Starting phenix.real_space_refine on Fri Sep 19 11:38:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7e_31768/09_2025/7v7e_31768.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7e_31768/09_2025/7v7e_31768.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/7v7e_31768/09_2025/7v7e_31768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7e_31768/09_2025/7v7e_31768.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7e_31768/09_2025/7v7e_31768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7e_31768/09_2025/7v7e_31768.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= -0.001 sd= 0.038 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 16103 2.51 5 N 4111 2.21 5 O 5015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25340 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8064 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 53, 'TRANS': 977} Chain breaks: 7 Chain: "B" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8064 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 53, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8064 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 53, 'TRANS': 977} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 15 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.38, per 1000 atoms: 0.25 Number of scatterers: 25340 At special positions: 0 Unit cell: (140.8, 151.8, 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 5015 8.00 N 4111 7.00 C 16103 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=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 343 " " NAG A2004 " - " ASN A 603 " " NAG A2005 " - " 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 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 122 " " NAG P 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 709 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 343 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 709 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " " NAG k 1 " - " ASN C1134 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5802 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 48 sheets defined 24.8% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.729A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 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: 3.960A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.982A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.603A 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 removed outlier: 3.519A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.540A 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 removed outlier: 3.548A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.631A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.843A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.593A 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 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.244A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.423A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (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: 3.682A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.981A 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 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.348A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) 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: 3.583A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.214A 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 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.231A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.613A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.349A 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 738 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.895A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.120A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.505A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.618A 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: 3.609A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.064A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (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: 8.308A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.171A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.811A 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: 3.580A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 144 removed outlier: 5.378A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.370A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.525A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.956A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.991A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.889A 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: 4.536A 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 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.519A 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: 4.706A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.929A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.639A 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: 6.918A 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: 4.034A 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: 3.587A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.159A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.966A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.446A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.111A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.674A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.582A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.582A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.584A 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: 4.994A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.775A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.502A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.559A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.559A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 10.577A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.600A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.352A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.155A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.616A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.538A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.875A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1096 994 hydrogen bonds defined for protein. 2721 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: 4.81 Time building geometry restraints manager: 2.87 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: 7985 1.34 - 1.46: 6307 1.46 - 1.58: 11462 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25892 Sorted by residual: bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 25887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 34064 1.57 - 3.13: 1037 3.13 - 4.70: 107 4.70 - 6.26: 17 6.26 - 7.83: 11 Bond angle restraints: 35236 Sorted by residual: angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.20 109.25 3.95 9.60e-01 1.09e+00 1.70e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 113.20 109.47 3.73 9.60e-01 1.09e+00 1.51e+01 angle pdb=" C ALA C 570 " pdb=" N ASP C 571 " pdb=" CA ASP C 571 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" N LEU B 455 " pdb=" CA LEU B 455 " pdb=" C LEU B 455 " ideal model delta sigma weight residual 114.56 110.72 3.84 1.27e+00 6.20e-01 9.13e+00 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.37 -3.67 1.22e+00 6.72e-01 9.04e+00 ... (remaining 35231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.89: 15418 22.89 - 45.77: 903 45.77 - 68.66: 126 68.66 - 91.54: 27 91.54 - 114.43: 17 Dihedral angle restraints: 16491 sinusoidal: 7479 harmonic: 9012 Sorted by residual: 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 -165.35 79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -165.02 79.02 1 1.00e+01 1.00e-02 7.77e+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 -161.80 75.80 1 1.00e+01 1.00e-02 7.25e+01 ... (remaining 16488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4035 0.101 - 0.203: 202 0.203 - 0.304: 3 0.304 - 0.406: 2 0.406 - 0.507: 2 Chirality restraints: 4244 Sorted by residual: 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 -1.89 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" C1 NAG B2003 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B2003 " pdb=" O5 NAG B2003 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 4241 not shown) Planarity restraints: 4501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO C 986 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO B 561 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO C 295 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " 0.028 5.00e-02 4.00e+02 ... (remaining 4498 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 464 2.66 - 3.22: 23721 3.22 - 3.78: 37221 3.78 - 4.34: 49349 4.34 - 4.90: 82561 Nonbonded interactions: 193316 Sorted by model distance: nonbonded pdb=" OG SER B 349 " pdb=" O ARG B 452 " model vdw 2.106 3.040 nonbonded pdb=" OE2 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.178 3.120 nonbonded pdb=" OE1 GLN B 804 " pdb=" O6 NAG V 1 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.245 3.040 ... (remaining 193311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 2004) selection = (chain 'B' and resid 14 through 2004) selection = chain 'C' } 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' } 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: 4.490 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.340 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.004 0.058 26011 Z= 0.198 Angle : 0.651 14.683 35556 Z= 0.319 Chirality : 0.049 0.507 4244 Planarity : 0.004 0.058 4453 Dihedral : 14.059 114.431 10578 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 aren not related in a simple way. whole: -0.18 (0.15), residues: 3045 helix: 1.92 (0.21), residues: 671 sheet: 0.45 (0.19), residues: 739 loop : -1.33 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.018 0.001 TYR B 636 PHE 0.024 0.001 PHE C 906 TRP 0.019 0.001 TRP C 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00419 (25892) covalent geometry : angle 0.61926 (35236) SS BOND : bond 0.00246 ( 37) SS BOND : angle 1.29775 ( 74) hydrogen bonds : bond 0.13011 ( 977) hydrogen bonds : angle 6.05294 ( 2721) link_BETA1-4 : bond 0.00492 ( 34) link_BETA1-4 : angle 1.81173 ( 102) link_NAG-ASN : bond 0.00440 ( 48) link_NAG-ASN : angle 2.76691 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.906 Fit side-chains REVERT: B 392 PHE cc_start: 0.7157 (m-80) cc_final: 0.6908 (m-80) REVERT: C 153 MET cc_start: 0.2890 (ptt) cc_final: 0.1720 (ppp) REVERT: C 351 TYR cc_start: 0.7493 (p90) cc_final: 0.6776 (p90) REVERT: C 436 TRP cc_start: 0.6982 (p-90) cc_final: 0.6686 (p-90) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.6181 time to fit residues: 65.8022 Evaluate side-chains 68 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 388 ASN B 901 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.086728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052513 restraints weight = 95625.256| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.20 r_work: 0.2841 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 26011 Z= 0.227 Angle : 0.649 13.453 35556 Z= 0.323 Chirality : 0.048 0.482 4244 Planarity : 0.004 0.060 4453 Dihedral : 8.725 99.890 5040 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 0.52 % Allowed : 6.45 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.15), residues: 3045 helix: 1.74 (0.21), residues: 681 sheet: 0.42 (0.19), residues: 729 loop : -1.35 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1039 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.002 PHE C 906 TRP 0.021 0.002 TRP B 436 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00536 (25892) covalent geometry : angle 0.61968 (35236) SS BOND : bond 0.00346 ( 37) SS BOND : angle 1.64372 ( 74) hydrogen bonds : bond 0.06129 ( 977) hydrogen bonds : angle 5.46109 ( 2721) link_BETA1-4 : bond 0.00322 ( 34) link_BETA1-4 : angle 1.65739 ( 102) link_NAG-ASN : bond 0.00405 ( 48) link_NAG-ASN : angle 2.57666 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.984 Fit side-chains REVERT: A 153 MET cc_start: 0.6948 (pmm) cc_final: 0.6640 (pmm) REVERT: A 869 MET cc_start: 0.9317 (mtt) cc_final: 0.9103 (mtp) REVERT: A 1002 GLN cc_start: 0.9097 (tp-100) cc_final: 0.8838 (tp-100) REVERT: B 125 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8649 (p0) REVERT: B 153 MET cc_start: 0.5019 (tpp) cc_final: 0.4487 (tpp) REVERT: C 338 PHE cc_start: 0.8602 (m-80) cc_final: 0.8339 (m-80) REVERT: C 351 TYR cc_start: 0.8103 (p90) cc_final: 0.7436 (p90) REVERT: C 408 ARG cc_start: 0.8300 (tmm160) cc_final: 0.7709 (ttp80) REVERT: C 1002 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8731 (mp10) outliers start: 14 outliers final: 6 residues processed: 76 average time/residue: 0.5727 time to fit residues: 52.1998 Evaluate side-chains 71 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 236 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 249 optimal weight: 0.0670 chunk 251 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 229 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.088060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053829 restraints weight = 94604.931| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.24 r_work: 0.2873 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26011 Z= 0.115 Angle : 0.567 13.221 35556 Z= 0.280 Chirality : 0.046 0.470 4244 Planarity : 0.004 0.054 4453 Dihedral : 8.067 94.278 5040 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.07 % Favored : 95.86 % Rotamer: Outliers : 0.81 % Allowed : 8.85 % Favored : 90.34 % 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 aren not related in a simple way. whole: -0.11 (0.15), residues: 3045 helix: 1.90 (0.21), residues: 683 sheet: 0.46 (0.19), residues: 746 loop : -1.26 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.016 0.001 TYR B1067 PHE 0.018 0.001 PHE B 157 TRP 0.015 0.001 TRP C 436 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00254 (25892) covalent geometry : angle 0.53950 (35236) SS BOND : bond 0.00274 ( 37) SS BOND : angle 1.23129 ( 74) hydrogen bonds : bond 0.05063 ( 977) hydrogen bonds : angle 5.08426 ( 2721) link_BETA1-4 : bond 0.00433 ( 34) link_BETA1-4 : angle 1.58307 ( 102) link_NAG-ASN : bond 0.00391 ( 48) link_NAG-ASN : angle 2.33829 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.878 Fit side-chains REVERT: A 53 ASP cc_start: 0.9145 (t0) cc_final: 0.8933 (t70) REVERT: A 153 MET cc_start: 0.6930 (pmm) cc_final: 0.6639 (pmm) REVERT: A 957 GLN cc_start: 0.9396 (tt0) cc_final: 0.8841 (tm-30) REVERT: B 153 MET cc_start: 0.5290 (tpp) cc_final: 0.4660 (tpp) REVERT: C 153 MET cc_start: 0.3547 (ptt) cc_final: 0.2124 (ppp) REVERT: C 351 TYR cc_start: 0.8088 (p90) cc_final: 0.7631 (p90) REVERT: C 436 TRP cc_start: 0.6520 (p90) cc_final: 0.5628 (p-90) REVERT: C 1002 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8720 (mp10) REVERT: C 1132 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9072 (pp) outliers start: 22 outliers final: 7 residues processed: 91 average time/residue: 0.5093 time to fit residues: 56.3923 Evaluate side-chains 79 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.086311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.051869 restraints weight = 95546.286| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.24 r_work: 0.2817 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 26011 Z= 0.245 Angle : 0.644 12.736 35556 Z= 0.320 Chirality : 0.047 0.471 4244 Planarity : 0.004 0.054 4453 Dihedral : 7.856 87.000 5040 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 1.47 % Allowed : 11.36 % 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 aren not related in a simple way. whole: -0.28 (0.15), residues: 3045 helix: 1.74 (0.21), residues: 679 sheet: 0.31 (0.19), residues: 743 loop : -1.32 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1039 TYR 0.020 0.001 TYR B1067 PHE 0.022 0.002 PHE B 559 TRP 0.023 0.002 TRP B 436 HIS 0.006 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00577 (25892) covalent geometry : angle 0.61616 (35236) SS BOND : bond 0.00351 ( 37) SS BOND : angle 1.56192 ( 74) hydrogen bonds : bond 0.06201 ( 977) hydrogen bonds : angle 5.32453 ( 2721) link_BETA1-4 : bond 0.00409 ( 34) link_BETA1-4 : angle 1.65666 ( 102) link_NAG-ASN : bond 0.00400 ( 48) link_NAG-ASN : angle 2.48052 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 70 time to evaluate : 0.958 Fit side-chains REVERT: A 53 ASP cc_start: 0.9183 (t0) cc_final: 0.8957 (t70) REVERT: A 153 MET cc_start: 0.6982 (pmm) cc_final: 0.6613 (pmm) REVERT: A 740 MET cc_start: 0.9567 (mmm) cc_final: 0.9336 (tpt) REVERT: A 900 MET cc_start: 0.9248 (mtp) cc_final: 0.9040 (mtt) REVERT: A 1002 GLN cc_start: 0.9457 (tt0) cc_final: 0.9001 (tp-100) REVERT: B 153 MET cc_start: 0.5490 (tpp) cc_final: 0.4798 (tpp) REVERT: C 338 PHE cc_start: 0.8158 (m-80) cc_final: 0.7931 (m-80) REVERT: C 351 TYR cc_start: 0.8136 (p90) cc_final: 0.7592 (p90) REVERT: C 434 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6805 (mp) REVERT: C 436 TRP cc_start: 0.6704 (p90) cc_final: 0.5733 (p-90) REVERT: C 1002 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8815 (mp10) REVERT: C 1132 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9144 (tt) outliers start: 40 outliers final: 19 residues processed: 101 average time/residue: 0.4340 time to fit residues: 54.8665 Evaluate side-chains 87 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 302 optimal weight: 0.7980 chunk 280 optimal weight: 0.3980 chunk 237 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 197 optimal weight: 0.7980 chunk 294 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 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 = 0.3864 r_free = 0.3864 target = 0.087216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053310 restraints weight = 94343.571| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.14 r_work: 0.2866 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26011 Z= 0.122 Angle : 0.568 12.573 35556 Z= 0.281 Chirality : 0.045 0.459 4244 Planarity : 0.004 0.052 4453 Dihedral : 7.426 82.925 5040 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 1.25 % Allowed : 12.46 % Favored : 86.28 % 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 aren not related in a simple way. whole: -0.11 (0.15), residues: 3045 helix: 1.92 (0.21), residues: 683 sheet: 0.46 (0.19), residues: 735 loop : -1.25 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE C 515 TRP 0.041 0.002 TRP A 353 HIS 0.003 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00274 (25892) covalent geometry : angle 0.54213 (35236) SS BOND : bond 0.00276 ( 37) SS BOND : angle 1.13614 ( 74) hydrogen bonds : bond 0.05195 ( 977) hydrogen bonds : angle 5.02838 ( 2721) link_BETA1-4 : bond 0.00413 ( 34) link_BETA1-4 : angle 1.57187 ( 102) link_NAG-ASN : bond 0.00341 ( 48) link_NAG-ASN : angle 2.31177 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9172 (t0) cc_final: 0.8957 (t70) REVERT: A 153 MET cc_start: 0.6919 (pmm) cc_final: 0.6594 (pmm) REVERT: A 740 MET cc_start: 0.9540 (mmm) cc_final: 0.9280 (tpt) REVERT: A 900 MET cc_start: 0.9123 (mtp) cc_final: 0.8908 (mtt) REVERT: A 957 GLN cc_start: 0.9416 (tt0) cc_final: 0.8884 (tm-30) REVERT: A 1002 GLN cc_start: 0.9408 (tt0) cc_final: 0.8938 (tp-100) REVERT: B 153 MET cc_start: 0.5631 (tpp) cc_final: 0.4954 (tpp) REVERT: C 338 PHE cc_start: 0.8232 (m-80) cc_final: 0.7916 (m-80) REVERT: C 351 TYR cc_start: 0.8284 (p90) cc_final: 0.7643 (p90) REVERT: C 408 ARG cc_start: 0.8388 (tmm160) cc_final: 0.7985 (ttp80) REVERT: C 434 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7407 (mp) REVERT: C 436 TRP cc_start: 0.6991 (p90) cc_final: 0.6003 (p-90) REVERT: C 984 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7818 (tm) REVERT: C 1002 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8735 (mp10) REVERT: C 1132 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9164 (tt) outliers start: 34 outliers final: 16 residues processed: 99 average time/residue: 0.5129 time to fit residues: 61.7107 Evaluate side-chains 87 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.086681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.051904 restraints weight = 94791.910| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.30 r_work: 0.2828 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26011 Z= 0.249 Angle : 0.646 13.482 35556 Z= 0.319 Chirality : 0.047 0.457 4244 Planarity : 0.004 0.050 4453 Dihedral : 7.021 77.092 5040 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.58 % Favored : 94.35 % Rotamer: Outliers : 1.81 % Allowed : 13.02 % Favored : 85.18 % 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 aren not related in a simple way. whole: -0.29 (0.15), residues: 3045 helix: 1.76 (0.21), residues: 679 sheet: 0.24 (0.19), residues: 752 loop : -1.31 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1039 TYR 0.020 0.001 TYR B1067 PHE 0.018 0.002 PHE B 559 TRP 0.021 0.002 TRP A 353 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00589 (25892) covalent geometry : angle 0.61473 (35236) SS BOND : bond 0.00355 ( 37) SS BOND : angle 1.52493 ( 74) hydrogen bonds : bond 0.06166 ( 977) hydrogen bonds : angle 5.24745 ( 2721) link_BETA1-4 : bond 0.00358 ( 34) link_BETA1-4 : angle 1.64003 ( 102) link_NAG-ASN : bond 0.00406 ( 48) link_NAG-ASN : angle 2.70941 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 66 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9176 (t0) cc_final: 0.8958 (t70) REVERT: A 153 MET cc_start: 0.6889 (pmm) cc_final: 0.6574 (pmm) REVERT: A 740 MET cc_start: 0.9555 (mmm) cc_final: 0.9314 (tpt) REVERT: A 900 MET cc_start: 0.9259 (mtp) cc_final: 0.9049 (mtt) REVERT: A 1002 GLN cc_start: 0.9460 (tt0) cc_final: 0.8979 (tp-100) REVERT: B 153 MET cc_start: 0.5940 (tpp) cc_final: 0.5174 (tpp) REVERT: B 759 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: C 338 PHE cc_start: 0.8166 (m-80) cc_final: 0.7957 (m-80) REVERT: C 351 TYR cc_start: 0.8232 (p90) cc_final: 0.7673 (p90) REVERT: C 368 LEU cc_start: 0.9066 (pt) cc_final: 0.8831 (mm) REVERT: C 434 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6802 (mp) REVERT: C 436 TRP cc_start: 0.6715 (p90) cc_final: 0.5761 (p-90) REVERT: C 1002 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8815 (mp10) REVERT: C 1132 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9143 (tt) outliers start: 49 outliers final: 29 residues processed: 103 average time/residue: 0.4375 time to fit residues: 56.7996 Evaluate side-chains 94 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 95 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 149 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.088121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.053768 restraints weight = 93547.142| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.21 r_work: 0.2867 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26011 Z= 0.112 Angle : 0.560 12.037 35556 Z= 0.277 Chirality : 0.045 0.444 4244 Planarity : 0.004 0.052 4453 Dihedral : 6.580 76.212 5040 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 1.33 % Allowed : 14.09 % Favored : 84.59 % 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 aren not related in a simple way. whole: -0.08 (0.15), residues: 3045 helix: 1.94 (0.21), residues: 685 sheet: 0.48 (0.19), residues: 739 loop : -1.24 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE B 392 TRP 0.019 0.001 TRP A 353 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00247 (25892) covalent geometry : angle 0.53446 (35236) SS BOND : bond 0.00237 ( 37) SS BOND : angle 1.14042 ( 74) hydrogen bonds : bond 0.04917 ( 977) hydrogen bonds : angle 4.91383 ( 2721) link_BETA1-4 : bond 0.00448 ( 34) link_BETA1-4 : angle 1.50980 ( 102) link_NAG-ASN : bond 0.00373 ( 48) link_NAG-ASN : angle 2.28625 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6950 (pmm) cc_final: 0.6644 (pmm) REVERT: A 957 GLN cc_start: 0.9425 (tt0) cc_final: 0.8891 (tm-30) REVERT: A 1141 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8399 (tm) REVERT: B 153 MET cc_start: 0.5936 (tpp) cc_final: 0.5186 (tpp) REVERT: B 759 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: C 153 MET cc_start: 0.4168 (ptt) cc_final: 0.2774 (ppp) REVERT: C 317 ASN cc_start: 0.9173 (p0) cc_final: 0.8828 (m-40) REVERT: C 338 PHE cc_start: 0.8152 (m-80) cc_final: 0.7937 (m-80) REVERT: C 351 TYR cc_start: 0.8214 (p90) cc_final: 0.7545 (p90) REVERT: C 368 LEU cc_start: 0.9001 (pt) cc_final: 0.8747 (mm) REVERT: C 434 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6735 (mp) REVERT: C 436 TRP cc_start: 0.6772 (p90) cc_final: 0.5823 (p-90) REVERT: C 466 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6277 (tpt90) REVERT: C 984 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7859 (tm) REVERT: C 1002 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8755 (mp10) REVERT: C 1132 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9135 (tt) outliers start: 36 outliers final: 23 residues processed: 103 average time/residue: 0.5157 time to fit residues: 65.0790 Evaluate side-chains 97 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 551 VAL 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 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 60 optimal weight: 0.0970 chunk 17 optimal weight: 9.9990 chunk 269 optimal weight: 0.7980 chunk 31 optimal weight: 30.0000 chunk 241 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 223 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 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 = 0.3867 r_free = 0.3867 target = 0.087831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053391 restraints weight = 93935.535| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.23 r_work: 0.2873 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26011 Z= 0.135 Angle : 0.567 11.615 35556 Z= 0.279 Chirality : 0.045 0.436 4244 Planarity : 0.004 0.051 4453 Dihedral : 6.298 65.775 5040 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 1.55 % Allowed : 14.27 % Favored : 84.18 % 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 aren not related in a simple way. whole: -0.03 (0.15), residues: 3045 helix: 1.98 (0.21), residues: 685 sheet: 0.51 (0.19), residues: 741 loop : -1.21 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.018 0.001 TYR B1067 PHE 0.031 0.001 PHE C 157 TRP 0.016 0.001 TRP A 353 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00312 (25892) covalent geometry : angle 0.54244 (35236) SS BOND : bond 0.00246 ( 37) SS BOND : angle 1.17838 ( 74) hydrogen bonds : bond 0.05065 ( 977) hydrogen bonds : angle 4.90555 ( 2721) link_BETA1-4 : bond 0.00389 ( 34) link_BETA1-4 : angle 1.52795 ( 102) link_NAG-ASN : bond 0.00311 ( 48) link_NAG-ASN : angle 2.25038 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 68 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6884 (pmm) cc_final: 0.6547 (pmm) REVERT: A 957 GLN cc_start: 0.9424 (tt0) cc_final: 0.8891 (tm-30) REVERT: A 1141 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8411 (tm) REVERT: B 153 MET cc_start: 0.6016 (tpp) cc_final: 0.5236 (tpp) REVERT: B 759 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: C 153 MET cc_start: 0.3981 (ptt) cc_final: 0.2467 (ppp) REVERT: C 317 ASN cc_start: 0.9139 (p0) cc_final: 0.8820 (m-40) REVERT: C 338 PHE cc_start: 0.8167 (m-80) cc_final: 0.7947 (m-80) REVERT: C 351 TYR cc_start: 0.8222 (p90) cc_final: 0.7561 (p90) REVERT: C 368 LEU cc_start: 0.9005 (pt) cc_final: 0.8747 (mm) REVERT: C 434 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.6713 (mp) REVERT: C 436 TRP cc_start: 0.6775 (p90) cc_final: 0.5837 (p-90) REVERT: C 466 ARG cc_start: 0.7235 (ttm-80) cc_final: 0.6279 (tpt90) REVERT: C 984 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7725 (tm) REVERT: C 1002 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8727 (mp10) REVERT: C 1132 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9141 (tt) outliers start: 42 outliers final: 29 residues processed: 104 average time/residue: 0.4464 time to fit residues: 57.5523 Evaluate side-chains 102 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 551 VAL 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 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 168 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 269 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 192 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 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 = 0.3874 r_free = 0.3874 target = 0.088229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.053759 restraints weight = 94111.291| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.29 r_work: 0.2884 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26011 Z= 0.119 Angle : 0.561 11.299 35556 Z= 0.276 Chirality : 0.045 0.424 4244 Planarity : 0.004 0.052 4453 Dihedral : 5.998 55.938 5040 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 1.44 % Allowed : 14.53 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 3045 helix: 2.03 (0.21), residues: 681 sheet: 0.56 (0.19), residues: 739 loop : -1.18 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.016 0.001 TYR B1067 PHE 0.027 0.001 PHE C 157 TRP 0.016 0.001 TRP A 353 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00272 (25892) covalent geometry : angle 0.53770 (35236) SS BOND : bond 0.00226 ( 37) SS BOND : angle 1.09862 ( 74) hydrogen bonds : bond 0.04822 ( 977) hydrogen bonds : angle 4.82243 ( 2721) link_BETA1-4 : bond 0.00421 ( 34) link_BETA1-4 : angle 1.50433 ( 102) link_NAG-ASN : bond 0.00311 ( 48) link_NAG-ASN : angle 2.15129 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 71 time to evaluate : 0.676 Fit side-chains REVERT: A 153 MET cc_start: 0.6879 (pmm) cc_final: 0.6536 (pmm) REVERT: A 957 GLN cc_start: 0.9425 (tt0) cc_final: 0.8893 (tm-30) REVERT: A 1141 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8415 (tm) REVERT: B 153 MET cc_start: 0.5960 (tpp) cc_final: 0.5249 (tpp) REVERT: B 759 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: C 153 MET cc_start: 0.3802 (ptt) cc_final: 0.2364 (ppp) REVERT: C 317 ASN cc_start: 0.9128 (p0) cc_final: 0.8852 (m-40) REVERT: C 338 PHE cc_start: 0.8160 (m-80) cc_final: 0.7939 (m-80) REVERT: C 351 TYR cc_start: 0.8225 (p90) cc_final: 0.7572 (p90) REVERT: C 368 LEU cc_start: 0.9035 (pt) cc_final: 0.8783 (mm) REVERT: C 434 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6744 (mp) REVERT: C 436 TRP cc_start: 0.6775 (p90) cc_final: 0.5841 (p-90) REVERT: C 466 ARG cc_start: 0.7233 (ttm-80) cc_final: 0.6545 (mmm160) REVERT: C 984 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7667 (tm) REVERT: C 1002 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8697 (mp10) REVERT: C 1132 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9143 (tt) outliers start: 39 outliers final: 27 residues processed: 102 average time/residue: 0.4923 time to fit residues: 61.5073 Evaluate side-chains 102 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 551 VAL 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 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 74 optimal weight: 0.6980 chunk 266 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 280 optimal weight: 0.0010 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 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 = 0.3855 r_free = 0.3855 target = 0.086971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052637 restraints weight = 94769.283| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.24 r_work: 0.2841 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26011 Z= 0.169 Angle : 0.587 11.098 35556 Z= 0.290 Chirality : 0.045 0.419 4244 Planarity : 0.004 0.051 4453 Dihedral : 5.933 55.807 5040 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 1.29 % Allowed : 14.79 % Favored : 83.92 % 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 aren not related in a simple way. whole: -0.04 (0.15), residues: 3045 helix: 1.96 (0.21), residues: 685 sheet: 0.49 (0.19), residues: 739 loop : -1.20 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.018 0.001 TYR B1067 PHE 0.026 0.001 PHE C 157 TRP 0.015 0.001 TRP A 353 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00394 (25892) covalent geometry : angle 0.56439 (35236) SS BOND : bond 0.00257 ( 37) SS BOND : angle 1.23626 ( 74) hydrogen bonds : bond 0.05272 ( 977) hydrogen bonds : angle 4.93516 ( 2721) link_BETA1-4 : bond 0.00369 ( 34) link_BETA1-4 : angle 1.53558 ( 102) link_NAG-ASN : bond 0.00299 ( 48) link_NAG-ASN : angle 2.19234 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6909 (pmm) cc_final: 0.6634 (pmm) REVERT: A 957 GLN cc_start: 0.9409 (tt0) cc_final: 0.8865 (tm-30) REVERT: A 1141 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8412 (tm) REVERT: B 153 MET cc_start: 0.6147 (tpp) cc_final: 0.5412 (tpp) REVERT: B 759 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: C 317 ASN cc_start: 0.9186 (p0) cc_final: 0.8916 (m-40) REVERT: C 338 PHE cc_start: 0.8149 (m-80) cc_final: 0.7940 (m-80) REVERT: C 351 TYR cc_start: 0.8285 (p90) cc_final: 0.7885 (p90) REVERT: C 434 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6744 (mp) REVERT: C 436 TRP cc_start: 0.6799 (p90) cc_final: 0.5862 (p-90) REVERT: C 466 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.6355 (mmm-85) REVERT: C 984 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7747 (tm) REVERT: C 1002 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8736 (mp10) REVERT: C 1132 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9137 (tt) outliers start: 35 outliers final: 27 residues processed: 99 average time/residue: 0.4646 time to fit residues: 57.0402 Evaluate side-chains 98 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 551 VAL 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 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 7 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 259 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 247 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 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 = 0.3856 r_free = 0.3856 target = 0.086854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052723 restraints weight = 94563.133| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 4.18 r_work: 0.2851 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26011 Z= 0.156 Angle : 0.583 10.955 35556 Z= 0.289 Chirality : 0.045 0.414 4244 Planarity : 0.004 0.051 4453 Dihedral : 5.834 55.651 5040 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.73 % Favored : 95.21 % Rotamer: Outliers : 1.59 % Allowed : 14.75 % Favored : 83.67 % 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 aren not related in a simple way. whole: -0.05 (0.15), residues: 3045 helix: 1.97 (0.21), residues: 685 sheet: 0.49 (0.19), residues: 743 loop : -1.22 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE C 157 TRP 0.015 0.001 TRP A 353 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00364 (25892) covalent geometry : angle 0.56013 (35236) SS BOND : bond 0.00252 ( 37) SS BOND : angle 1.24962 ( 74) hydrogen bonds : bond 0.05265 ( 977) hydrogen bonds : angle 4.93056 ( 2721) link_BETA1-4 : bond 0.00378 ( 34) link_BETA1-4 : angle 1.52854 ( 102) link_NAG-ASN : bond 0.00294 ( 48) link_NAG-ASN : angle 2.18315 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9666.67 seconds wall clock time: 165 minutes 10.79 seconds (9910.79 seconds total)