) cc_final: 0.8029 (t0) REVERT: B 513 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8805 (pp) REVERT: B 725 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 775 ASP cc_start: 0.8862 (m-30) cc_final: 0.8608 (m-30) REVERT: B 902 MET cc_start: 0.9011 (tpp) cc_final: 0.8635 (tpp) REVERT: B 916 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8448 (pp) REVERT: B 936 ASP cc_start: 0.9170 (m-30) cc_final: 0.8769 (t0) REVERT: B 1001 LEU cc_start: 0.9787 (tt) cc_final: 0.9493 (pp) REVERT: B 1021 SER cc_start: 0.9712 (m) cc_final: 0.9425 (p) REVERT: B 1038 LYS cc_start: 0.9479 (mttt) cc_final: 0.9018 (mmmt) REVERT: B 1052 PHE cc_start: 0.9538 (m-80) cc_final: 0.9261 (m-10) REVERT: B 1123 SER cc_start: 0.7909 (t) cc_final: 0.7527 (t) REVERT: B 1125 ASN cc_start: 0.8217 (t0) cc_final: 0.7934 (t0) REVERT: C 175 PHE cc_start: 0.9583 (m-80) cc_final: 0.9264 (m-80) REVERT: C 513 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8809 (pp) REVERT: C 773 GLU cc_start: 0.9290 (tt0) cc_final: 0.8013 (tm-30) REVERT: C 775 ASP cc_start: 0.8823 (m-30) cc_final: 0.8436 (m-30) REVERT: C 869 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8804 (ptp) REVERT: C 936 ASP cc_start: 0.9149 (m-30) cc_final: 0.8784 (t0) REVERT: C 1001 LEU cc_start: 0.9821 (tp) cc_final: 0.9406 (pp) REVERT: C 1021 SER cc_start: 0.9692 (m) cc_final: 0.9429 (p) REVERT: C 1031 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8537 (mm-30) REVERT: C 1123 SER cc_start: 0.7693 (t) cc_final: 0.7397 (t) REVERT: C 1125 ASN cc_start: 0.8213 (t0) cc_final: 0.7945 (t0) REVERT: L 4 MET cc_start: 0.6611 (mmm) cc_final: 0.6038 (tpp) REVERT: L 11 LEU cc_start: 0.9522 (tt) cc_final: 0.9210 (pp) REVERT: H 39 MET cc_start: 0.5650 (mpp) cc_final: 0.5277 (mmm) REVERT: H 91 MET cc_start: 0.7076 (mpp) cc_final: 0.6667 (mpp) REVERT: H 115 MET cc_start: 0.7587 (mmm) cc_final: 0.7057 (tpp) REVERT: H 159 ASP cc_start: 0.9482 (m-30) cc_final: 0.9061 (p0) REVERT: M 4 MET cc_start: 0.6225 (mmm) cc_final: 0.5539 (tpp) REVERT: M 11 LEU cc_start: 0.9487 (tt) cc_final: 0.9233 (pp) REVERT: I 39 MET cc_start: 0.5659 (mpp) cc_final: 0.5286 (mmm) REVERT: I 91 MET cc_start: 0.6970 (mpp) cc_final: 0.6587 (mpp) REVERT: I 159 ASP cc_start: 0.9479 (m-30) cc_final: 0.9069 (p0) REVERT: N 4 MET cc_start: 0.6569 (mmm) cc_final: 0.5833 (tpp) REVERT: J 91 MET cc_start: 0.7173 (mpp) cc_final: 0.6855 (mpp) REVERT: J 115 MET cc_start: 0.8449 (mmm) cc_final: 0.7892 (mmm) REVERT: J 159 ASP cc_start: 0.9439 (m-30) cc_final: 0.9029 (p0) REVERT: J 225 LYS cc_start: 0.9245 (tptt) cc_final: 0.9032 (tptp) outliers start: 98 outliers final: 64 residues processed: 323 average time/residue: 0.2377 time to fit residues: 122.6550 Evaluate side-chains 296 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 224 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 414 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 280 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 926 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.054714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.039422 restraints weight = 289195.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.040667 restraints weight = 165492.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.041504 restraints weight = 111629.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.042084 restraints weight = 83669.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.042467 restraints weight = 67776.218| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 36051 Z= 0.164 Angle : 0.651 11.528 49215 Z= 0.329 Chirality : 0.044 0.310 5766 Planarity : 0.004 0.080 6204 Dihedral : 4.892 22.138 4728 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 2.38 % Allowed : 10.16 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4353 helix: 1.35 (0.20), residues: 684 sheet: 0.19 (0.14), residues: 1287 loop : -0.01 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1019 TYR 0.040 0.001 TYR A1067 PHE 0.024 0.002 PHE A1052 TRP 0.010 0.001 TRP C 436 HIS 0.010 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (35916) covalent geometry : angle 0.63332 / 0.33 (48867) SS BOND : bond 0.00353 / 0.25 ( 57) SS BOND : angle 0.85076 / 0.58 ( 114) hydrogen bonds : bond 0.04356 / 2.81 ( 1430) hydrogen bonds : angle 6.26510 / 4.29 ( 3897) link_BETA1-4 : bond 0.00487 / 0.31 ( 33) link_BETA1-4 : angle 1.67171 / 1.13 ( 99) link_NAG-ASN : bond 0.00429 / 0.21 ( 45) link_NAG-ASN : angle 2.56773 / 1.97 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 228 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8148 (t80) cc_final: 0.7851 (t80) REVERT: A 226 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8988 (mt) REVERT: A 513 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8700 (pp) REVERT: A 725 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 775 ASP cc_start: 0.8874 (m-30) cc_final: 0.8542 (m-30) REVERT: A 936 ASP cc_start: 0.9183 (m-30) cc_final: 0.8824 (t0) REVERT: A 945 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8931 (pp) REVERT: A 1017 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8942 (pp20) REVERT: A 1021 SER cc_start: 0.9736 (m) cc_final: 0.9511 (p) REVERT: A 1038 LYS cc_start: 0.9538 (mttt) cc_final: 0.9141 (mmmt) REVERT: A 1047 TYR cc_start: 0.4564 (OUTLIER) cc_final: 0.4096 (m-80) REVERT: A 1123 SER cc_start: 0.7858 (t) cc_final: 0.7501 (t) REVERT: A 1125 ASN cc_start: 0.8356 (t0) cc_final: 0.8100 (t0) REVERT: B 513 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8837 (pp) REVERT: B 725 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 775 ASP cc_start: 0.8936 (m-30) cc_final: 0.8695 (m-30) REVERT: B 902 MET cc_start: 0.9052 (tpp) cc_final: 0.8559 (tpp) REVERT: B 916 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8445 (pp) REVERT: B 936 ASP cc_start: 0.9195 (m-30) cc_final: 0.8811 (t0) REVERT: B 1001 LEU cc_start: 0.9793 (tt) cc_final: 0.9490 (pp) REVERT: B 1123 SER cc_start: 0.8014 (t) cc_final: 0.7642 (t) REVERT: B 1125 ASN cc_start: 0.8269 (t0) cc_final: 0.7969 (t0) REVERT: C 175 PHE cc_start: 0.9599 (m-80) cc_final: 0.9219 (m-80) REVERT: C 513 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8817 (pp) REVERT: C 725 GLU cc_start: 0.8685 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 775 ASP cc_start: 0.8828 (m-30) cc_final: 0.8428 (m-30) REVERT: C 780 GLU cc_start: 0.9032 (tp30) cc_final: 0.8814 (tt0) REVERT: C 869 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8828 (ptp) REVERT: C 936 ASP cc_start: 0.9172 (m-30) cc_final: 0.8806 (t0) REVERT: C 1001 LEU cc_start: 0.9850 (tp) cc_final: 0.9416 (pp) REVERT: C 1021 SER cc_start: 0.9686 (m) cc_final: 0.9421 (p) REVERT: C 1031 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8585 (mm-30) REVERT: C 1038 LYS cc_start: 0.9558 (mttt) cc_final: 0.9341 (mttp) REVERT: C 1123 SER cc_start: 0.7746 (t) cc_final: 0.7447 (t) REVERT: C 1125 ASN cc_start: 0.8252 (t0) cc_final: 0.7969 (t0) REVERT: L 4 MET cc_start: 0.6574 (mmm) cc_final: 0.6026 (tpp) REVERT: L 11 LEU cc_start: 0.9550 (tt) cc_final: 0.9248 (pt) REVERT: H 39 MET cc_start: 0.5670 (mpp) cc_final: 0.5337 (mmm) REVERT: H 91 MET cc_start: 0.7059 (mpp) cc_final: 0.6653 (mpp) REVERT: H 115 MET cc_start: 0.7540 (mmm) cc_final: 0.6963 (tpp) REVERT: H 159 ASP cc_start: 0.9479 (m-30) cc_final: 0.9062 (p0) REVERT: M 4 MET cc_start: 0.6926 (mmm) cc_final: 0.5622 (tpp) REVERT: M 11 LEU cc_start: 0.9522 (tt) cc_final: 0.9264 (pp) REVERT: I 39 MET cc_start: 0.5768 (mpp) cc_final: 0.5337 (mmm) REVERT: I 91 MET cc_start: 0.6925 (mpp) cc_final: 0.6565 (mpp) REVERT: I 115 MET cc_start: 0.7600 (mmm) cc_final: 0.7003 (tpp) REVERT: I 159 ASP cc_start: 0.9459 (m-30) cc_final: 0.9051 (p0) REVERT: N 4 MET cc_start: 0.6957 (mmm) cc_final: 0.6157 (tpp) REVERT: N 11 LEU cc_start: 0.9304 (tp) cc_final: 0.8919 (pp) REVERT: J 91 MET cc_start: 0.7141 (mpp) cc_final: 0.6820 (mpp) REVERT: J 115 MET cc_start: 0.8457 (mmm) cc_final: 0.7935 (mmm) REVERT: J 159 ASP cc_start: 0.9449 (m-30) cc_final: 0.9030 (p0) outliers start: 91 outliers final: 65 residues processed: 299 average time/residue: 0.2391 time to fit residues: 113.5481 Evaluate side-chains 291 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 218 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 403 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 247 optimal weight: 0.0270 chunk 289 optimal weight: 3.9990 chunk 414 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 308 optimal weight: 1.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN A 913 GLN A 926 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 913 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN L 167 GLN ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 167 GLN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 167 GLN N 209 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.052581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.037352 restraints weight = 299195.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.038552 restraints weight = 169901.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.039350 restraints weight = 114218.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.039901 restraints weight = 85840.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.040276 restraints weight = 69639.015| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 36051 Z= 0.218 Angle : 0.693 10.714 49215 Z= 0.352 Chirality : 0.045 0.289 5766 Planarity : 0.005 0.065 6204 Dihedral : 5.024 26.250 4728 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.16 % Rotamer: Outliers : 2.36 % Allowed : 11.00 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.26 (0.13), residues: 4353 helix: 1.30 (0.20), residues: 705 sheet: 0.17 (0.14), residues: 1266 loop : -0.07 (0.14), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1091 TYR 0.042 0.002 TYR A1067 PHE 0.024 0.002 PHE B 759 TRP 0.010 0.002 TRP B1102 HIS 0.007 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (35916) covalent geometry : angle 0.67551 / 0.35 (48867) SS BOND : bond 0.00465 / 0.33 ( 57) SS BOND : angle 0.99764 / 0.70 ( 114) hydrogen bonds : bond 0.04530 / 2.93 ( 1430) hydrogen bonds : angle 6.30207 / 4.30 ( 3897) link_BETA1-4 : bond 0.00501 / 0.32 ( 33) link_BETA1-4 : angle 1.78151 / 1.20 ( 99) link_NAG-ASN : bond 0.00474 / 0.25 ( 45) link_NAG-ASN : angle 2.59169 / 2.03 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 217 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9158 (mt) REVERT: A 513 LEU cc_start: 0.9130 (tp) cc_final: 0.8792 (pp) REVERT: A 725 GLU cc_start: 0.8592 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 740 MET cc_start: 0.8832 (mmm) cc_final: 0.8286 (mmt) REVERT: A 775 ASP cc_start: 0.8869 (m-30) cc_final: 0.8576 (m-30) REVERT: A 869 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8850 (ptp) REVERT: A 936 ASP cc_start: 0.9236 (m-30) cc_final: 0.8881 (t0) REVERT: A 1002 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8759 (tp40) REVERT: A 1017 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8882 (pp20) REVERT: A 1031 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8639 (mm-30) REVERT: A 1038 LYS cc_start: 0.9556 (mttt) cc_final: 0.9212 (mmmt) REVERT: A 1123 SER cc_start: 0.8016 (t) cc_final: 0.7678 (t) REVERT: A 1125 ASN cc_start: 0.8397 (t0) cc_final: 0.8146 (t0) REVERT: A 1138 TYR cc_start: 0.7838 (m-80) cc_final: 0.7576 (m-80) REVERT: B 513 LEU cc_start: 0.9156 (tp) cc_final: 0.8868 (pp) REVERT: B 775 ASP cc_start: 0.8930 (m-30) cc_final: 0.8715 (m-30) REVERT: B 776 LYS cc_start: 0.9478 (tptp) cc_final: 0.9041 (tptp) REVERT: B 916 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8625 (pp) REVERT: B 936 ASP cc_start: 0.9210 (m-30) cc_final: 0.8863 (t0) REVERT: B 1001 LEU cc_start: 0.9791 (tt) cc_final: 0.9492 (pp) REVERT: B 1038 LYS cc_start: 0.9522 (mttt) cc_final: 0.9279 (mmtt) REVERT: B 1123 SER cc_start: 0.8152 (t) cc_final: 0.7826 (t) REVERT: B 1125 ASN cc_start: 0.8375 (t0) cc_final: 0.8072 (t0) REVERT: B 1138 TYR cc_start: 0.8034 (m-80) cc_final: 0.7806 (m-80) REVERT: C 513 LEU cc_start: 0.9225 (tp) cc_final: 0.8863 (pp) REVERT: C 725 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 740 MET cc_start: 0.8769 (mmm) cc_final: 0.8334 (mmt) REVERT: C 775 ASP cc_start: 0.8872 (m-30) cc_final: 0.8576 (m-30) REVERT: C 902 MET cc_start: 0.9333 (tpp) cc_final: 0.8987 (tpp) REVERT: C 936 ASP cc_start: 0.9198 (m-30) cc_final: 0.8833 (t0) REVERT: C 1001 LEU cc_start: 0.9868 (tp) cc_final: 0.9459 (pp) REVERT: C 1031 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8591 (mm-30) REVERT: C 1123 SER cc_start: 0.8010 (t) cc_final: 0.7668 (t) REVERT: C 1125 ASN cc_start: 0.8363 (t0) cc_final: 0.8096 (t0) REVERT: C 1138 TYR cc_start: 0.7725 (m-80) cc_final: 0.7519 (m-80) REVERT: L 4 MET cc_start: 0.7067 (mmm) cc_final: 0.6150 (tpp) REVERT: L 11 LEU cc_start: 0.9576 (tt) cc_final: 0.9283 (pt) REVERT: L 162 ARG cc_start: 0.9149 (tpt90) cc_final: 0.8657 (tpp80) REVERT: H 39 MET cc_start: 0.5605 (mpp) cc_final: 0.5399 (mmm) REVERT: H 84 LYS cc_start: 0.8858 (tptp) cc_final: 0.8191 (pttt) REVERT: H 91 MET cc_start: 0.7155 (mpp) cc_final: 0.6765 (mpp) REVERT: H 115 MET cc_start: 0.7465 (mmm) cc_final: 0.7008 (tpp) REVERT: H 159 ASP cc_start: 0.9499 (m-30) cc_final: 0.9104 (p0) REVERT: M 4 MET cc_start: 0.7014 (mmm) cc_final: 0.5905 (tpp) REVERT: M 11 LEU cc_start: 0.9556 (tt) cc_final: 0.9276 (pt) REVERT: M 162 ARG cc_start: 0.9172 (tpt90) cc_final: 0.8698 (tpp80) REVERT: I 39 MET cc_start: 0.5771 (mpp) cc_final: 0.4610 (mmm) REVERT: I 91 MET cc_start: 0.7040 (mpp) cc_final: 0.6655 (mpp) REVERT: I 115 MET cc_start: 0.7704 (mmm) cc_final: 0.7152 (tpp) REVERT: I 159 ASP cc_start: 0.9491 (m-30) cc_final: 0.9107 (p0) REVERT: N 3 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8634 (pp30) REVERT: N 4 MET cc_start: 0.6888 (mmm) cc_final: 0.6038 (tpp) REVERT: N 11 LEU cc_start: 0.9323 (tp) cc_final: 0.8934 (pt) REVERT: N 162 ARG cc_start: 0.9182 (tpt90) cc_final: 0.8744 (tpp80) REVERT: J 91 MET cc_start: 0.7222 (mpp) cc_final: 0.6887 (mpp) REVERT: J 115 MET cc_start: 0.8561 (mmm) cc_final: 0.7978 (mmm) REVERT: J 159 ASP cc_start: 0.9494 (m-30) cc_final: 0.9099 (p0) outliers start: 90 outliers final: 63 residues processed: 292 average time/residue: 0.2422 time to fit residues: 111.6622 Evaluate side-chains 270 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 202 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 29 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 302 optimal weight: 0.9980 chunk 350 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 403 optimal weight: 10.0000 chunk 290 optimal weight: 0.8980 chunk 253 optimal weight: 0.6980 chunk 351 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN H 186 GLN ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN I 186 GLN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.053311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.037859 restraints weight = 295342.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.039098 restraints weight = 167406.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.039926 restraints weight = 112317.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.040488 restraints weight = 84228.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.040854 restraints weight = 68334.406| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 36051 Z= 0.144 Angle : 0.647 12.566 49215 Z= 0.324 Chirality : 0.045 0.334 5766 Planarity : 0.004 0.063 6204 Dihedral : 4.867 25.569 4728 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 1.94 % Allowed : 12.20 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.28 (0.13), residues: 4353 helix: 1.22 (0.20), residues: 702 sheet: 0.20 (0.14), residues: 1263 loop : -0.04 (0.14), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1019 TYR 0.026 0.001 TYR B1067 PHE 0.020 0.002 PHE B1052 TRP 0.012 0.001 TRP C 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (35916) covalent geometry : angle 0.63197 / 0.32 (48867) SS BOND : bond 0.00349 / 0.25 ( 57) SS BOND : angle 0.81537 / 0.55 ( 114) hydrogen bonds : bond 0.04160 / 2.68 ( 1430) hydrogen bonds : angle 6.11693 / 4.17 ( 3897) link_BETA1-4 : bond 0.00489 / 0.31 ( 33) link_BETA1-4 : angle 1.63182 / 1.10 ( 99) link_NAG-ASN : bond 0.00418 / 0.19 ( 45) link_NAG-ASN : angle 2.38294 / 1.83 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 221 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9215 (mt) REVERT: A 513 LEU cc_start: 0.9119 (tp) cc_final: 0.8768 (pp) REVERT: A 725 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8438 (tm-30) REVERT: A 740 MET cc_start: 0.8738 (mmm) cc_final: 0.8298 (mmt) REVERT: A 775 ASP cc_start: 0.8916 (m-30) cc_final: 0.8676 (m-30) REVERT: A 869 MET cc_start: 0.9211 (mtp) cc_final: 0.8846 (ptp) REVERT: A 936 ASP cc_start: 0.9226 (m-30) cc_final: 0.8859 (t0) REVERT: A 1002 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8700 (tp40) REVERT: A 1017 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8937 (pp20) REVERT: A 1038 LYS cc_start: 0.9532 (mttt) cc_final: 0.9251 (mmmt) REVERT: A 1123 SER cc_start: 0.8020 (t) cc_final: 0.7673 (t) REVERT: A 1125 ASN cc_start: 0.8474 (t0) cc_final: 0.8174 (t0) REVERT: A 1138 TYR cc_start: 0.7868 (m-80) cc_final: 0.7645 (m-80) REVERT: B 513 LEU cc_start: 0.9150 (tp) cc_final: 0.8838 (pp) REVERT: B 916 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8536 (pp) REVERT: B 936 ASP cc_start: 0.9206 (m-30) cc_final: 0.8849 (t0) REVERT: B 1001 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9480 (pp) REVERT: B 1123 SER cc_start: 0.8077 (t) cc_final: 0.7771 (t) REVERT: B 1125 ASN cc_start: 0.8248 (t0) cc_final: 0.7936 (t0) REVERT: B 1138 TYR cc_start: 0.7948 (m-80) cc_final: 0.7748 (m-80) REVERT: C 513 LEU cc_start: 0.9220 (tp) cc_final: 0.8843 (pp) REVERT: C 725 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8056 (tm-30) REVERT: C 740 MET cc_start: 0.8656 (mmm) cc_final: 0.8356 (mmt) REVERT: C 775 ASP cc_start: 0.8880 (m-30) cc_final: 0.8588 (m-30) REVERT: C 902 MET cc_start: 0.9392 (tpp) cc_final: 0.9001 (tpp) REVERT: C 936 ASP cc_start: 0.9217 (m-30) cc_final: 0.8835 (t0) REVERT: C 1001 LEU cc_start: 0.9860 (tp) cc_final: 0.9429 (pp) REVERT: C 1031 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8554 (mm-30) REVERT: C 1123 SER cc_start: 0.7946 (t) cc_final: 0.7703 (t) REVERT: C 1125 ASN cc_start: 0.8358 (t0) cc_final: 0.8055 (t0) REVERT: C 1138 TYR cc_start: 0.7599 (m-80) cc_final: 0.7378 (m-80) REVERT: L 4 MET cc_start: 0.7242 (mmm) cc_final: 0.6330 (tpp) REVERT: L 11 LEU cc_start: 0.9571 (tt) cc_final: 0.9254 (pt) REVERT: H 39 MET cc_start: 0.5589 (mpp) cc_final: 0.4709 (mmm) REVERT: H 84 LYS cc_start: 0.8852 (tptp) cc_final: 0.8230 (ptmt) REVERT: H 91 MET cc_start: 0.7110 (mpp) cc_final: 0.6723 (mpp) REVERT: H 115 MET cc_start: 0.7418 (mmm) cc_final: 0.6921 (tpp) REVERT: H 159 ASP cc_start: 0.9503 (m-30) cc_final: 0.9104 (p0) REVERT: M 4 MET cc_start: 0.7070 (mmm) cc_final: 0.5981 (tpp) REVERT: M 11 LEU cc_start: 0.9535 (tt) cc_final: 0.9280 (pt) REVERT: I 39 MET cc_start: 0.5747 (mpp) cc_final: 0.4575 (mmm) REVERT: I 91 MET cc_start: 0.7047 (mpp) cc_final: 0.6684 (mpp) REVERT: I 115 MET cc_start: 0.7445 (mmm) cc_final: 0.6906 (tpp) REVERT: I 159 ASP cc_start: 0.9486 (m-30) cc_final: 0.9106 (p0) REVERT: N 4 MET cc_start: 0.6946 (mmm) cc_final: 0.5891 (tpp) REVERT: N 11 LEU cc_start: 0.9220 (tp) cc_final: 0.8857 (pt) REVERT: J 91 MET cc_start: 0.7213 (mpp) cc_final: 0.6878 (mpp) REVERT: J 115 MET cc_start: 0.8514 (mmm) cc_final: 0.7902 (mmm) REVERT: J 159 ASP cc_start: 0.9481 (m-30) cc_final: 0.9063 (p0) outliers start: 74 outliers final: 62 residues processed: 283 average time/residue: 0.2350 time to fit residues: 104.8839 Evaluate side-chains 272 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 431 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 432 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 434 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 359 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 935 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.053318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.038035 restraints weight = 300261.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.039270 restraints weight = 168123.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.040087 restraints weight = 111953.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.040645 restraints weight = 83611.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.041028 restraints weight = 67628.248| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 36051 Z= 0.144 Angle : 0.641 12.450 49215 Z= 0.320 Chirality : 0.044 0.352 5766 Planarity : 0.004 0.048 6204 Dihedral : 4.790 25.178 4728 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 1.86 % Allowed : 12.31 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4353 helix: 1.24 (0.20), residues: 720 sheet: 0.23 (0.14), residues: 1299 loop : -0.07 (0.14), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1019 TYR 0.025 0.001 TYR A1110 PHE 0.048 0.002 PHE C 782 TRP 0.018 0.001 TRP C 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (35916) covalent geometry : angle 0.62598 / 0.32 (48867) SS BOND : bond 0.00365 / 0.26 ( 57) SS BOND : angle 0.84401 / 0.57 ( 114) hydrogen bonds : bond 0.04085 / 2.63 ( 1430) hydrogen bonds : angle 6.06202 / 4.13 ( 3897) link_BETA1-4 : bond 0.00497 / 0.32 ( 33) link_BETA1-4 : angle 1.61075 / 1.09 ( 99) link_NAG-ASN : bond 0.00418 / 0.19 ( 45) link_NAG-ASN : angle 2.33987 / 1.81 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 214 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9220 (mt) REVERT: A 513 LEU cc_start: 0.9116 (tp) cc_final: 0.8759 (pp) REVERT: A 725 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8452 (tm-30) REVERT: A 740 MET cc_start: 0.8683 (mmm) cc_final: 0.8222 (mmt) REVERT: A 775 ASP cc_start: 0.8874 (m-30) cc_final: 0.8583 (m-30) REVERT: A 869 MET cc_start: 0.9209 (mtp) cc_final: 0.8538 (ptp) REVERT: A 877 LEU cc_start: 0.9650 (mt) cc_final: 0.9381 (mt) REVERT: A 936 ASP cc_start: 0.9219 (m-30) cc_final: 0.8860 (t0) REVERT: A 954 GLN cc_start: 0.9376 (mt0) cc_final: 0.9147 (pt0) REVERT: A 1002 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8701 (tp40) REVERT: A 1017 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8902 (pp20) REVERT: A 1038 LYS cc_start: 0.9453 (mttt) cc_final: 0.9009 (mmmt) REVERT: A 1123 SER cc_start: 0.8059 (t) cc_final: 0.7697 (t) REVERT: A 1125 ASN cc_start: 0.8479 (t0) cc_final: 0.8167 (t0) REVERT: A 1138 TYR cc_start: 0.7906 (m-80) cc_final: 0.7695 (m-80) REVERT: B 513 LEU cc_start: 0.9172 (tp) cc_final: 0.8809 (pp) REVERT: B 936 ASP cc_start: 0.9185 (m-30) cc_final: 0.8849 (t0) REVERT: B 1001 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9481 (pp) REVERT: B 1038 LYS cc_start: 0.9388 (ptpt) cc_final: 0.8968 (mmmt) REVERT: B 1092 GLU cc_start: 0.8803 (mp0) cc_final: 0.7607 (mp0) REVERT: B 1107 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.5650 (tpt170) REVERT: B 1123 SER cc_start: 0.8057 (t) cc_final: 0.7757 (t) REVERT: B 1125 ASN cc_start: 0.8224 (t0) cc_final: 0.7893 (t0) REVERT: C 513 LEU cc_start: 0.9205 (tp) cc_final: 0.8814 (pp) REVERT: C 725 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 740 MET cc_start: 0.8608 (mmm) cc_final: 0.8349 (mmt) REVERT: C 775 ASP cc_start: 0.8858 (m-30) cc_final: 0.8564 (m-30) REVERT: C 902 MET cc_start: 0.9340 (tpp) cc_final: 0.8950 (tpp) REVERT: C 936 ASP cc_start: 0.9194 (m-30) cc_final: 0.8836 (t0) REVERT: C 954 GLN cc_start: 0.9332 (mt0) cc_final: 0.9061 (pt0) REVERT: C 1001 LEU cc_start: 0.9856 (tp) cc_final: 0.9424 (pp) REVERT: C 1031 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8510 (mm-30) REVERT: C 1123 SER cc_start: 0.7959 (t) cc_final: 0.7710 (t) REVERT: C 1125 ASN cc_start: 0.8370 (t0) cc_final: 0.8053 (t0) REVERT: C 1138 TYR cc_start: 0.7633 (m-80) cc_final: 0.7432 (m-80) REVERT: L 1 ASP cc_start: 0.8581 (m-30) cc_final: 0.8239 (t0) REVERT: L 4 MET cc_start: 0.7208 (mmm) cc_final: 0.6176 (tpp) REVERT: L 11 LEU cc_start: 0.9576 (tt) cc_final: 0.9257 (pt) REVERT: H 39 MET cc_start: 0.5572 (mpp) cc_final: 0.4664 (mmm) REVERT: H 84 LYS cc_start: 0.8811 (tptp) cc_final: 0.8264 (ptmt) REVERT: H 91 MET cc_start: 0.7069 (mpp) cc_final: 0.6676 (mpp) REVERT: H 115 MET cc_start: 0.7426 (mmm) cc_final: 0.6910 (tpp) REVERT: H 159 ASP cc_start: 0.9496 (m-30) cc_final: 0.9105 (p0) REVERT: M 4 MET cc_start: 0.6972 (mmm) cc_final: 0.5816 (tpp) REVERT: M 11 LEU cc_start: 0.9539 (tt) cc_final: 0.9315 (pt) REVERT: I 39 MET cc_start: 0.5612 (mpp) cc_final: 0.4557 (mmm) REVERT: I 91 MET cc_start: 0.6984 (mpp) cc_final: 0.6622 (mpp) REVERT: I 115 MET cc_start: 0.7403 (mmm) cc_final: 0.6860 (tpp) REVERT: I 159 ASP cc_start: 0.9515 (m-30) cc_final: 0.9151 (p0) REVERT: N 4 MET cc_start: 0.7101 (mmm) cc_final: 0.6287 (tpp) REVERT: N 11 LEU cc_start: 0.9226 (tp) cc_final: 0.8859 (pt) REVERT: J 91 MET cc_start: 0.7157 (mpp) cc_final: 0.6826 (mpp) REVERT: J 115 MET cc_start: 0.8549 (mmm) cc_final: 0.7962 (mmm) REVERT: J 159 ASP cc_start: 0.9487 (m-30) cc_final: 0.9078 (p0) outliers start: 71 outliers final: 59 residues processed: 274 average time/residue: 0.2395 time to fit residues: 103.3934 Evaluate side-chains 271 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 188 optimal weight: 2.9990 chunk 362 optimal weight: 1.9990 chunk 346 optimal weight: 7.9990 chunk 350 optimal weight: 8.9990 chunk 339 optimal weight: 30.0000 chunk 168 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 376 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 394 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 935 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 913 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN L 3 GLN L 219 GLN ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 219 GLN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 219 GLN ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.051432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.036167 restraints weight = 307006.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.037348 restraints weight = 173143.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.038134 restraints weight = 116304.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.038671 restraints weight = 87449.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.039028 restraints weight = 71181.803| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 36051 Z= 0.227 Angle : 0.705 17.059 49215 Z= 0.354 Chirality : 0.045 0.320 5766 Planarity : 0.004 0.045 6204 Dihedral : 4.995 28.234 4728 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 1.89 % Allowed : 12.33 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.17 (0.13), residues: 4353 helix: 1.25 (0.20), residues: 693 sheet: 0.15 (0.14), residues: 1227 loop : -0.16 (0.13), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 905 TYR 0.031 0.002 TYR A 904 PHE 0.025 0.002 PHE B 759 TRP 0.016 0.002 TRP C 886 HIS 0.008 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 (35916) covalent geometry : angle 0.68909 / 0.35 (48867) SS BOND : bond 0.00480 / 0.35 ( 57) SS BOND : angle 0.96612 / 0.67 ( 114) hydrogen bonds : bond 0.04460 / 2.89 ( 1430) hydrogen bonds : angle 6.26924 / 4.27 ( 3897) link_BETA1-4 : bond 0.00491 / 0.30 ( 33) link_BETA1-4 : angle 1.75026 / 1.18 ( 99) link_NAG-ASN : bond 0.00475 / 0.24 ( 45) link_NAG-ASN : angle 2.46530 / 1.89 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9234 (mt) REVERT: A 513 LEU cc_start: 0.9187 (tp) cc_final: 0.8821 (pp) REVERT: A 725 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8443 (tm-30) REVERT: A 740 MET cc_start: 0.8802 (mmm) cc_final: 0.8368 (mmt) REVERT: A 936 ASP cc_start: 0.9277 (m-30) cc_final: 0.8956 (t0) REVERT: A 954 GLN cc_start: 0.9402 (mt0) cc_final: 0.9186 (pt0) REVERT: A 1002 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8799 (tp40) REVERT: A 1038 LYS cc_start: 0.9458 (mttt) cc_final: 0.9021 (mmmt) REVERT: A 1092 GLU cc_start: 0.8880 (mp0) cc_final: 0.8430 (pm20) REVERT: A 1123 SER cc_start: 0.8251 (t) cc_final: 0.7917 (t) REVERT: B 513 LEU cc_start: 0.9184 (tp) cc_final: 0.8859 (pp) REVERT: B 796 ASP cc_start: 0.8950 (m-30) cc_final: 0.8590 (p0) REVERT: B 936 ASP cc_start: 0.9238 (m-30) cc_final: 0.8918 (t0) REVERT: B 1001 LEU cc_start: 0.9777 (tt) cc_final: 0.9494 (pp) REVERT: B 1038 LYS cc_start: 0.9121 (ptpt) cc_final: 0.8905 (mmtm) REVERT: B 1107 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7201 (mpt180) REVERT: B 1123 SER cc_start: 0.8265 (t) cc_final: 0.7945 (t) REVERT: C 513 LEU cc_start: 0.9169 (tp) cc_final: 0.8820 (pp) REVERT: C 725 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 775 ASP cc_start: 0.8906 (m-30) cc_final: 0.8615 (m-30) REVERT: C 902 MET cc_start: 0.9372 (tpp) cc_final: 0.8950 (tpp) REVERT: C 936 ASP cc_start: 0.9245 (m-30) cc_final: 0.8905 (t0) REVERT: C 954 GLN cc_start: 0.9365 (mt0) cc_final: 0.9129 (pt0) REVERT: C 1001 LEU cc_start: 0.9871 (tp) cc_final: 0.9457 (pp) REVERT: C 1031 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8557 (mm-30) REVERT: C 1107 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6161 (tpt170) REVERT: C 1123 SER cc_start: 0.8115 (t) cc_final: 0.7837 (t) REVERT: L 4 MET cc_start: 0.7306 (mmm) cc_final: 0.6767 (tpp) REVERT: L 11 LEU cc_start: 0.9602 (tt) cc_final: 0.9311 (pt) REVERT: L 162 ARG cc_start: 0.9217 (tpt90) cc_final: 0.8686 (tpp80) REVERT: H 39 MET cc_start: 0.5570 (mpp) cc_final: 0.4681 (mmm) REVERT: H 91 MET cc_start: 0.7120 (mpp) cc_final: 0.6728 (mpp) REVERT: H 115 MET cc_start: 0.7512 (mmm) cc_final: 0.7013 (tpp) REVERT: H 159 ASP cc_start: 0.9521 (m-30) cc_final: 0.9159 (p0) REVERT: M 4 MET cc_start: 0.7382 (mmm) cc_final: 0.6556 (tpp) REVERT: M 11 LEU cc_start: 0.9524 (tt) cc_final: 0.9261 (pt) REVERT: M 162 ARG cc_start: 0.9223 (tpt90) cc_final: 0.8719 (tpp80) REVERT: I 39 MET cc_start: 0.5560 (mpp) cc_final: 0.4640 (mmm) REVERT: I 91 MET cc_start: 0.6894 (mpp) cc_final: 0.6502 (mpp) REVERT: I 115 MET cc_start: 0.7455 (mmm) cc_final: 0.6911 (tpp) REVERT: I 159 ASP cc_start: 0.9505 (m-30) cc_final: 0.9160 (p0) REVERT: N 4 MET cc_start: 0.7151 (mmm) cc_final: 0.6220 (tpp) REVERT: N 11 LEU cc_start: 0.9250 (tp) cc_final: 0.8870 (pt) REVERT: N 162 ARG cc_start: 0.9184 (tpt90) cc_final: 0.8693 (tpp80) REVERT: J 91 MET cc_start: 0.7239 (mpp) cc_final: 0.6906 (mpp) REVERT: J 115 MET cc_start: 0.8495 (mmm) cc_final: 0.7896 (mmm) REVERT: J 159 ASP cc_start: 0.9519 (m-30) cc_final: 0.9130 (p0) outliers start: 72 outliers final: 60 residues processed: 257 average time/residue: 0.2327 time to fit residues: 94.1575 Evaluate side-chains 257 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 193 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 42 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 340 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.051283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.036030 restraints weight = 303820.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.037213 restraints weight = 171183.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.038002 restraints weight = 114739.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.038499 restraints weight = 86214.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.038874 restraints weight = 70456.529| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.262 36051 Z= 0.268 Angle : 0.826 59.194 49215 Z= 0.440 Chirality : 0.046 0.724 5766 Planarity : 0.005 0.170 6204 Dihedral : 4.994 28.251 4728 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 1.70 % Allowed : 12.62 % Favored : 85.68 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 6.49 % 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: 0.16 (0.13), residues: 4353 helix: 1.24 (0.20), residues: 693 sheet: 0.12 (0.14), residues: 1257 loop : -0.16 (0.14), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.076 0.001 ARG A 905 TYR 0.029 0.002 TYR A1067 PHE 0.023 0.002 PHE B 759 TRP 0.016 0.002 TRP C 886 HIS 0.007 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.27 (35916) covalent geometry : angle 0.81403 / 0.44 (48867) SS BOND : bond 0.00474 / 0.34 ( 57) SS BOND : angle 0.95372 / 0.66 ( 114) hydrogen bonds : bond 0.04451 / 2.88 ( 1430) hydrogen bonds : angle 6.27493 / 4.27 ( 3897) link_BETA1-4 : bond 0.00494 / 0.31 ( 33) link_BETA1-4 : angle 1.73286 / 1.17 ( 99) link_NAG-ASN : bond 0.00470 / 0.24 ( 45) link_NAG-ASN : angle 2.46505 / 1.89 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6966.21 seconds wall clock time: 121 minutes 46.70 seconds (7306.70 seconds total)