Starting phenix.real_space_refine on Mon Sep 14 00:53:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zge_11203/09_2026/6zge_11203.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zge_11203/09_2026/6zge_11203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zge_11203/09_2026/6zge_11203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zge_11203/09_2026/6zge_11203.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6zge_11203/09_2026/6zge_11203.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zge_11203/09_2026/6zge_11203.cif" model { file = "/net/cci-nas-00/data/ceres_data/6zge_11203/09_2026/6zge_11203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zge_11203/09_2026/6zge_11203.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.208 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17121 2.51 5 N 4395 2.21 5 O 5355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26991 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "B" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "C" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 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: 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: "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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 9.62, per 1000 atoms: 0.36 Number of scatterers: 26991 At special positions: 0 Unit cell: (151.093, 150.006, 179.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5355 8.00 N 4395 7.00 C 17121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1307 " - " ASN A 149 " " NAG A1312 " - " ASN A 282 " " NAG A1313 " - " ASN A 331 " " NAG A1314 " - " ASN A 343 " " NAG A1317 " - " ASN A 657 " " NAG A1318 " - " ASN A 709 " " NAG A1323 " - " ASN A1074 " " NAG B1307 " - " ASN B 149 " " NAG B1312 " - " ASN B 282 " " NAG B1313 " - " ASN B 331 " " NAG B1314 " - " ASN B 343 " " NAG B1317 " - " ASN B 657 " " NAG B1318 " - " ASN B 709 " " NAG B1323 " - " ASN B1074 " " NAG C1307 " - " ASN C 149 " " NAG C1312 " - " ASN C 282 " " NAG C1313 " - " ASN C 331 " " NAG C1314 " - " ASN C 343 " " NAG C1317 " - " ASN C 657 " " NAG C1318 " - " ASN C 709 " " NAG C1323 " - " ASN C1074 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 61 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 61 " " NAG Y 1 " - " ASN C 17 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.7 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 24.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.209A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.209A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.138A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.210A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.205A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.877A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 163 removed outlier: 6.624A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.322A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.205A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.876A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 151 through 163 removed outlier: 6.624A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.335A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.204A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.029A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.877A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 151 through 163 removed outlier: 6.624A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.071A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1056 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8310 1.34 - 1.47: 7203 1.47 - 1.59: 11889 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 27552 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" CB ASP B 228 " pdb=" CG ASP B 228 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.81e+00 bond pdb=" CB ASP A 228 " pdb=" CG ASP A 228 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.80e+00 ... (remaining 27547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 36229 2.34 - 4.69: 1169 4.69 - 7.03: 78 7.03 - 9.38: 12 9.38 - 11.72: 6 Bond angle restraints: 37494 Sorted by residual: angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 110.80 119.19 -8.39 2.13e+00 2.20e-01 1.55e+01 angle pdb=" CA LEU B 241 " pdb=" CB LEU B 241 " pdb=" CG LEU B 241 " ideal model delta sigma weight residual 116.30 128.02 -11.72 3.50e+00 8.16e-02 1.12e+01 angle pdb=" CA LEU A 241 " pdb=" CB LEU A 241 " pdb=" CG LEU A 241 " ideal model delta sigma weight residual 116.30 128.02 -11.72 3.50e+00 8.16e-02 1.12e+01 ... (remaining 37489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 14701 17.58 - 35.16: 842 35.16 - 52.74: 132 52.74 - 70.32: 59 70.32 - 87.90: 28 Dihedral angle restraints: 15762 sinusoidal: 6156 harmonic: 9606 Sorted by residual: dihedral pdb=" CA HIS C 66 " pdb=" C HIS C 66 " pdb=" N ALA C 67 " pdb=" CA ALA C 67 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA HIS A 66 " pdb=" C HIS A 66 " pdb=" N ALA A 67 " pdb=" CA ALA A 67 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA HIS B 66 " pdb=" C HIS B 66 " pdb=" N ALA B 67 " pdb=" CA ALA B 67 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 15759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2960 0.062 - 0.124: 1323 0.124 - 0.186: 158 0.186 - 0.248: 14 0.248 - 0.310: 3 Chirality restraints: 4458 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 4455 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 539 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL B 539 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL B 539 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 540 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 539 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL C 539 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL C 539 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN C 540 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 539 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C VAL A 539 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL A 539 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN A 540 " -0.023 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 9045 2.86 - 3.37: 21969 3.37 - 3.88: 43388 3.88 - 4.39: 50567 4.39 - 4.90: 87089 Nonbonded interactions: 212058 Sorted by model distance: nonbonded pdb=" OD1 ASN A 777 " pdb=" NH1BARG A1019 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASN B 777 " pdb=" NH1BARG B1019 " model vdw 2.345 3.120 nonbonded pdb=" OD1 ASN C 777 " pdb=" NH1BARG C1019 " model vdw 2.345 3.120 nonbonded pdb=" O SER B 477 " pdb=" OG1 THR B 478 " model vdw 2.347 3.040 nonbonded pdb=" O SER A 477 " pdb=" OG1 THR A 478 " model vdw 2.347 3.040 ... (remaining 212053 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: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1323)) selection = (chain 'B' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1323)) selection = (chain 'C' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1323)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.060 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.160 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 : 0.010 0.080 27678 Z= 0.406 Angle : 0.975 12.623 37827 Z= 0.516 Chirality : 0.063 0.310 4458 Planarity : 0.005 0.039 4755 Dihedral : 12.627 87.897 9459 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 0.73 % Allowed : 3.24 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3270 helix: 0.91 (0.19), residues: 711 sheet: 0.39 (0.18), residues: 777 loop : -1.87 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1039 TYR 0.024 0.003 TYR C 265 PHE 0.022 0.004 PHE A 592 TRP 0.017 0.003 TRP B 886 HIS 0.008 0.002 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00983 / 0.41 (27552) covalent geometry : angle 0.94125 / 0.51 (37494) SS BOND : bond 0.01125 / 0.77 ( 45) SS BOND : angle 2.26032 / 1.61 ( 90) hydrogen bonds : bond 0.14378 / 9.35 ( 1056) hydrogen bonds : angle 6.58130 / 4.57 ( 2856) link_BETA1-4 : bond 0.00483 / 0.32 ( 30) link_BETA1-4 : angle 1.54371 / 1.05 ( 90) link_NAG-ASN : bond 0.00540 / 0.31 ( 51) link_NAG-ASN : angle 3.70711 / 2.54 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 408 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8415 (m-40) cc_final: 0.8139 (m110) REVERT: A 158 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7992 (mtt90) REVERT: A 505 TYR cc_start: 0.7701 (m-80) cc_final: 0.7267 (t80) REVERT: A 765 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7713 (mtp180) REVERT: A 904 TYR cc_start: 0.7986 (m-10) cc_final: 0.7220 (m-10) REVERT: A 947 LYS cc_start: 0.8420 (mttm) cc_final: 0.8208 (mppt) REVERT: A 957 GLN cc_start: 0.8066 (tt0) cc_final: 0.7760 (tp40) REVERT: B 88 ASP cc_start: 0.7743 (m-30) cc_final: 0.7510 (m-30) REVERT: B 259 THR cc_start: 0.8180 (t) cc_final: 0.7974 (m) REVERT: B 321 GLN cc_start: 0.8447 (mm110) cc_final: 0.8176 (mm110) REVERT: B 430 THR cc_start: 0.8451 (m) cc_final: 0.8228 (m) REVERT: B 505 TYR cc_start: 0.7829 (m-80) cc_final: 0.7442 (t80) REVERT: B 646 ARG cc_start: 0.8255 (mtm180) cc_final: 0.8028 (mtp180) REVERT: B 705 VAL cc_start: 0.8419 (t) cc_final: 0.8190 (t) REVERT: B 738 CYS cc_start: 0.6106 (t) cc_final: 0.5567 (t) REVERT: B 916 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8311 (tt) REVERT: B 947 LYS cc_start: 0.8456 (mttm) cc_final: 0.8087 (mppt) REVERT: B 955 ASN cc_start: 0.7895 (m-40) cc_final: 0.7549 (m110) REVERT: B 1005 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8106 (tp-100) REVERT: B 1107 ARG cc_start: 0.7740 (mpp80) cc_final: 0.6820 (mtt180) REVERT: B 1125 ASN cc_start: 0.7878 (p0) cc_final: 0.7545 (p0) REVERT: B 1141 LEU cc_start: 0.8269 (tp) cc_final: 0.8009 (tm) REVERT: C 88 ASP cc_start: 0.7651 (m-30) cc_final: 0.7437 (m-30) REVERT: C 505 TYR cc_start: 0.7755 (m-80) cc_final: 0.7257 (t80) REVERT: C 759 PHE cc_start: 0.7238 (m-80) cc_final: 0.6975 (m-80) REVERT: C 869 MET cc_start: 0.8716 (mtt) cc_final: 0.8461 (mtp) REVERT: C 904 TYR cc_start: 0.7968 (m-10) cc_final: 0.6945 (m-10) REVERT: C 947 LYS cc_start: 0.8261 (mttm) cc_final: 0.7907 (mppt) REVERT: C 1073 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7421 (tttp) outliers start: 21 outliers final: 3 residues processed: 426 average time/residue: 0.7062 time to fit residues: 347.9876 Evaluate side-chains 261 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 257 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.0060 chunk 298 optimal weight: 0.9980 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A 218 GLN A 239 GLN A 245 HIS A 394 ASN A 440 ASN A 474 GLN A 501 ASN A 540 ASN A 563 GLN A 580 GLN A 641 ASN A 658 ASN A 751 ASN A 925 ASN A 954 GLN A 969 ASN A1023 ASN A1036 GLN A1064 HIS B 99 ASN B 146 HIS B 239 GLN B 245 HIS B 394 ASN B 474 GLN B 501 ASN B 540 ASN B 580 GLN B 641 ASN B 658 ASN B 675 GLN B 751 ASN B 925 ASN B1023 ASN B1036 GLN B1064 HIS C 99 ASN C 188 ASN C 207 HIS C 218 GLN C 239 GLN C 245 HIS C 394 ASN C 474 GLN C 501 ASN C 540 ASN C 580 GLN C 641 ASN C 658 ASN C 703 ASN C 751 ASN C 925 ASN C1023 ASN C1036 GLN C1064 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.148264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.116256 restraints weight = 36662.609| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.09 r_work: 0.3097 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (17 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27678 Z= 0.144 Angle : 0.698 16.056 37827 Z= 0.353 Chirality : 0.049 0.459 4458 Planarity : 0.004 0.045 4755 Dihedral : 5.446 55.597 3563 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.80 % Favored : 96.05 % Rotamer: Outliers : 1.32 % Allowed : 7.97 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.74 (0.14), residues: 3270 helix: 1.27 (0.20), residues: 714 sheet: 0.49 (0.19), residues: 765 loop : -1.77 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 246 TYR 0.017 0.001 TYR B 265 PHE 0.016 0.001 PHE A 59 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (27552) covalent geometry : angle 0.65197 / 0.34 (37494) SS BOND : bond 0.00857 / 0.40 ( 45) SS BOND : angle 2.46111 / 1.63 ( 90) hydrogen bonds : bond 0.06022 / 4.03 ( 1056) hydrogen bonds : angle 5.56132 / 3.83 ( 2856) link_BETA1-4 : bond 0.00410 / 0.26 ( 30) link_BETA1-4 : angle 1.21585 / 0.86 ( 90) link_NAG-ASN : bond 0.00909 / 0.55 ( 51) link_NAG-ASN : angle 3.43216 / 2.43 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.7949 (mtt180) REVERT: A 271 GLN cc_start: 0.8572 (mt0) cc_final: 0.8330 (mt0) REVERT: A 312 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8984 (tt) REVERT: A 394 ASN cc_start: 0.8614 (m-40) cc_final: 0.8127 (m110) REVERT: A 505 TYR cc_start: 0.8463 (m-80) cc_final: 0.7606 (t80) REVERT: A 738 CYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7639 (t) REVERT: A 745 ASP cc_start: 0.7743 (m-30) cc_final: 0.7339 (m-30) REVERT: A 869 MET cc_start: 0.8941 (mtt) cc_final: 0.8645 (mtm) REVERT: A 904 TYR cc_start: 0.8480 (m-10) cc_final: 0.7441 (m-10) REVERT: A 947 LYS cc_start: 0.8662 (mttm) cc_final: 0.8135 (mppt) REVERT: A 955 ASN cc_start: 0.7778 (m-40) cc_final: 0.7559 (m110) REVERT: A 957 GLN cc_start: 0.8707 (tt0) cc_final: 0.8386 (tp40) REVERT: B 80 ASP cc_start: 0.7951 (m-30) cc_final: 0.7739 (m-30) REVERT: B 153 MET cc_start: 0.7823 (ptm) cc_final: 0.7545 (ptt) REVERT: B 312 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8925 (tp) REVERT: B 321 GLN cc_start: 0.8602 (mm110) cc_final: 0.8254 (mm110) REVERT: B 505 TYR cc_start: 0.8484 (m-80) cc_final: 0.7604 (t80) REVERT: B 646 ARG cc_start: 0.8335 (mtm180) cc_final: 0.8015 (mtp180) REVERT: B 661 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: B 705 VAL cc_start: 0.8311 (t) cc_final: 0.8034 (t) REVERT: B 738 CYS cc_start: 0.8142 (t) cc_final: 0.7818 (t) REVERT: B 745 ASP cc_start: 0.7491 (m-30) cc_final: 0.7231 (m-30) REVERT: B 916 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8252 (tt) REVERT: B 947 LYS cc_start: 0.8545 (mttm) cc_final: 0.7934 (mppt) REVERT: B 955 ASN cc_start: 0.7833 (m-40) cc_final: 0.7509 (m-40) REVERT: B 1073 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7813 (tttm) REVERT: B 1091 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8200 (mtt-85) REVERT: B 1107 ARG cc_start: 0.8081 (mpp80) cc_final: 0.7249 (mtt180) REVERT: B 1125 ASN cc_start: 0.8070 (p0) cc_final: 0.7649 (p0) REVERT: C 187 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7306 (mmtm) REVERT: C 202 LYS cc_start: 0.9133 (mttt) cc_final: 0.8892 (mtpm) REVERT: C 246 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7249 (mtt90) REVERT: C 505 TYR cc_start: 0.8499 (m-80) cc_final: 0.7600 (t80) REVERT: C 738 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7670 (t) REVERT: C 745 ASP cc_start: 0.7653 (m-30) cc_final: 0.7444 (m-30) REVERT: C 904 TYR cc_start: 0.8524 (m-10) cc_final: 0.7376 (m-10) REVERT: C 947 LYS cc_start: 0.8564 (mttm) cc_final: 0.8001 (mppt) REVERT: C 1073 LYS cc_start: 0.8012 (ttpt) cc_final: 0.7592 (tttp) outliers start: 38 outliers final: 14 residues processed: 341 average time/residue: 0.6600 time to fit residues: 262.9536 Evaluate side-chains 305 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 248 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 307 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 314 GLN A 563 GLN A 613 GLN A 954 GLN A1054 GLN B 99 ASN B 658 ASN B 762 GLN B 969 ASN B1054 GLN C 99 ASN C 207 HIS C 658 ASN C 762 GLN C 787 GLN C 901 GLN C1005 GLN C1054 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109693 restraints weight = 50170.060| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.76 r_work: 0.2954 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 27678 Z= 0.240 Angle : 0.803 16.002 37827 Z= 0.414 Chirality : 0.054 0.524 4458 Planarity : 0.005 0.053 4755 Dihedral : 5.665 56.033 3563 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.47 % Favored : 95.37 % Rotamer: Outliers : 2.51 % Allowed : 8.35 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.93 (0.14), residues: 3270 helix: 0.89 (0.19), residues: 717 sheet: 0.55 (0.18), residues: 756 loop : -1.87 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1000 TYR 0.027 0.002 TYR B 265 PHE 0.022 0.003 PHE A 802 TRP 0.017 0.002 TRP A 152 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 (27552) covalent geometry : angle 0.76227 / 0.40 (37494) SS BOND : bond 0.00991 / 0.67 ( 45) SS BOND : angle 3.32278 / 2.22 ( 90) hydrogen bonds : bond 0.07864 / 5.27 ( 1056) hydrogen bonds : angle 5.67468 / 3.93 ( 2856) link_BETA1-4 : bond 0.00385 / 0.26 ( 30) link_BETA1-4 : angle 1.09677 / 0.77 ( 90) link_NAG-ASN : bond 0.00627 / 0.37 ( 51) link_NAG-ASN : angle 3.13501 / 2.16 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 284 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8588 (mtt-85) cc_final: 0.8355 (mtt90) REVERT: A 312 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8993 (tt) REVERT: A 394 ASN cc_start: 0.8618 (m-40) cc_final: 0.8137 (m110) REVERT: A 505 TYR cc_start: 0.8408 (m-80) cc_final: 0.7846 (t80) REVERT: A 705 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.7961 (t) REVERT: A 869 MET cc_start: 0.9035 (mtt) cc_final: 0.8810 (mtm) REVERT: A 904 TYR cc_start: 0.8462 (m-10) cc_final: 0.7321 (m-10) REVERT: A 947 LYS cc_start: 0.8743 (mttm) cc_final: 0.8275 (mppt) REVERT: A 955 ASN cc_start: 0.8051 (m-40) cc_final: 0.7776 (m110) REVERT: A 957 GLN cc_start: 0.8675 (tt0) cc_final: 0.8382 (tp40) REVERT: B 154 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: B 218 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: B 321 GLN cc_start: 0.8617 (mm110) cc_final: 0.8292 (mm110) REVERT: B 430 THR cc_start: 0.8740 (m) cc_final: 0.8497 (m) REVERT: B 505 TYR cc_start: 0.8388 (m-80) cc_final: 0.7720 (t80) REVERT: B 646 ARG cc_start: 0.8466 (mtm180) cc_final: 0.8098 (mtp180) REVERT: B 661 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: B 738 CYS cc_start: 0.7719 (t) cc_final: 0.7318 (t) REVERT: B 916 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8420 (tt) REVERT: B 947 LYS cc_start: 0.8599 (mttm) cc_final: 0.8013 (mppt) REVERT: B 955 ASN cc_start: 0.7964 (m-40) cc_final: 0.7658 (m-40) REVERT: B 1125 ASN cc_start: 0.8130 (p0) cc_final: 0.7727 (p0) REVERT: C 246 ARG cc_start: 0.7660 (mtp85) cc_final: 0.7398 (mtt90) REVERT: C 505 TYR cc_start: 0.8412 (m-80) cc_final: 0.7710 (t80) REVERT: C 738 CYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7462 (t) REVERT: C 745 ASP cc_start: 0.7568 (m-30) cc_final: 0.7280 (m-30) REVERT: C 759 PHE cc_start: 0.7272 (m-80) cc_final: 0.6949 (m-80) REVERT: C 947 LYS cc_start: 0.8450 (mttm) cc_final: 0.7963 (mppt) REVERT: C 1045 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8151 (tttp) REVERT: C 1073 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7621 (tttp) outliers start: 72 outliers final: 39 residues processed: 328 average time/residue: 0.6242 time to fit residues: 239.9114 Evaluate side-chains 312 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 326 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 474 GLN A 563 GLN A 613 GLN A 954 GLN B 99 ASN B 440 ASN B 474 GLN B 658 ASN B 779 GLN C 99 ASN C 207 HIS C 314 GLN C 474 GLN C 613 GLN C 658 ASN C 901 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111886 restraints weight = 45674.718| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.67 r_work: 0.3006 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27678 Z= 0.168 Angle : 0.712 12.041 37827 Z= 0.365 Chirality : 0.050 0.439 4458 Planarity : 0.005 0.055 4755 Dihedral : 5.431 55.783 3561 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 2.09 % Allowed : 9.43 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3270 helix: 1.07 (0.20), residues: 714 sheet: 0.61 (0.18), residues: 759 loop : -1.87 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.022 0.002 TYR B 265 PHE 0.023 0.002 PHE C 133 TRP 0.013 0.001 TRP A 152 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (27552) covalent geometry : angle 0.66980 / 0.35 (37494) SS BOND : bond 0.00600 / 0.40 ( 45) SS BOND : angle 3.29888 / 2.34 ( 90) hydrogen bonds : bond 0.06600 / 4.43 ( 1056) hydrogen bonds : angle 5.50210 / 3.81 ( 2856) link_BETA1-4 : bond 0.00359 / 0.24 ( 30) link_BETA1-4 : angle 1.09973 / 0.78 ( 90) link_NAG-ASN : bond 0.00518 / 0.29 ( 51) link_NAG-ASN : angle 2.89483 / 1.97 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.8734 (m-40) cc_final: 0.8245 (m110) REVERT: A 505 TYR cc_start: 0.8536 (m-80) cc_final: 0.7782 (t80) REVERT: A 613 GLN cc_start: 0.8637 (mt0) cc_final: 0.8357 (mt0) REVERT: A 869 MET cc_start: 0.9034 (mtt) cc_final: 0.8782 (mtm) REVERT: A 904 TYR cc_start: 0.8566 (m-10) cc_final: 0.7422 (m-10) REVERT: A 947 LYS cc_start: 0.8802 (mttm) cc_final: 0.8192 (mppt) REVERT: A 955 ASN cc_start: 0.8071 (m-40) cc_final: 0.7822 (m110) REVERT: A 957 GLN cc_start: 0.8747 (tt0) cc_final: 0.8438 (tp40) REVERT: A 994 ASP cc_start: 0.8149 (t70) cc_final: 0.7933 (t70) REVERT: B 154 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: B 321 GLN cc_start: 0.8605 (mm110) cc_final: 0.8262 (mm110) REVERT: B 394 ASN cc_start: 0.8944 (m-40) cc_final: 0.8582 (m110) REVERT: B 505 TYR cc_start: 0.8595 (m-80) cc_final: 0.7706 (t80) REVERT: B 646 ARG cc_start: 0.8449 (mtm180) cc_final: 0.8078 (mtp180) REVERT: B 661 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7934 (mm-30) REVERT: B 738 CYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7942 (t) REVERT: B 947 LYS cc_start: 0.8657 (mttm) cc_final: 0.7946 (mppt) REVERT: B 955 ASN cc_start: 0.7894 (m-40) cc_final: 0.7645 (m-40) REVERT: B 1073 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7890 (tttm) REVERT: B 1113 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: B 1125 ASN cc_start: 0.8109 (p0) cc_final: 0.7637 (p0) REVERT: C 202 LYS cc_start: 0.9198 (mttt) cc_final: 0.8990 (mtpm) REVERT: C 246 ARG cc_start: 0.7492 (mtt90) cc_final: 0.7033 (mtt90) REVERT: C 505 TYR cc_start: 0.8686 (m-80) cc_final: 0.7760 (t80) REVERT: C 738 CYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7776 (t) REVERT: C 745 ASP cc_start: 0.7670 (m-30) cc_final: 0.7406 (m-30) REVERT: C 947 LYS cc_start: 0.8515 (mttm) cc_final: 0.7891 (mppt) REVERT: C 1045 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8241 (tttp) REVERT: C 1073 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7727 (ttpp) outliers start: 60 outliers final: 32 residues processed: 312 average time/residue: 0.6171 time to fit residues: 226.5229 Evaluate side-chains 299 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 222 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 563 GLN A 954 GLN B 99 ASN B 218 GLN B 658 ASN B 762 GLN C 99 ASN C 207 HIS C 658 ASN C 901 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111684 restraints weight = 50040.697| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.20 r_work: 0.2964 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 27678 Z= 0.190 Angle : 0.732 18.506 37827 Z= 0.376 Chirality : 0.051 0.484 4458 Planarity : 0.005 0.056 4755 Dihedral : 5.376 56.138 3557 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.05 % Allowed : 10.02 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3270 helix: 1.01 (0.20), residues: 714 sheet: 0.62 (0.18), residues: 765 loop : -1.90 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1000 TYR 0.023 0.002 TYR B 265 PHE 0.019 0.002 PHE C 133 TRP 0.016 0.002 TRP A 152 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (27552) covalent geometry : angle 0.69430 / 0.37 (37494) SS BOND : bond 0.00797 / 0.53 ( 45) SS BOND : angle 3.17110 / 2.18 ( 90) hydrogen bonds : bond 0.07006 / 4.70 ( 1056) hydrogen bonds : angle 5.51010 / 3.82 ( 2856) link_BETA1-4 : bond 0.00366 / 0.25 ( 30) link_BETA1-4 : angle 1.02478 / 0.72 ( 90) link_NAG-ASN : bond 0.00455 / 0.24 ( 51) link_NAG-ASN : angle 2.81935 / 1.92 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 274 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8324 (mttt) REVERT: A 153 MET cc_start: 0.7917 (ptt) cc_final: 0.7398 (ptt) REVERT: A 158 ARG cc_start: 0.8595 (mtt90) cc_final: 0.8291 (mtt180) REVERT: A 394 ASN cc_start: 0.8628 (m-40) cc_final: 0.8170 (m110) REVERT: A 505 TYR cc_start: 0.8362 (m-80) cc_final: 0.7887 (t80) REVERT: A 613 GLN cc_start: 0.8576 (mt0) cc_final: 0.8332 (mt0) REVERT: A 705 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.7976 (t) REVERT: A 869 MET cc_start: 0.9009 (mtt) cc_final: 0.8776 (mtm) REVERT: A 904 TYR cc_start: 0.8459 (m-10) cc_final: 0.7444 (m-10) REVERT: A 947 LYS cc_start: 0.8738 (mttm) cc_final: 0.8265 (mppt) REVERT: A 955 ASN cc_start: 0.8012 (m-40) cc_final: 0.7744 (m110) REVERT: A 957 GLN cc_start: 0.8709 (tt0) cc_final: 0.8428 (tp40) REVERT: B 154 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: B 215 ASP cc_start: 0.7306 (m-30) cc_final: 0.6926 (m-30) REVERT: B 321 GLN cc_start: 0.8602 (mm110) cc_final: 0.8312 (mm110) REVERT: B 394 ASN cc_start: 0.8747 (m-40) cc_final: 0.8460 (m110) REVERT: B 505 TYR cc_start: 0.8441 (m-80) cc_final: 0.7839 (t80) REVERT: B 646 ARG cc_start: 0.8346 (mtm180) cc_final: 0.7984 (mtp180) REVERT: B 661 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: B 738 CYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7701 (t) REVERT: B 947 LYS cc_start: 0.8625 (mttm) cc_final: 0.8033 (mppt) REVERT: B 955 ASN cc_start: 0.7849 (m-40) cc_final: 0.7580 (m-40) REVERT: B 1113 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: B 1125 ASN cc_start: 0.8111 (p0) cc_final: 0.7712 (p0) REVERT: C 66 HIS cc_start: 0.8018 (m-70) cc_final: 0.7628 (m-70) REVERT: C 187 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7665 (mppt) REVERT: C 246 ARG cc_start: 0.7694 (mtt90) cc_final: 0.7284 (mtt90) REVERT: C 357 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8091 (tpp-160) REVERT: C 505 TYR cc_start: 0.8509 (m-80) cc_final: 0.7861 (t80) REVERT: C 738 CYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7505 (t) REVERT: C 947 LYS cc_start: 0.8461 (mttm) cc_final: 0.7916 (mppt) REVERT: C 1045 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8167 (tttp) REVERT: C 1073 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7664 (ttpp) outliers start: 59 outliers final: 37 residues processed: 307 average time/residue: 0.6151 time to fit residues: 222.0305 Evaluate side-chains 302 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 176 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 290 optimal weight: 0.5980 chunk 246 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 563 GLN A 954 GLN B 30 ASN B 99 ASN B 164 ASN B 218 GLN B 474 GLN B 658 ASN C 99 ASN C 164 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113778 restraints weight = 51879.491| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.28 r_work: 0.2992 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 27678 Z= 0.145 Angle : 0.700 19.888 37827 Z= 0.355 Chirality : 0.049 0.423 4458 Planarity : 0.004 0.052 4755 Dihedral : 5.118 56.252 3557 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 1.88 % Allowed : 10.68 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3270 helix: 1.27 (0.20), residues: 711 sheet: 0.74 (0.18), residues: 744 loop : -1.84 (0.12), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.020 0.001 TYR B 265 PHE 0.023 0.001 PHE C 133 TRP 0.011 0.001 TRP A 152 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (27552) covalent geometry : angle 0.66199 / 0.34 (37494) SS BOND : bond 0.00675 / 0.41 ( 45) SS BOND : angle 3.16709 / 2.28 ( 90) hydrogen bonds : bond 0.05976 / 4.01 ( 1056) hydrogen bonds : angle 5.35694 / 3.71 ( 2856) link_BETA1-4 : bond 0.00363 / 0.24 ( 30) link_BETA1-4 : angle 1.04078 / 0.73 ( 90) link_NAG-ASN : bond 0.00499 / 0.26 ( 51) link_NAG-ASN : angle 2.68194 / 1.84 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8305 (mttt) REVERT: A 153 MET cc_start: 0.7808 (ptt) cc_final: 0.7374 (ptt) REVERT: A 158 ARG cc_start: 0.8492 (mtt90) cc_final: 0.8185 (mtt180) REVERT: A 394 ASN cc_start: 0.8607 (m-40) cc_final: 0.8157 (m110) REVERT: A 505 TYR cc_start: 0.8310 (m-80) cc_final: 0.7858 (t80) REVERT: A 613 GLN cc_start: 0.8528 (mt0) cc_final: 0.8276 (mt0) REVERT: A 738 CYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7542 (t) REVERT: A 762 GLN cc_start: 0.8474 (tt0) cc_final: 0.8114 (mt0) REVERT: A 869 MET cc_start: 0.8980 (mtt) cc_final: 0.8715 (mtm) REVERT: A 904 TYR cc_start: 0.8403 (m-10) cc_final: 0.7419 (m-10) REVERT: A 947 LYS cc_start: 0.8694 (mttm) cc_final: 0.8268 (mppt) REVERT: A 955 ASN cc_start: 0.7932 (m-40) cc_final: 0.7655 (m110) REVERT: A 957 GLN cc_start: 0.8703 (tt0) cc_final: 0.8416 (tp40) REVERT: B 154 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: B 215 ASP cc_start: 0.7318 (m-30) cc_final: 0.6944 (m-30) REVERT: B 321 GLN cc_start: 0.8574 (mm110) cc_final: 0.8290 (mm110) REVERT: B 394 ASN cc_start: 0.8690 (m-40) cc_final: 0.8434 (m110) REVERT: B 505 TYR cc_start: 0.8415 (m-80) cc_final: 0.7837 (t80) REVERT: B 646 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8083 (mtp180) REVERT: B 661 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7812 (mm-30) REVERT: B 738 CYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7693 (t) REVERT: B 817 PHE cc_start: 0.8530 (t80) cc_final: 0.8136 (t80) REVERT: B 834 ILE cc_start: 0.7848 (mm) cc_final: 0.7647 (mm) REVERT: B 947 LYS cc_start: 0.8549 (mttm) cc_final: 0.7992 (mppt) REVERT: B 955 ASN cc_start: 0.7760 (m-40) cc_final: 0.7512 (m-40) REVERT: B 1017 GLU cc_start: 0.7938 (tt0) cc_final: 0.7714 (mt-10) REVERT: B 1073 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7823 (tttm) REVERT: B 1113 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: B 1125 ASN cc_start: 0.8021 (p0) cc_final: 0.7620 (p0) REVERT: C 187 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7589 (mppt) REVERT: C 246 ARG cc_start: 0.7624 (mtt90) cc_final: 0.7237 (mtt90) REVERT: C 505 TYR cc_start: 0.8468 (m-80) cc_final: 0.7852 (t80) REVERT: C 738 CYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7535 (t) REVERT: C 947 LYS cc_start: 0.8370 (mttm) cc_final: 0.7939 (mppt) REVERT: C 1045 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8134 (tttp) REVERT: C 1073 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7623 (ttpp) outliers start: 54 outliers final: 28 residues processed: 295 average time/residue: 0.6494 time to fit residues: 224.2787 Evaluate side-chains 295 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 195 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 259 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 4 optimal weight: 0.0070 chunk 262 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 289 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN A 787 GLN A 954 GLN B 99 ASN B 658 ASN B 762 GLN C 99 ASN C 207 HIS C 658 ASN C 901 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113122 restraints weight = 47407.838| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.25 r_work: 0.3004 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 27678 Z= 0.155 Angle : 0.704 19.607 37827 Z= 0.358 Chirality : 0.049 0.417 4458 Planarity : 0.004 0.051 4755 Dihedral : 5.092 55.929 3557 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 2.09 % Allowed : 10.86 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.74 (0.14), residues: 3270 helix: 1.29 (0.20), residues: 711 sheet: 0.72 (0.18), residues: 744 loop : -1.87 (0.12), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.022 0.002 TYR B 265 PHE 0.014 0.002 PHE A 643 TRP 0.010 0.001 TRP A 152 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (27552) covalent geometry : angle 0.66592 / 0.35 (37494) SS BOND : bond 0.00694 / 0.43 ( 45) SS BOND : angle 3.27353 / 2.30 ( 90) hydrogen bonds : bond 0.06161 / 4.13 ( 1056) hydrogen bonds : angle 5.36163 / 3.71 ( 2856) link_BETA1-4 : bond 0.00357 / 0.24 ( 30) link_BETA1-4 : angle 1.02130 / 0.72 ( 90) link_NAG-ASN : bond 0.00441 / 0.22 ( 51) link_NAG-ASN : angle 2.65546 / 1.84 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8294 (mttt) REVERT: A 153 MET cc_start: 0.7819 (ptt) cc_final: 0.7437 (ptt) REVERT: A 158 ARG cc_start: 0.8563 (mtt90) cc_final: 0.8267 (mtt180) REVERT: A 394 ASN cc_start: 0.8619 (m-40) cc_final: 0.8157 (m110) REVERT: A 505 TYR cc_start: 0.8277 (m-80) cc_final: 0.7850 (t80) REVERT: A 613 GLN cc_start: 0.8501 (mt0) cc_final: 0.8269 (mt0) REVERT: A 705 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.7973 (t) REVERT: A 762 GLN cc_start: 0.8481 (tt0) cc_final: 0.8103 (mt0) REVERT: A 776 LYS cc_start: 0.8784 (ttmp) cc_final: 0.8566 (ttmm) REVERT: A 869 MET cc_start: 0.8979 (mtt) cc_final: 0.8727 (mtm) REVERT: A 904 TYR cc_start: 0.8396 (m-10) cc_final: 0.7392 (m-10) REVERT: A 947 LYS cc_start: 0.8698 (mttm) cc_final: 0.8247 (mppt) REVERT: A 955 ASN cc_start: 0.7899 (m-40) cc_final: 0.7456 (m110) REVERT: A 957 GLN cc_start: 0.8684 (tt0) cc_final: 0.8399 (tp40) REVERT: B 154 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: B 321 GLN cc_start: 0.8575 (mm110) cc_final: 0.8290 (mm110) REVERT: B 394 ASN cc_start: 0.8739 (m-40) cc_final: 0.8456 (m110) REVERT: B 505 TYR cc_start: 0.8397 (m-80) cc_final: 0.7842 (t80) REVERT: B 646 ARG cc_start: 0.8342 (mtm180) cc_final: 0.7968 (mtp180) REVERT: B 661 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7743 (mm-30) REVERT: B 738 CYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7581 (t) REVERT: B 817 PHE cc_start: 0.8514 (t80) cc_final: 0.8100 (t80) REVERT: B 947 LYS cc_start: 0.8552 (mttm) cc_final: 0.7984 (mppt) REVERT: B 955 ASN cc_start: 0.7747 (m-40) cc_final: 0.7496 (m-40) REVERT: B 1073 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7775 (tttm) REVERT: B 1125 ASN cc_start: 0.7999 (p0) cc_final: 0.7586 (p0) REVERT: C 66 HIS cc_start: 0.7950 (m-70) cc_final: 0.7546 (m-70) REVERT: C 158 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8408 (mmm-85) REVERT: C 187 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7615 (mppt) REVERT: C 246 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7302 (mtt90) REVERT: C 323 THR cc_start: 0.8415 (p) cc_final: 0.8157 (p) REVERT: C 505 TYR cc_start: 0.8421 (m-80) cc_final: 0.7832 (t80) REVERT: C 738 CYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7469 (t) REVERT: C 947 LYS cc_start: 0.8369 (mttm) cc_final: 0.7925 (mppt) REVERT: C 1045 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8128 (tttp) REVERT: C 1073 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7592 (ttpp) outliers start: 60 outliers final: 33 residues processed: 301 average time/residue: 0.6576 time to fit residues: 231.8222 Evaluate side-chains 303 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 191 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 307 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN A 954 GLN B 99 ASN B 658 ASN C 99 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113144 restraints weight = 42206.357| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.55 r_work: 0.3021 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 27678 Z= 0.166 Angle : 0.710 19.557 37827 Z= 0.362 Chirality : 0.050 0.432 4458 Planarity : 0.004 0.050 4755 Dihedral : 5.144 56.241 3557 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 1.98 % Allowed : 11.10 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3270 helix: 1.25 (0.20), residues: 711 sheet: 0.78 (0.18), residues: 774 loop : -1.89 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1000 TYR 0.023 0.002 TYR B 265 PHE 0.015 0.002 PHE A 643 TRP 0.010 0.002 TRP A 152 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (27552) covalent geometry : angle 0.67350 / 0.35 (37494) SS BOND : bond 0.00718 / 0.46 ( 45) SS BOND : angle 3.15248 / 2.21 ( 90) hydrogen bonds : bond 0.06457 / 4.33 ( 1056) hydrogen bonds : angle 5.38115 / 3.73 ( 2856) link_BETA1-4 : bond 0.00356 / 0.24 ( 30) link_BETA1-4 : angle 1.01212 / 0.71 ( 90) link_NAG-ASN : bond 0.00427 / 0.21 ( 51) link_NAG-ASN : angle 2.63324 / 1.81 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8256 (mttt) REVERT: A 153 MET cc_start: 0.7791 (ptt) cc_final: 0.7403 (ptt) REVERT: A 158 ARG cc_start: 0.8547 (mtt90) cc_final: 0.8315 (mtt180) REVERT: A 394 ASN cc_start: 0.8731 (m-40) cc_final: 0.8259 (m110) REVERT: A 505 TYR cc_start: 0.8471 (m-80) cc_final: 0.7749 (t80) REVERT: A 613 GLN cc_start: 0.8591 (mt0) cc_final: 0.8276 (mt0) REVERT: A 705 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.7931 (t) REVERT: A 869 MET cc_start: 0.9020 (mtt) cc_final: 0.8777 (mtm) REVERT: A 904 TYR cc_start: 0.8474 (m-10) cc_final: 0.7430 (m-10) REVERT: A 947 LYS cc_start: 0.8764 (mttm) cc_final: 0.8156 (mppt) REVERT: A 955 ASN cc_start: 0.7984 (m-40) cc_final: 0.7551 (m110) REVERT: A 957 GLN cc_start: 0.8744 (tt0) cc_final: 0.8448 (tp40) REVERT: B 321 GLN cc_start: 0.8586 (mm110) cc_final: 0.8271 (mm110) REVERT: B 394 ASN cc_start: 0.8904 (m-40) cc_final: 0.8578 (m110) REVERT: B 505 TYR cc_start: 0.8575 (m-80) cc_final: 0.7741 (t80) REVERT: B 646 ARG cc_start: 0.8327 (mtm180) cc_final: 0.7934 (mtp180) REVERT: B 661 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: B 738 CYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7872 (t) REVERT: B 947 LYS cc_start: 0.8652 (mttm) cc_final: 0.7942 (mppt) REVERT: B 955 ASN cc_start: 0.7842 (m-40) cc_final: 0.7598 (m-40) REVERT: B 1073 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7766 (tttm) REVERT: B 1125 ASN cc_start: 0.7964 (p0) cc_final: 0.7510 (p0) REVERT: C 66 HIS cc_start: 0.7925 (m-70) cc_final: 0.7526 (m-70) REVERT: C 158 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8368 (mmm-85) REVERT: C 187 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7277 (mmtm) REVERT: C 246 ARG cc_start: 0.7470 (mtt90) cc_final: 0.7099 (mtt90) REVERT: C 323 THR cc_start: 0.8412 (p) cc_final: 0.8145 (p) REVERT: C 505 TYR cc_start: 0.8592 (m-80) cc_final: 0.7747 (t80) REVERT: C 738 CYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7708 (t) REVERT: C 947 LYS cc_start: 0.8486 (mttm) cc_final: 0.7918 (mppt) REVERT: C 1045 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8208 (tttp) outliers start: 57 outliers final: 39 residues processed: 294 average time/residue: 0.6120 time to fit residues: 212.3788 Evaluate side-chains 305 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 79 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 130 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 563 GLN A 954 GLN B 66 HIS B 99 ASN B 658 ASN C 30 ASN C 99 ASN C 207 HIS C 658 ASN C 901 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113841 restraints weight = 47517.994| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.18 r_work: 0.3004 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27678 Z= 0.143 Angle : 0.675 18.745 37827 Z= 0.343 Chirality : 0.048 0.436 4458 Planarity : 0.004 0.049 4755 Dihedral : 5.024 56.297 3557 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.89 % Favored : 96.05 % Rotamer: Outliers : 1.77 % Allowed : 11.31 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3270 helix: 1.36 (0.20), residues: 711 sheet: 0.81 (0.18), residues: 774 loop : -1.86 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.020 0.001 TYR B 265 PHE 0.016 0.001 PHE A 643 TRP 0.010 0.001 TRP A 152 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (27552) covalent geometry : angle 0.64037 / 0.33 (37494) SS BOND : bond 0.00697 / 0.42 ( 45) SS BOND : angle 2.92466 / 2.03 ( 90) hydrogen bonds : bond 0.05913 / 3.97 ( 1056) hydrogen bonds : angle 5.29565 / 3.66 ( 2856) link_BETA1-4 : bond 0.00359 / 0.24 ( 30) link_BETA1-4 : angle 1.00096 / 0.70 ( 90) link_NAG-ASN : bond 0.00407 / 0.19 ( 51) link_NAG-ASN : angle 2.52704 / 1.73 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7787 (ptt) cc_final: 0.7405 (ptt) REVERT: A 158 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8299 (mtt180) REVERT: A 394 ASN cc_start: 0.8591 (m-40) cc_final: 0.8169 (m110) REVERT: A 505 TYR cc_start: 0.8321 (m-80) cc_final: 0.7869 (t80) REVERT: A 613 GLN cc_start: 0.8499 (mt0) cc_final: 0.8277 (mt0) REVERT: A 705 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.7974 (t) REVERT: A 762 GLN cc_start: 0.8441 (tt0) cc_final: 0.8089 (mt0) REVERT: A 776 LYS cc_start: 0.8785 (ttmp) cc_final: 0.8568 (ttmm) REVERT: A 869 MET cc_start: 0.8955 (mtt) cc_final: 0.8695 (mtm) REVERT: A 904 TYR cc_start: 0.8379 (m-10) cc_final: 0.7391 (m-10) REVERT: A 947 LYS cc_start: 0.8676 (mttm) cc_final: 0.8249 (mppt) REVERT: A 955 ASN cc_start: 0.7904 (m-40) cc_final: 0.7468 (m110) REVERT: A 957 GLN cc_start: 0.8678 (tt0) cc_final: 0.8393 (tp40) REVERT: B 321 GLN cc_start: 0.8577 (mm110) cc_final: 0.8294 (mm110) REVERT: B 394 ASN cc_start: 0.8713 (m-40) cc_final: 0.8411 (m110) REVERT: B 505 TYR cc_start: 0.8362 (m-80) cc_final: 0.7823 (t80) REVERT: B 646 ARG cc_start: 0.8355 (mtm180) cc_final: 0.7982 (mtp180) REVERT: B 661 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: B 738 CYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7574 (t) REVERT: B 817 PHE cc_start: 0.8497 (t80) cc_final: 0.8085 (t80) REVERT: B 947 LYS cc_start: 0.8535 (mttm) cc_final: 0.7990 (mppt) REVERT: B 955 ASN cc_start: 0.7733 (m-40) cc_final: 0.7494 (m-40) REVERT: B 1073 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7772 (tttm) REVERT: B 1125 ASN cc_start: 0.7992 (p0) cc_final: 0.7550 (p0) REVERT: C 66 HIS cc_start: 0.7916 (m-70) cc_final: 0.7505 (m-70) REVERT: C 158 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8357 (mmm-85) REVERT: C 187 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7360 (mmtm) REVERT: C 246 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7305 (mtt90) REVERT: C 323 THR cc_start: 0.8405 (p) cc_final: 0.8146 (p) REVERT: C 505 TYR cc_start: 0.8404 (m-80) cc_final: 0.7845 (t80) REVERT: C 738 CYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7494 (t) REVERT: C 947 LYS cc_start: 0.8342 (mttm) cc_final: 0.7923 (mppt) REVERT: C 1045 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8112 (tttp) REVERT: C 1073 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7631 (ttpp) outliers start: 51 outliers final: 37 residues processed: 295 average time/residue: 0.6367 time to fit residues: 220.5741 Evaluate side-chains 307 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 198 optimal weight: 0.0370 chunk 127 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN A 954 GLN B 99 ASN B 658 ASN B 762 GLN B 787 GLN C 99 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113579 restraints weight = 50840.672| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.28 r_work: 0.2999 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27678 Z= 0.146 Angle : 0.673 18.293 37827 Z= 0.343 Chirality : 0.048 0.425 4458 Planarity : 0.004 0.048 4755 Dihedral : 5.022 56.361 3557 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 1.60 % Allowed : 11.73 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.64 (0.14), residues: 3270 helix: 1.36 (0.20), residues: 711 sheet: 0.80 (0.18), residues: 774 loop : -1.85 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.021 0.001 TYR B 265 PHE 0.018 0.001 PHE A 643 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (27552) covalent geometry : angle 0.64021 / 0.33 (37494) SS BOND : bond 0.00681 / 0.42 ( 45) SS BOND : angle 2.88646 / 1.99 ( 90) hydrogen bonds : bond 0.05990 / 4.02 ( 1056) hydrogen bonds : angle 5.28883 / 3.66 ( 2856) link_BETA1-4 : bond 0.00361 / 0.24 ( 30) link_BETA1-4 : angle 0.99305 / 0.70 ( 90) link_NAG-ASN : bond 0.00403 / 0.19 ( 51) link_NAG-ASN : angle 2.49117 / 1.70 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7780 (ptt) cc_final: 0.7401 (ptt) REVERT: A 158 ARG cc_start: 0.8532 (mtt90) cc_final: 0.8324 (mtt180) REVERT: A 394 ASN cc_start: 0.8609 (m-40) cc_final: 0.8179 (m110) REVERT: A 505 TYR cc_start: 0.8367 (m-80) cc_final: 0.7881 (t80) REVERT: A 613 GLN cc_start: 0.8522 (mt0) cc_final: 0.8275 (mt0) REVERT: A 705 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.7970 (t) REVERT: A 762 GLN cc_start: 0.8459 (tt0) cc_final: 0.8094 (mt0) REVERT: A 776 LYS cc_start: 0.8810 (ttmp) cc_final: 0.8588 (ttmm) REVERT: A 869 MET cc_start: 0.8958 (mtt) cc_final: 0.8696 (mtm) REVERT: A 904 TYR cc_start: 0.8430 (m-10) cc_final: 0.7418 (m-10) REVERT: A 947 LYS cc_start: 0.8673 (mttm) cc_final: 0.8248 (mppt) REVERT: A 955 ASN cc_start: 0.7901 (m-40) cc_final: 0.7488 (m110) REVERT: A 957 GLN cc_start: 0.8694 (tt0) cc_final: 0.8409 (tp40) REVERT: B 321 GLN cc_start: 0.8621 (mm110) cc_final: 0.8320 (mm110) REVERT: B 394 ASN cc_start: 0.8760 (m-40) cc_final: 0.8470 (m110) REVERT: B 505 TYR cc_start: 0.8386 (m-80) cc_final: 0.7824 (t80) REVERT: B 646 ARG cc_start: 0.8359 (mtm180) cc_final: 0.7980 (mtp180) REVERT: B 661 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: B 738 CYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7614 (t) REVERT: B 947 LYS cc_start: 0.8534 (mttm) cc_final: 0.8006 (mppt) REVERT: B 955 ASN cc_start: 0.7750 (m-40) cc_final: 0.7516 (m-40) REVERT: B 1073 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7760 (tttm) REVERT: B 1125 ASN cc_start: 0.7982 (p0) cc_final: 0.7533 (p0) REVERT: C 187 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7355 (mmtm) REVERT: C 218 GLN cc_start: 0.8271 (mt0) cc_final: 0.8063 (mt0) REVERT: C 246 ARG cc_start: 0.7635 (mtt90) cc_final: 0.7297 (mtt90) REVERT: C 323 THR cc_start: 0.8414 (p) cc_final: 0.8156 (p) REVERT: C 505 TYR cc_start: 0.8426 (m-80) cc_final: 0.7846 (t80) REVERT: C 738 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7549 (t) REVERT: C 947 LYS cc_start: 0.8355 (mttm) cc_final: 0.7942 (mppt) REVERT: C 1045 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8116 (tttp) outliers start: 46 outliers final: 36 residues processed: 293 average time/residue: 0.6366 time to fit residues: 219.3555 Evaluate side-chains 302 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 231 optimal weight: 2.9990 chunk 223 optimal weight: 0.0570 chunk 27 optimal weight: 0.0040 chunk 151 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.7714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 99 ASN A 563 GLN A 954 GLN B 99 ASN B 658 ASN C 99 ASN C 207 HIS C 658 ASN C 901 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113633 restraints weight = 56429.668| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.67 r_work: 0.2977 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27678 Z= 0.142 Angle : 0.663 17.945 37827 Z= 0.338 Chirality : 0.048 0.420 4458 Planarity : 0.004 0.050 4755 Dihedral : 4.997 56.621 3557 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 1.70 % Allowed : 11.76 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.62 (0.14), residues: 3270 helix: 1.38 (0.20), residues: 711 sheet: 0.81 (0.18), residues: 774 loop : -1.84 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.020 0.001 TYR B 265 PHE 0.020 0.001 PHE A 643 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (27552) covalent geometry : angle 0.63114 / 0.33 (37494) SS BOND : bond 0.00653 / 0.40 ( 45) SS BOND : angle 2.79940 / 1.92 ( 90) hydrogen bonds : bond 0.05877 / 3.94 ( 1056) hydrogen bonds : angle 5.27934 / 3.65 ( 2856) link_BETA1-4 : bond 0.00362 / 0.24 ( 30) link_BETA1-4 : angle 0.98531 / 0.69 ( 90) link_NAG-ASN : bond 0.00392 / 0.18 ( 51) link_NAG-ASN : angle 2.44979 / 1.67 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11228.60 seconds wall clock time: 191 minutes 25.40 seconds (11485.40 seconds total)