Starting phenix.real_space_refine on Sun Jul 5 04:07:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v7s_31780/07_2026/7v7s_31780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7s_31780/07_2026/7v7s_31780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v7s_31780/07_2026/7v7s_31780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7s_31780/07_2026/7v7s_31780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v7s_31780/07_2026/7v7s_31780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7s_31780/07_2026/7v7s_31780.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v7s_31780/07_2026/7v7s_31780.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v7s_31780/07_2026/7v7s_31780.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.038 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 108 5.16 5 C 16039 2.51 5 N 4113 2.21 5 O 4995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25255 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8028 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 53, 'TRANS': 974} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.48, per 1000 atoms: 0.22 Number of scatterers: 25255 At special positions: 0 Unit cell: (140.8, 145.2, 199.1, 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 108 16.00 O 4995 8.00 N 4113 7.00 C 16039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.04 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 163 " " NAG A2004 " - " ASN A 232 " " NAG A2005 " - " ASN A 601 " " NAG A2006 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 280 " " NAG E 1 " - " ASN A 329 " " NAG F 1 " - " ASN A 341 " " NAG G 1 " - " ASN A 614 " " NAG H 1 " - " ASN A 707 " " NAG I 1 " - " ASN A 715 " " NAG J 1 " - " ASN A 799 " " NAG K 1 " - " ASN A1072 " " NAG L 1 " - " ASN A1096 " " NAG M 1 " - " ASN A1132 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 163 " " NAG P 1 " - " ASN B 280 " " NAG Q 1 " - " ASN B 341 " " NAG R 1 " - " ASN B 614 " " NAG S 1 " - " ASN B 707 " " NAG T 1 " - " ASN B 715 " " NAG U 1 " - " ASN B 799 " " NAG V 1 " - " ASN B1072 " " NAG W 1 " - " ASN B1096 " " NAG X 1 " - " ASN B1132 " " NAG Y 1 " - " ASN C 122 " " NAG Z 1 " - " ASN C 163 " " NAG a 1 " - " ASN C 232 " " NAG b 1 " - " ASN C 280 " " NAG c 1 " - " ASN C 341 " " NAG d 1 " - " ASN C 614 " " NAG e 1 " - " ASN C 707 " " NAG f 1 " - " ASN C 715 " " NAG g 1 " - " ASN C 799 " " NAG h 1 " - " ASN C1072 " " NAG i 1 " - " ASN C1096 " " NAG j 1 " - " ASN C1132 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 962.7 milliseconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 46 sheets defined 24.6% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.438A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 removed outlier: 4.277A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 753 removed outlier: 4.097A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.290A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.644A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.531A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.019A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.582A pdb=" N LEU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.294A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.738A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.684A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.628A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.078A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.579A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.552A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.351A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.811A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 381 through 388 removed outlier: 4.549A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.818A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.627A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 757 through 781 removed outlier: 3.511A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.597A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 939 removed outlier: 4.319A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.508A pdb=" N GLN C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.715A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.434A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.606A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.863A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.130A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 103 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 126 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 128 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 130 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU A 132 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLN A 134 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA A 161 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 317 removed outlier: 7.111A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.790A pdb=" N ASN A 540 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA9, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.165A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.029A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.511A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.548A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.484A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB6, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 30 removed outlier: 8.615A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.164A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.506A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.181A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.506A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.345A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.440A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 573 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 564 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC5, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.258A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AC7, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC8, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.007A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.974A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.089A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.535A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD4, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.081A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.620A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.195A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU C 132 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLN C 134 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASN C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.130A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 323 through 324 Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 3.516A pdb=" N CYS C 523 " --> pdb=" O CYS C 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 removed outlier: 3.743A pdb=" N TYR C 471 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C 487 " --> pdb=" O TYR C 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 564 through 565 removed outlier: 6.741A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.022A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.570A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA C1076 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE C1093 " --> pdb=" O ALA C1076 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN C1104 " --> pdb=" O GLU C1109 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU C1109 " --> pdb=" O GLN C1104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.540A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.516A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1118 through 1120 1006 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 3.00 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: 7977 1.34 - 1.46: 6421 1.46 - 1.58: 11272 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25802 Sorted by residual: bond pdb=" C PRO A 984 " pdb=" N PRO A 985 " ideal model delta sigma weight residual 1.333 1.376 -0.043 1.44e-02 4.82e+03 8.88e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C1 NAG B2004 " pdb=" O5 NAG B2004 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.70e+00 ... (remaining 25797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 34042 1.55 - 3.10: 945 3.10 - 4.64: 92 4.64 - 6.19: 19 6.19 - 7.74: 11 Bond angle restraints: 35109 Sorted by residual: angle pdb=" C SER B 170 " pdb=" N GLN B 171 " pdb=" CA GLN B 171 " ideal model delta sigma weight residual 120.49 125.03 -4.54 1.42e+00 4.96e-01 1.02e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.55 -3.85 1.22e+00 6.72e-01 9.98e+00 angle pdb=" C ASN A 329 " pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta sigma weight residual 121.97 127.51 -5.54 1.80e+00 3.09e-01 9.47e+00 angle pdb=" N PRO A 559 " pdb=" CA PRO A 559 " pdb=" C PRO A 559 " ideal model delta sigma weight residual 112.47 118.68 -6.21 2.06e+00 2.36e-01 9.09e+00 angle pdb=" N PRO C 559 " pdb=" CA PRO C 559 " pdb=" C PRO C 559 " ideal model delta sigma weight residual 112.47 118.26 -5.79 2.06e+00 2.36e-01 7.89e+00 ... (remaining 35104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 13163 17.28 - 34.55: 1268 34.55 - 51.83: 241 51.83 - 69.10: 35 69.10 - 86.38: 34 Dihedral angle restraints: 14741 sinusoidal: 5754 harmonic: 8987 Sorted by residual: dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual -86.00 -0.91 -85.09 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -169.13 83.13 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual -86.00 -166.07 80.07 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 14738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3661 0.073 - 0.146: 539 0.146 - 0.219: 20 0.219 - 0.291: 1 0.291 - 0.364: 3 Chirality restraints: 4224 Sorted by residual: chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1 NAG A2005 " pdb=" ND2 ASN A 601 " pdb=" C2 NAG A2005 " pdb=" O5 NAG A2005 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C1 NAG A2004 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG A2004 " pdb=" O5 NAG A2004 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 4221 not shown) Planarity restraints: 4490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.025 2.00e-02 2.50e+03 2.31e-02 6.69e+00 pdb=" CG ASN A 329 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 558 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO C 559 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 559 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 559 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 984 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.026 5.00e-02 4.00e+02 ... (remaining 4487 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1862 2.74 - 3.28: 24679 3.28 - 3.82: 39948 3.82 - 4.36: 44918 4.36 - 4.90: 80399 Nonbonded interactions: 191806 Sorted by model distance: nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.206 3.040 nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 189 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.231 3.040 ... (remaining 191801 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 619 or resid 635 through 825 or resid 853 throu \ gh 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 2004)) } 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' } 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.320 Find NCS groups from input model: 1.070 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: 0.000 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 0.049 25923 Z= 0.188 Angle : 0.624 11.453 35432 Z= 0.296 Chirality : 0.047 0.364 4224 Planarity : 0.004 0.050 4442 Dihedral : 13.812 86.376 8835 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3040 helix: 2.30 (0.22), residues: 656 sheet: 0.52 (0.19), residues: 719 loop : -1.07 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.016 0.001 TYR A 503 PHE 0.019 0.001 PHE B 904 TRP 0.023 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (25802) covalent geometry : angle 0.59023 / 0.29 (35109) SS BOND : bond 0.00285 / 0.18 ( 40) SS BOND : angle 1.58207 / 0.95 ( 80) hydrogen bonds : bond 0.11920 / 7.69 ( 1003) hydrogen bonds : angle 5.58193 / 3.68 ( 2748) link_BETA1-4 : bond 0.00360 / 0.24 ( 33) link_BETA1-4 : angle 1.93685 / 1.25 ( 99) link_NAG-ASN : bond 0.00397 / 0.26 ( 48) link_NAG-ASN : angle 2.62068 / 2.18 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 569 ASP cc_start: 0.6995 (t0) cc_final: 0.6793 (OUTLIER) outliers start: 0 outliers final: 1 residues processed: 87 average time/residue: 0.5096 time to fit residues: 53.8505 Evaluate side-chains 59 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN B1000 GLN C 269 GLN C 386 ASN C1003 GLN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.085546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.050605 restraints weight = 86531.081| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 4.37 r_work: 0.2690 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25923 Z= 0.263 Angle : 0.652 13.337 35432 Z= 0.324 Chirality : 0.047 0.362 4224 Planarity : 0.004 0.054 4442 Dihedral : 4.331 23.761 3310 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 0.41 % Allowed : 6.78 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.15), residues: 3040 helix: 2.23 (0.21), residues: 657 sheet: 0.38 (0.19), residues: 728 loop : -1.15 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1037 TYR 0.017 0.001 TYR A1065 PHE 0.024 0.002 PHE C 904 TRP 0.016 0.002 TRP C 351 HIS 0.004 0.001 HIS B1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (25802) covalent geometry : angle 0.62487 / 0.32 (35109) SS BOND : bond 0.00423 / 0.28 ( 40) SS BOND : angle 1.76740 / 1.10 ( 80) hydrogen bonds : bond 0.06720 / 4.52 ( 1003) hydrogen bonds : angle 5.24166 / 3.51 ( 2748) link_BETA1-4 : bond 0.00270 / 0.18 ( 33) link_BETA1-4 : angle 1.64582 / 1.07 ( 99) link_NAG-ASN : bond 0.00453 / 0.28 ( 48) link_NAG-ASN : angle 2.43352 / 2.09 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8316 (t0) cc_final: 0.8077 (t0) REVERT: A 898 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.9227 (mtp) REVERT: B 867 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.9037 (mtp) REVERT: C 988 GLU cc_start: 0.8502 (pp20) cc_final: 0.8185 (pm20) outliers start: 11 outliers final: 3 residues processed: 69 average time/residue: 0.5545 time to fit residues: 46.6047 Evaluate side-chains 66 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 155 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 304 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.085699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.050634 restraints weight = 86485.479| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 4.36 r_work: 0.2720 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25923 Z= 0.224 Angle : 0.619 11.456 35432 Z= 0.307 Chirality : 0.046 0.356 4224 Planarity : 0.004 0.052 4442 Dihedral : 4.300 23.584 3310 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 0.67 % Allowed : 10.59 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 3040 helix: 2.24 (0.21), residues: 656 sheet: 0.35 (0.19), residues: 727 loop : -1.14 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1037 TYR 0.017 0.001 TYR A1065 PHE 0.020 0.001 PHE C 904 TRP 0.014 0.001 TRP C 884 HIS 0.003 0.001 HIS C1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (25802) covalent geometry : angle 0.59183 / 0.30 (35109) SS BOND : bond 0.00392 / 0.26 ( 40) SS BOND : angle 1.64988 / 1.03 ( 80) hydrogen bonds : bond 0.06440 / 4.36 ( 1003) hydrogen bonds : angle 5.14971 / 3.46 ( 2748) link_BETA1-4 : bond 0.00267 / 0.19 ( 33) link_BETA1-4 : angle 1.61305 / 1.05 ( 99) link_NAG-ASN : bond 0.00427 / 0.26 ( 48) link_NAG-ASN : angle 2.39179 / 2.09 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8047 (t0) cc_final: 0.7800 (t0) REVERT: A 898 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9082 (mtp) REVERT: B 867 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.9078 (mtp) REVERT: B 1000 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8354 (tm-30) outliers start: 18 outliers final: 6 residues processed: 71 average time/residue: 0.4706 time to fit residues: 40.9664 Evaluate side-chains 68 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 147 optimal weight: 6.9990 chunk 161 optimal weight: 0.0870 chunk 243 optimal weight: 40.0000 chunk 299 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 234 optimal weight: 30.0000 chunk 214 optimal weight: 6.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.086003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050731 restraints weight = 85648.701| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 4.43 r_work: 0.2698 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25923 Z= 0.181 Angle : 0.590 11.351 35432 Z= 0.291 Chirality : 0.046 0.355 4224 Planarity : 0.004 0.050 4442 Dihedral : 4.190 22.940 3310 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 1.22 % Allowed : 12.44 % Favored : 86.34 % 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 are not related in a simple way. whole: 0.07 (0.15), residues: 3040 helix: 2.40 (0.21), residues: 648 sheet: 0.38 (0.19), residues: 724 loop : -1.12 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1037 TYR 0.017 0.001 TYR A1065 PHE 0.017 0.001 PHE A 106 TRP 0.024 0.001 TRP A 351 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (25802) covalent geometry : angle 0.56205 / 0.29 (35109) SS BOND : bond 0.00353 / 0.23 ( 40) SS BOND : angle 1.51448 / 0.95 ( 80) hydrogen bonds : bond 0.06076 / 4.13 ( 1003) hydrogen bonds : angle 5.02636 / 3.38 ( 2748) link_BETA1-4 : bond 0.00277 / 0.20 ( 33) link_BETA1-4 : angle 1.58789 / 1.03 ( 99) link_NAG-ASN : bond 0.00411 / 0.26 ( 48) link_NAG-ASN : angle 2.35728 / 2.08 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.9076 (t0) cc_final: 0.8654 (m110) REVERT: A 569 ASP cc_start: 0.8329 (t0) cc_final: 0.8079 (t0) REVERT: A 898 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9252 (mtp) REVERT: B 867 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8973 (mtp) REVERT: C 434 TRP cc_start: 0.7473 (t60) cc_final: 0.7250 (p-90) outliers start: 33 outliers final: 13 residues processed: 85 average time/residue: 0.4752 time to fit residues: 50.6225 Evaluate side-chains 75 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 298 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 275 optimal weight: 0.0970 chunk 245 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.086183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051001 restraints weight = 85750.378| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.42 r_work: 0.2708 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25923 Z= 0.165 Angle : 0.588 11.237 35432 Z= 0.288 Chirality : 0.045 0.356 4224 Planarity : 0.004 0.052 4442 Dihedral : 4.146 22.381 3310 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 1.41 % Allowed : 13.44 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3040 helix: 2.48 (0.21), residues: 642 sheet: 0.44 (0.19), residues: 718 loop : -1.09 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1037 TYR 0.016 0.001 TYR A1065 PHE 0.014 0.001 PHE C1119 TRP 0.013 0.001 TRP A 351 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (25802) covalent geometry : angle 0.56074 / 0.28 (35109) SS BOND : bond 0.00345 / 0.23 ( 40) SS BOND : angle 1.44213 / 0.89 ( 80) hydrogen bonds : bond 0.05867 / 4.00 ( 1003) hydrogen bonds : angle 4.94335 / 3.33 ( 2748) link_BETA1-4 : bond 0.00283 / 0.20 ( 33) link_BETA1-4 : angle 1.59067 / 1.03 ( 99) link_NAG-ASN : bond 0.00406 / 0.26 ( 48) link_NAG-ASN : angle 2.34820 / 2.07 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.9106 (t0) cc_final: 0.8707 (m110) REVERT: A 569 ASP cc_start: 0.8338 (t0) cc_final: 0.8083 (t0) REVERT: A 898 MET cc_start: 0.9458 (OUTLIER) cc_final: 0.9227 (mtp) REVERT: B 867 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8955 (mtp) REVERT: C 434 TRP cc_start: 0.7455 (t60) cc_final: 0.7194 (p-90) REVERT: C 876 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8954 (tt) outliers start: 38 outliers final: 19 residues processed: 92 average time/residue: 0.4693 time to fit residues: 53.9384 Evaluate side-chains 83 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 98 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 302 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.087150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052141 restraints weight = 85968.585| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.38 r_work: 0.2749 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25923 Z= 0.114 Angle : 0.568 12.523 35432 Z= 0.275 Chirality : 0.045 0.352 4224 Planarity : 0.004 0.051 4442 Dihedral : 3.948 21.221 3310 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 1.55 % Allowed : 14.18 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3040 helix: 2.57 (0.22), residues: 646 sheet: 0.54 (0.19), residues: 718 loop : -1.03 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.016 0.001 TYR A1065 PHE 0.019 0.001 PHE B 454 TRP 0.012 0.001 TRP A 351 HIS 0.002 0.000 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (25802) covalent geometry : angle 0.54239 / 0.27 (35109) SS BOND : bond 0.00279 / 0.18 ( 40) SS BOND : angle 1.23476 / 0.75 ( 80) hydrogen bonds : bond 0.05075 / 3.47 ( 1003) hydrogen bonds : angle 4.73705 / 3.19 ( 2748) link_BETA1-4 : bond 0.00352 / 0.24 ( 33) link_BETA1-4 : angle 1.54190 / 1.00 ( 99) link_NAG-ASN : bond 0.00407 / 0.26 ( 48) link_NAG-ASN : angle 2.27072 / 2.04 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 66 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6540 (p) REVERT: A 389 CYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7136 (p) REVERT: A 569 ASP cc_start: 0.8289 (t0) cc_final: 0.7958 (t0) REVERT: A 898 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9187 (mtp) REVERT: B 867 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8940 (mtp) REVERT: B 1000 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7972 (tm-30) REVERT: C 242 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7745 (tm) REVERT: C 434 TRP cc_start: 0.7506 (t60) cc_final: 0.7205 (p-90) REVERT: C 876 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8924 (tt) outliers start: 42 outliers final: 16 residues processed: 98 average time/residue: 0.4565 time to fit residues: 56.4229 Evaluate side-chains 83 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 255 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.086986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051925 restraints weight = 85790.046| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.42 r_work: 0.2739 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25923 Z= 0.125 Angle : 0.569 11.611 35432 Z= 0.277 Chirality : 0.045 0.353 4224 Planarity : 0.004 0.051 4442 Dihedral : 3.921 20.262 3310 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 1.37 % Allowed : 14.66 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3040 helix: 2.56 (0.21), residues: 647 sheet: 0.53 (0.19), residues: 720 loop : -1.01 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.018 0.001 TYR B 447 PHE 0.020 0.001 PHE C 375 TRP 0.011 0.001 TRP C 884 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (25802) covalent geometry : angle 0.54330 / 0.27 (35109) SS BOND : bond 0.00280 / 0.18 ( 40) SS BOND : angle 1.24790 / 0.76 ( 80) hydrogen bonds : bond 0.05157 / 3.52 ( 1003) hydrogen bonds : angle 4.71814 / 3.18 ( 2748) link_BETA1-4 : bond 0.00314 / 0.22 ( 33) link_BETA1-4 : angle 1.54996 / 1.01 ( 99) link_NAG-ASN : bond 0.00400 / 0.26 ( 48) link_NAG-ASN : angle 2.25237 / 2.02 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7031 (OUTLIER) cc_final: 0.6552 (p) REVERT: A 389 CYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7202 (p) REVERT: A 569 ASP cc_start: 0.8321 (t0) cc_final: 0.8015 (t0) REVERT: A 898 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9175 (mtp) REVERT: B 867 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8984 (mtp) REVERT: B 988 GLU cc_start: 0.8745 (pp20) cc_final: 0.8444 (pm20) REVERT: B 1000 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 242 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7773 (tm) REVERT: C 434 TRP cc_start: 0.7555 (t60) cc_final: 0.7285 (p-90) REVERT: C 778 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8967 (pp20) REVERT: C 876 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8950 (tt) outliers start: 37 outliers final: 22 residues processed: 93 average time/residue: 0.4470 time to fit residues: 52.0329 Evaluate side-chains 90 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 231 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 chunk 289 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.086254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.051326 restraints weight = 86048.202| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.34 r_work: 0.2721 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25923 Z= 0.168 Angle : 0.592 11.226 35432 Z= 0.290 Chirality : 0.045 0.355 4224 Planarity : 0.004 0.052 4442 Dihedral : 4.014 20.292 3310 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.79 % Rotamer: Outliers : 1.18 % Allowed : 15.33 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3040 helix: 2.56 (0.22), residues: 643 sheet: 0.46 (0.19), residues: 725 loop : -1.02 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1037 TYR 0.016 0.001 TYR A1065 PHE 0.022 0.001 PHE C 375 TRP 0.012 0.001 TRP C 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (25802) covalent geometry : angle 0.56687 / 0.28 (35109) SS BOND : bond 0.00326 / 0.21 ( 40) SS BOND : angle 1.37538 / 0.85 ( 80) hydrogen bonds : bond 0.05668 / 3.85 ( 1003) hydrogen bonds : angle 4.80536 / 3.24 ( 2748) link_BETA1-4 : bond 0.00273 / 0.19 ( 33) link_BETA1-4 : angle 1.57343 / 1.02 ( 99) link_NAG-ASN : bond 0.00403 / 0.26 ( 48) link_NAG-ASN : angle 2.26888 / 2.03 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7056 (OUTLIER) cc_final: 0.6573 (p) REVERT: A 569 ASP cc_start: 0.8334 (t0) cc_final: 0.8071 (t0) REVERT: A 898 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.9209 (mtp) REVERT: B 867 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8995 (mtp) REVERT: B 988 GLU cc_start: 0.8760 (pp20) cc_final: 0.8394 (pm20) REVERT: C 242 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7773 (tm) REVERT: C 434 TRP cc_start: 0.7608 (t60) cc_final: 0.7333 (p-90) REVERT: C 876 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8948 (tt) outliers start: 32 outliers final: 23 residues processed: 85 average time/residue: 0.4589 time to fit residues: 48.7106 Evaluate side-chains 88 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 39 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 65 optimal weight: 0.0270 chunk 237 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN C1003 GLN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.087338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.052774 restraints weight = 85329.909| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.25 r_work: 0.2761 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25923 Z= 0.109 Angle : 0.561 10.929 35432 Z= 0.273 Chirality : 0.045 0.351 4224 Planarity : 0.004 0.051 4442 Dihedral : 3.851 19.422 3310 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 1.04 % Allowed : 15.73 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3040 helix: 2.63 (0.21), residues: 642 sheet: 0.59 (0.19), residues: 714 loop : -0.98 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 464 TYR 0.018 0.001 TYR B 447 PHE 0.019 0.001 PHE C 375 TRP 0.037 0.001 TRP C 351 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (25802) covalent geometry : angle 0.53565 / 0.27 (35109) SS BOND : bond 0.00244 / 0.15 ( 40) SS BOND : angle 1.36506 / 0.84 ( 80) hydrogen bonds : bond 0.04863 / 3.33 ( 1003) hydrogen bonds : angle 4.63097 / 3.12 ( 2748) link_BETA1-4 : bond 0.00358 / 0.24 ( 33) link_BETA1-4 : angle 1.52251 / 0.99 ( 99) link_NAG-ASN : bond 0.00413 / 0.27 ( 48) link_NAG-ASN : angle 2.20542 / 2.00 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7128 (OUTLIER) cc_final: 0.6634 (p) REVERT: A 569 ASP cc_start: 0.8277 (t0) cc_final: 0.7969 (t0) REVERT: A 898 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9167 (mtp) REVERT: B 867 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8944 (mtp) REVERT: B 988 GLU cc_start: 0.8760 (pp20) cc_final: 0.8461 (pm20) REVERT: B 1000 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 242 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7870 (tm) REVERT: C 434 TRP cc_start: 0.7807 (t60) cc_final: 0.7509 (p-90) outliers start: 28 outliers final: 21 residues processed: 87 average time/residue: 0.4636 time to fit residues: 50.0130 Evaluate side-chains 87 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 chunk 224 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 278 optimal weight: 0.3980 chunk 133 optimal weight: 8.9990 chunk 266 optimal weight: 2.9990 chunk 174 optimal weight: 0.0050 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.086983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.052349 restraints weight = 86450.435| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 4.28 r_work: 0.2742 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25923 Z= 0.126 Angle : 0.565 10.779 35432 Z= 0.276 Chirality : 0.045 0.351 4224 Planarity : 0.004 0.052 4442 Dihedral : 3.853 19.277 3310 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 1.11 % Allowed : 15.81 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3040 helix: 2.56 (0.22), residues: 647 sheet: 0.58 (0.19), residues: 714 loop : -0.96 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.016 0.001 TYR A1065 PHE 0.020 0.001 PHE C 375 TRP 0.024 0.001 TRP C 351 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (25802) covalent geometry : angle 0.54033 / 0.27 (35109) SS BOND : bond 0.00267 / 0.17 ( 40) SS BOND : angle 1.33420 / 0.81 ( 80) hydrogen bonds : bond 0.05042 / 3.43 ( 1003) hydrogen bonds : angle 4.64473 / 3.13 ( 2748) link_BETA1-4 : bond 0.00312 / 0.21 ( 33) link_BETA1-4 : angle 1.53306 / 1.00 ( 99) link_NAG-ASN : bond 0.00395 / 0.26 ( 48) link_NAG-ASN : angle 2.20045 / 1.99 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6619 (p) REVERT: A 569 ASP cc_start: 0.8298 (t0) cc_final: 0.8001 (t0) REVERT: A 898 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9152 (mtp) REVERT: B 867 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8964 (mtp) REVERT: B 988 GLU cc_start: 0.8769 (pp20) cc_final: 0.8471 (pm20) REVERT: B 1000 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 242 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7934 (tm) REVERT: C 434 TRP cc_start: 0.7792 (t60) cc_final: 0.7499 (p-90) outliers start: 30 outliers final: 22 residues processed: 83 average time/residue: 0.4662 time to fit residues: 47.6804 Evaluate side-chains 86 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 212 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 234 optimal weight: 30.0000 chunk 161 optimal weight: 0.1980 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.086573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051706 restraints weight = 86226.793| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.31 r_work: 0.2725 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25923 Z= 0.153 Angle : 0.578 10.598 35432 Z= 0.283 Chirality : 0.045 0.352 4224 Planarity : 0.004 0.052 4442 Dihedral : 3.931 19.627 3310 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 1.15 % Allowed : 15.88 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3040 helix: 2.48 (0.22), residues: 651 sheet: 0.50 (0.19), residues: 720 loop : -0.95 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1037 TYR 0.018 0.001 TYR B 447 PHE 0.021 0.001 PHE C 375 TRP 0.024 0.001 TRP C 351 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (25802) covalent geometry : angle 0.55340 / 0.28 (35109) SS BOND : bond 0.00294 / 0.19 ( 40) SS BOND : angle 1.40640 / 0.86 ( 80) hydrogen bonds : bond 0.05424 / 3.69 ( 1003) hydrogen bonds : angle 4.70892 / 3.17 ( 2748) link_BETA1-4 : bond 0.00290 / 0.20 ( 33) link_BETA1-4 : angle 1.54890 / 1.00 ( 99) link_NAG-ASN : bond 0.00396 / 0.25 ( 48) link_NAG-ASN : angle 2.20365 / 1.99 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7979.14 seconds wall clock time: 137 minutes 3.85 seconds (8223.85 seconds total)