Starting phenix.real_space_refine on Sun Jul 5 05:14:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v7f_31769/07_2026/7v7f_31769.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7f_31769/07_2026/7v7f_31769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7f_31769/07_2026/7v7f_31769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7f_31769/07_2026/7v7f_31769.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v7f_31769/07_2026/7v7f_31769.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v7f_31769/07_2026/7v7f_31769.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v7f_31769/07_2026/7v7f_31769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7f_31769/07_2026/7v7f_31769.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.037 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 111 5.16 5 C 16203 2.51 5 N 4137 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25503 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.88, per 1000 atoms: 0.23 Number of scatterers: 25503 At special positions: 0 Unit cell: (140.8, 150.7, 198, 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 111 16.00 O 5052 8.00 N 4137 7.00 C 16203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 603 " " NAG A2003 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 234 " " NAG B2003 " - " ASN B 331 " " NAG B2004 " - " ASN B 603 " " NAG B2005 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 331 " " NAG C2003 " - " ASN C 603 " " NAG C2004 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 343 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN A 709 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 343 " " NAG U 1 " - " ASN B 616 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 165 " " NAG d 1 " - " ASN C 234 " " NAG e 1 " - " ASN C 282 " " NAG f 1 " - " ASN C 343 " " NAG g 1 " - " ASN C 616 " " NAG h 1 " - " ASN C 709 " " NAG i 1 " - " ASN C 717 " " NAG j 1 " - " ASN C 801 " " NAG k 1 " - " ASN C1074 " " NAG l 1 " - " ASN C1098 " " NAG m 1 " - " ASN C1134 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 992.9 milliseconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5832 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 51 sheets defined 25.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.092A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.919A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.638A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.109A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.889A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.512A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.636A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.647A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.711A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.529A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.775A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.554A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.836A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.524A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.908A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.576A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.195A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.745A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.503A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.526A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.387A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.571A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.907A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.041A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.572A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.639A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.769A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.879A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.119A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.812A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.894A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.574A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.402A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.542A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.887A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.688A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.391A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.487A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 3.600A pdb=" N ASN C 703 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.426A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1096 removed outlier: 4.820A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.588A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.887A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.086A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.515A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.185A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.568A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 removed outlier: 7.683A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.362A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.066A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.555A pdb=" N ILE C 788 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.760A pdb=" N HIS B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.539A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.009A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.509A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.014A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.850A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.066A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.598A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.710A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 143 through 144 removed outlier: 5.517A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.544A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.358A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.088A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.831A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.787A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1096 975 hydrogen bonds defined for protein. 2649 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: 5.89 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8030 1.34 - 1.46: 6487 1.46 - 1.58: 11406 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26061 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 ... (remaining 26056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 34500 1.75 - 3.49: 888 3.49 - 5.24: 57 5.24 - 6.99: 17 6.99 - 8.73: 7 Bond angle restraints: 35469 Sorted by residual: angle pdb=" N ASP A1101 " pdb=" CA ASP A1101 " pdb=" CB ASP A1101 " ideal model delta sigma weight residual 114.17 109.62 4.55 1.14e+00 7.69e-01 1.59e+01 angle pdb=" CG1 ILE C 233 " pdb=" CB ILE C 233 " pdb=" CG2 ILE C 233 " ideal model delta sigma weight residual 110.70 101.97 8.73 3.00e+00 1.11e-01 8.47e+00 angle pdb=" N TRP A1102 " pdb=" CA TRP A1102 " pdb=" C TRP A1102 " ideal model delta sigma weight residual 110.80 116.74 -5.94 2.13e+00 2.20e-01 7.77e+00 angle pdb=" CA VAL B 729 " pdb=" C VAL B 729 " pdb=" N SER B 730 " ideal model delta sigma weight residual 116.60 120.40 -3.80 1.45e+00 4.76e-01 6.87e+00 angle pdb=" N PRO A 561 " pdb=" CA PRO A 561 " pdb=" C PRO A 561 " ideal model delta sigma weight residual 112.47 117.77 -5.30 2.06e+00 2.36e-01 6.63e+00 ... (remaining 35464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13436 17.96 - 35.91: 1142 35.91 - 53.87: 199 53.87 - 71.83: 34 71.83 - 89.78: 21 Dihedral angle restraints: 14832 sinusoidal: 5769 harmonic: 9063 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 4.14 88.86 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -164.01 78.01 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -163.98 77.98 1 1.00e+01 1.00e-02 7.60e+01 ... (remaining 14829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 4251 0.161 - 0.322: 15 0.322 - 0.483: 3 0.483 - 0.644: 1 0.644 - 0.806: 2 Chirality restraints: 4272 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" C1 NAG k 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG k 1 " pdb=" O5 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" C1 NAG B2002 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B2002 " pdb=" O5 NAG B2002 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 4269 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.017 2.00e-02 2.50e+03 1.63e-02 4.63e+00 pdb=" CG PHE A 906 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.69e+00 pdb=" N PRO C 295 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " -0.015 2.00e-02 2.50e+03 1.41e-02 3.48e+00 pdb=" CG PHE C 906 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " -0.002 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 334 2.63 - 3.20: 22793 3.20 - 3.76: 37246 3.76 - 4.33: 50369 4.33 - 4.90: 84519 Nonbonded interactions: 195261 Sorted by model distance: nonbonded pdb=" OG SER B 349 " pdb=" O ARG B 452 " model vdw 2.061 3.040 nonbonded pdb=" OD1 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 2.157 3.040 nonbonded pdb=" OE2 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.196 3.120 nonbonded pdb=" O ASP B 405 " pdb=" NH1 ARG B 408 " model vdw 2.224 3.120 nonbonded pdb=" NE2 GLN A 314 " pdb=" O THR A 315 " model vdw 2.226 3.120 ... (remaining 195256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 2003) selection = (chain 'C' and resid 14 through 2003) } 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' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.380 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 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:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26182 Z= 0.214 Angle : 0.705 21.303 35795 Z= 0.330 Chirality : 0.051 0.806 4272 Planarity : 0.004 0.048 4479 Dihedral : 13.675 89.783 8889 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.13 (0.15), residues: 3066 helix: 2.01 (0.21), residues: 649 sheet: 0.56 (0.19), residues: 760 loop : -1.33 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1039 TYR 0.015 0.001 TYR B1067 PHE 0.038 0.001 PHE A 906 TRP 0.014 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (26061) covalent geometry : angle 0.62822 / 0.31 (35469) SS BOND : bond 0.00277 / 0.16 ( 37) SS BOND : angle 1.48443 / 1.00 ( 74) hydrogen bonds : bond 0.12298 / 8.04 ( 971) hydrogen bonds : angle 5.94249 / 4.00 ( 2649) link_BETA1-4 : bond 0.00403 / 0.24 ( 36) link_BETA1-4 : angle 2.17142 / 1.51 ( 108) link_NAG-ASN : bond 0.00676 / 0.55 ( 48) link_NAG-ASN : angle 4.66936 / 3.29 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 449 TYR cc_start: 0.8675 (m-10) cc_final: 0.8318 (m-80) outliers start: 0 outliers final: 1 residues processed: 74 average time/residue: 0.5549 time to fit residues: 49.1866 Evaluate side-chains 49 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 740 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN B 14 GLN B 66 HIS B 81 ASN B 914 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.081159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.053083 restraints weight = 87694.632| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 5.07 r_work: 0.2804 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26182 Z= 0.189 Angle : 0.655 19.576 35795 Z= 0.313 Chirality : 0.048 0.507 4272 Planarity : 0.004 0.049 4479 Dihedral : 4.276 55.028 3342 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 0.44 % Allowed : 5.88 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3066 helix: 1.95 (0.21), residues: 669 sheet: 0.53 (0.19), residues: 753 loop : -1.36 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1039 TYR 0.015 0.001 TYR B1067 PHE 0.024 0.001 PHE C 906 TRP 0.019 0.001 TRP A 258 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (26061) covalent geometry : angle 0.58686 / 0.30 (35469) SS BOND : bond 0.00334 / 0.19 ( 37) SS BOND : angle 1.65565 / 1.10 ( 74) hydrogen bonds : bond 0.05687 / 3.70 ( 971) hydrogen bonds : angle 5.28451 / 3.60 ( 2649) link_BETA1-4 : bond 0.00266 / 0.16 ( 36) link_BETA1-4 : angle 1.70364 / 1.22 ( 108) link_NAG-ASN : bond 0.00605 / 0.49 ( 48) link_NAG-ASN : angle 4.26981 / 3.02 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ASN cc_start: 0.5940 (OUTLIER) cc_final: 0.5617 (p0) REVERT: B 636 TYR cc_start: 0.3516 (OUTLIER) cc_final: 0.2093 (p90) REVERT: C 1002 GLN cc_start: 0.9003 (tp40) cc_final: 0.8664 (tp-100) outliers start: 12 outliers final: 3 residues processed: 58 average time/residue: 0.5292 time to fit residues: 37.5646 Evaluate side-chains 54 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 940 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 205 optimal weight: 0.8980 chunk 138 optimal weight: 0.2980 chunk 268 optimal weight: 3.9990 chunk 207 optimal weight: 0.0980 chunk 304 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.071458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.046255 restraints weight = 102583.551| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.21 r_work: 0.2853 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 26182 Z= 0.107 Angle : 0.595 18.233 35795 Z= 0.281 Chirality : 0.046 0.487 4272 Planarity : 0.004 0.054 4479 Dihedral : 3.946 18.679 3339 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 0.51 % Allowed : 8.86 % Favored : 90.63 % 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: 0.04 (0.15), residues: 3066 helix: 2.02 (0.21), residues: 671 sheet: 0.73 (0.19), residues: 735 loop : -1.21 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.013 0.001 TYR A1067 PHE 0.017 0.001 PHE C 133 TRP 0.013 0.001 TRP A 258 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (26061) covalent geometry : angle 0.52757 / 0.27 (35469) SS BOND : bond 0.00275 / 0.17 ( 37) SS BOND : angle 1.36264 / 0.89 ( 74) hydrogen bonds : bond 0.04707 / 3.04 ( 971) hydrogen bonds : angle 4.96956 / 3.39 ( 2649) link_BETA1-4 : bond 0.00439 / 0.27 ( 36) link_BETA1-4 : angle 1.65166 / 1.16 ( 108) link_NAG-ASN : bond 0.00652 / 0.53 ( 48) link_NAG-ASN : angle 4.06405 / 2.88 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 636 TYR cc_start: 0.3526 (OUTLIER) cc_final: 0.2121 (p90) REVERT: C 1002 GLN cc_start: 0.9085 (tp40) cc_final: 0.8606 (tp-100) outliers start: 14 outliers final: 5 residues processed: 62 average time/residue: 0.4824 time to fit residues: 36.9324 Evaluate side-chains 54 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 292 optimal weight: 5.9990 chunk 295 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.070479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.045113 restraints weight = 102140.655| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 4.18 r_work: 0.2818 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26182 Z= 0.176 Angle : 0.620 18.061 35795 Z= 0.296 Chirality : 0.046 0.483 4272 Planarity : 0.004 0.053 4479 Dihedral : 4.003 17.875 3339 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.09 % Favored : 94.81 % Rotamer: Outliers : 1.10 % Allowed : 10.36 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3066 helix: 2.07 (0.21), residues: 667 sheet: 0.60 (0.19), residues: 746 loop : -1.28 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.016 0.001 TYR B 449 PHE 0.020 0.001 PHE C 133 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (26061) covalent geometry : angle 0.55816 / 0.28 (35469) SS BOND : bond 0.00319 / 0.19 ( 37) SS BOND : angle 1.52036 / 1.00 ( 74) hydrogen bonds : bond 0.05221 / 3.38 ( 971) hydrogen bonds : angle 4.99327 / 3.42 ( 2649) link_BETA1-4 : bond 0.00311 / 0.19 ( 36) link_BETA1-4 : angle 1.59063 / 1.11 ( 108) link_NAG-ASN : bond 0.00568 / 0.46 ( 48) link_NAG-ASN : angle 3.97494 / 2.82 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 52 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8689 (p) REVERT: A 1132 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9036 (tp) REVERT: B 636 TYR cc_start: 0.3567 (OUTLIER) cc_final: 0.2595 (p90) REVERT: C 1002 GLN cc_start: 0.9115 (tp40) cc_final: 0.8601 (tp-100) outliers start: 30 outliers final: 10 residues processed: 76 average time/residue: 0.4168 time to fit residues: 40.1842 Evaluate side-chains 62 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 103 optimal weight: 20.0000 chunk 80 optimal weight: 0.3980 chunk 231 optimal weight: 4.9990 chunk 253 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.070696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.045362 restraints weight = 101638.254| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 4.19 r_work: 0.2826 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26182 Z= 0.142 Angle : 0.600 17.036 35795 Z= 0.285 Chirality : 0.046 0.478 4272 Planarity : 0.004 0.053 4479 Dihedral : 3.973 18.891 3339 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 0.99 % Allowed : 11.83 % Favored : 87.17 % 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: -0.00 (0.15), residues: 3066 helix: 2.08 (0.21), residues: 667 sheet: 0.64 (0.19), residues: 733 loop : -1.24 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.017 0.001 TYR C 369 PHE 0.016 0.001 PHE A1121 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (26061) covalent geometry : angle 0.54001 / 0.27 (35469) SS BOND : bond 0.00285 / 0.16 ( 37) SS BOND : angle 1.45144 / 0.95 ( 74) hydrogen bonds : bond 0.04947 / 3.20 ( 971) hydrogen bonds : angle 4.91547 / 3.36 ( 2649) link_BETA1-4 : bond 0.00350 / 0.21 ( 36) link_BETA1-4 : angle 1.55539 / 1.09 ( 108) link_NAG-ASN : bond 0.00572 / 0.47 ( 48) link_NAG-ASN : angle 3.85763 / 2.74 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8620 (mp) cc_final: 0.8248 (pp) REVERT: A 1132 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9046 (tp) REVERT: B 636 TYR cc_start: 0.3619 (OUTLIER) cc_final: 0.2682 (p90) REVERT: C 742 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9115 (tt) REVERT: C 878 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9187 (tt) REVERT: C 1002 GLN cc_start: 0.9147 (tp40) cc_final: 0.8605 (tp-100) outliers start: 27 outliers final: 11 residues processed: 72 average time/residue: 0.4831 time to fit residues: 42.7736 Evaluate side-chains 61 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 106 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 5 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 262 optimal weight: 0.2980 chunk 240 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.071781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.046580 restraints weight = 102886.968| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 4.25 r_work: 0.2865 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26182 Z= 0.098 Angle : 0.565 15.777 35795 Z= 0.267 Chirality : 0.045 0.477 4272 Planarity : 0.004 0.056 4479 Dihedral : 3.760 17.440 3339 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 0.88 % Allowed : 12.79 % Favored : 86.33 % 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: 0.19 (0.15), residues: 3066 helix: 2.20 (0.21), residues: 670 sheet: 0.87 (0.19), residues: 723 loop : -1.14 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.016 0.001 TYR B 449 PHE 0.019 0.001 PHE A 140 TRP 0.011 0.001 TRP B 436 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (26061) covalent geometry : angle 0.50799 / 0.25 (35469) SS BOND : bond 0.00233 / 0.14 ( 37) SS BOND : angle 1.11426 / 0.73 ( 74) hydrogen bonds : bond 0.04218 / 2.72 ( 971) hydrogen bonds : angle 4.71572 / 3.23 ( 2649) link_BETA1-4 : bond 0.00419 / 0.26 ( 36) link_BETA1-4 : angle 1.54035 / 1.07 ( 108) link_NAG-ASN : bond 0.00615 / 0.50 ( 48) link_NAG-ASN : angle 3.66895 / 2.61 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8616 (mp) cc_final: 0.8210 (pp) REVERT: A 581 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8720 (p) REVERT: A 878 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9265 (tp) REVERT: B 636 TYR cc_start: 0.3644 (OUTLIER) cc_final: 0.2646 (p90) REVERT: C 878 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9170 (tt) REVERT: C 979 ASP cc_start: 0.8558 (t0) cc_final: 0.8259 (t0) REVERT: C 1002 GLN cc_start: 0.9128 (tp40) cc_final: 0.8563 (tp-100) outliers start: 24 outliers final: 11 residues processed: 75 average time/residue: 0.4602 time to fit residues: 41.9753 Evaluate side-chains 63 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 297 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 281 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 294 optimal weight: 0.8980 chunk 237 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.071149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045797 restraints weight = 102441.204| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.22 r_work: 0.2841 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26182 Z= 0.129 Angle : 0.584 15.500 35795 Z= 0.275 Chirality : 0.045 0.470 4272 Planarity : 0.004 0.055 4479 Dihedral : 3.790 17.405 3339 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 0.99 % Allowed : 13.23 % Favored : 85.78 % 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: 0.18 (0.15), residues: 3066 helix: 2.19 (0.21), residues: 669 sheet: 0.82 (0.19), residues: 722 loop : -1.13 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.014 0.001 TYR C 369 PHE 0.015 0.001 PHE A1121 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (26061) covalent geometry : angle 0.53198 / 0.26 (35469) SS BOND : bond 0.00252 / 0.14 ( 37) SS BOND : angle 1.23054 / 0.81 ( 74) hydrogen bonds : bond 0.04571 / 2.95 ( 971) hydrogen bonds : angle 4.72198 / 3.23 ( 2649) link_BETA1-4 : bond 0.00402 / 0.27 ( 36) link_BETA1-4 : angle 1.84598 / 1.25 ( 108) link_NAG-ASN : bond 0.00566 / 0.47 ( 48) link_NAG-ASN : angle 3.43323 / 2.41 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8710 (mp) cc_final: 0.8339 (pp) REVERT: A 581 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8709 (p) REVERT: A 1132 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9049 (tp) REVERT: B 636 TYR cc_start: 0.3780 (OUTLIER) cc_final: 0.2938 (p90) REVERT: C 242 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8760 (mm) REVERT: C 878 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9200 (tt) REVERT: C 979 ASP cc_start: 0.8608 (t0) cc_final: 0.8303 (t0) REVERT: C 1002 GLN cc_start: 0.9111 (tp40) cc_final: 0.8550 (tp-100) outliers start: 27 outliers final: 13 residues processed: 76 average time/residue: 0.3993 time to fit residues: 38.1727 Evaluate side-chains 64 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 116 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 139 optimal weight: 0.2980 chunk 159 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.071154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.046653 restraints weight = 102819.201| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.39 r_work: 0.2820 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26182 Z= 0.133 Angle : 0.580 14.984 35795 Z= 0.275 Chirality : 0.045 0.469 4272 Planarity : 0.004 0.054 4479 Dihedral : 3.808 17.713 3339 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 0.96 % Allowed : 13.52 % Favored : 85.52 % 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: 0.16 (0.15), residues: 3066 helix: 2.16 (0.21), residues: 670 sheet: 0.75 (0.19), residues: 728 loop : -1.11 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.014 0.001 TYR B 449 PHE 0.021 0.001 PHE A 140 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (26061) covalent geometry : angle 0.53099 / 0.26 (35469) SS BOND : bond 0.00257 / 0.14 ( 37) SS BOND : angle 1.29553 / 0.88 ( 74) hydrogen bonds : bond 0.04662 / 3.01 ( 971) hydrogen bonds : angle 4.72729 / 3.24 ( 2649) link_BETA1-4 : bond 0.00347 / 0.21 ( 36) link_BETA1-4 : angle 1.72761 / 1.18 ( 108) link_NAG-ASN : bond 0.00544 / 0.45 ( 48) link_NAG-ASN : angle 3.34161 / 2.35 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8723 (mp) cc_final: 0.8398 (pp) REVERT: A 581 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8716 (p) REVERT: A 1132 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9074 (tp) REVERT: A 1138 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.6891 (p90) REVERT: B 636 TYR cc_start: 0.3700 (OUTLIER) cc_final: 0.2809 (p90) REVERT: C 242 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8784 (mm) REVERT: C 878 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9208 (tt) REVERT: C 979 ASP cc_start: 0.8615 (t0) cc_final: 0.8332 (t0) REVERT: C 1002 GLN cc_start: 0.9150 (tp40) cc_final: 0.8592 (tp-100) outliers start: 26 outliers final: 15 residues processed: 73 average time/residue: 0.4333 time to fit residues: 39.5824 Evaluate side-chains 69 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 137 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 8 optimal weight: 0.0270 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.071577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.046256 restraints weight = 103002.463| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.25 r_work: 0.2852 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26182 Z= 0.104 Angle : 0.566 14.167 35795 Z= 0.268 Chirality : 0.045 0.470 4272 Planarity : 0.004 0.055 4479 Dihedral : 3.713 17.399 3339 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 0.88 % Allowed : 14.08 % Favored : 85.04 % 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: 0.23 (0.15), residues: 3066 helix: 2.19 (0.21), residues: 672 sheet: 0.78 (0.19), residues: 733 loop : -1.05 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.014 0.001 TYR A1067 PHE 0.014 0.001 PHE C 133 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (26061) covalent geometry : angle 0.51823 / 0.26 (35469) SS BOND : bond 0.00229 / 0.13 ( 37) SS BOND : angle 1.12193 / 0.75 ( 74) hydrogen bonds : bond 0.04332 / 2.80 ( 971) hydrogen bonds : angle 4.66584 / 3.19 ( 2649) link_BETA1-4 : bond 0.00384 / 0.23 ( 36) link_BETA1-4 : angle 1.70757 / 1.17 ( 108) link_NAG-ASN : bond 0.00573 / 0.47 ( 48) link_NAG-ASN : angle 3.25708 / 2.29 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8819 (mp) cc_final: 0.8513 (pp) REVERT: A 581 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8719 (p) REVERT: A 1132 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9045 (tp) REVERT: B 636 TYR cc_start: 0.3580 (OUTLIER) cc_final: 0.2652 (p90) REVERT: C 242 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8761 (mm) REVERT: C 742 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9014 (mt) REVERT: C 878 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9193 (tt) REVERT: C 979 ASP cc_start: 0.8578 (t0) cc_final: 0.8294 (t0) REVERT: C 1002 GLN cc_start: 0.9104 (tp40) cc_final: 0.8547 (tp-100) outliers start: 24 outliers final: 14 residues processed: 72 average time/residue: 0.4335 time to fit residues: 38.9576 Evaluate side-chains 68 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 150 optimal weight: 10.0000 chunk 305 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 251 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 160 optimal weight: 0.6980 chunk 20 optimal weight: 30.0000 chunk 273 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.070566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.045068 restraints weight = 102778.416| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.23 r_work: 0.2817 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26182 Z= 0.166 Angle : 0.600 14.354 35795 Z= 0.286 Chirality : 0.046 0.464 4272 Planarity : 0.004 0.054 4479 Dihedral : 3.867 17.745 3339 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 0.96 % Allowed : 14.04 % Favored : 85.01 % 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: 0.14 (0.15), residues: 3066 helix: 2.15 (0.21), residues: 668 sheet: 0.76 (0.19), residues: 716 loop : -1.12 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.016 0.001 TYR B 449 PHE 0.025 0.001 PHE A 140 TRP 0.011 0.001 TRP C1102 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (26061) covalent geometry : angle 0.55333 / 0.28 (35469) SS BOND : bond 0.00282 / 0.15 ( 37) SS BOND : angle 1.41459 / 0.96 ( 74) hydrogen bonds : bond 0.04991 / 3.22 ( 971) hydrogen bonds : angle 4.79902 / 3.29 ( 2649) link_BETA1-4 : bond 0.00304 / 0.19 ( 36) link_BETA1-4 : angle 1.70716 / 1.17 ( 108) link_NAG-ASN : bond 0.00508 / 0.42 ( 48) link_NAG-ASN : angle 3.27774 / 2.30 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8870 (mp) cc_final: 0.8584 (pp) REVERT: A 581 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8712 (p) REVERT: A 1132 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9077 (tp) REVERT: A 1138 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.6878 (p90) REVERT: B 636 TYR cc_start: 0.3579 (OUTLIER) cc_final: 0.3002 (p90) REVERT: C 742 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9086 (tt) REVERT: C 878 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9202 (tt) REVERT: C 979 ASP cc_start: 0.8625 (t0) cc_final: 0.8342 (t0) REVERT: C 1002 GLN cc_start: 0.9136 (tp40) cc_final: 0.8582 (tp-100) outliers start: 26 outliers final: 19 residues processed: 75 average time/residue: 0.3925 time to fit residues: 37.3585 Evaluate side-chains 75 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 235 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 274 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.070344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.044830 restraints weight = 102093.573| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.23 r_work: 0.2810 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26182 Z= 0.181 Angle : 0.610 14.202 35795 Z= 0.293 Chirality : 0.046 0.463 4272 Planarity : 0.004 0.055 4479 Dihedral : 3.932 18.656 3339 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.89 % Favored : 95.04 % Rotamer: Outliers : 0.99 % Allowed : 14.22 % Favored : 84.79 % 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: 0.06 (0.15), residues: 3066 helix: 2.09 (0.21), residues: 668 sheet: 0.69 (0.19), residues: 720 loop : -1.16 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.017 0.001 TYR C 369 PHE 0.021 0.001 PHE B 456 TRP 0.011 0.001 TRP B1102 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (26061) covalent geometry : angle 0.56464 / 0.28 (35469) SS BOND : bond 0.00288 / 0.16 ( 37) SS BOND : angle 1.46390 / 1.00 ( 74) hydrogen bonds : bond 0.05143 / 3.32 ( 971) hydrogen bonds : angle 4.84748 / 3.32 ( 2649) link_BETA1-4 : bond 0.00308 / 0.19 ( 36) link_BETA1-4 : angle 1.70188 / 1.16 ( 108) link_NAG-ASN : bond 0.00506 / 0.42 ( 48) link_NAG-ASN : angle 3.27903 / 2.30 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7104.81 seconds wall clock time: 122 minutes 16.00 seconds (7336.00 seconds total)