Starting phenix.real_space_refine on Sun Jun 22 02:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7s_31780/06_2025/7v7s_31780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7s_31780/06_2025/7v7s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7s_31780/06_2025/7v7s_31780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7s_31780/06_2025/7v7s_31780.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7s_31780/06_2025/7v7s_31780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7s_31780/06_2025/7v7s_31780.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 18 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.81, per 1000 atoms: 0.63 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: 7.27 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 4.17 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: 14.88 Time building geometry restraints manager: 8.41 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: 14681 17.28 - 34.55: 1361 34.55 - 51.83: 299 51.83 - 69.10: 67 69.10 - 86.38: 34 Dihedral angle restraints: 16442 sinusoidal: 7455 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 16439 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 1144 or resid 2001 through 2004)) selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 1144 or resid 2001 through 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 1144 or resid 2001 thr \ ough 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 65.040 Find NCS groups from input model: 3.550 Set up NCS constraints: 1.070 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: 0.040 Load rotamer database and sin/cos tables:21.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 13.700 86.376 10536 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 PHE 0.019 0.001 PHE B 904 TYR 0.016 0.001 TYR A 503 ARG 0.003 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 48) link_NAG-ASN : angle 2.62068 ( 144) link_BETA1-4 : bond 0.00360 ( 33) link_BETA1-4 : angle 1.93685 ( 99) hydrogen bonds : bond 0.11920 ( 1003) hydrogen bonds : angle 5.58193 ( 2748) SS BOND : bond 0.00285 ( 40) SS BOND : angle 1.58207 ( 80) covalent geometry : bond 0.00393 (25802) covalent geometry : angle 0.59023 (35109) *********************** 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 : 3.573 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: 1.1061 time to fit residues: 118.6227 Evaluate side-chains 61 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 240 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN A 899 GLN C 386 ASN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.086196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051311 restraints weight = 85353.286| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.29 r_work: 0.2705 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25923 Z= 0.197 Angle : 0.607 11.445 35432 Z= 0.302 Chirality : 0.046 0.375 4224 Planarity : 0.004 0.054 4442 Dihedral : 7.477 58.321 5011 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 0.44 % Allowed : 6.15 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3040 helix: 2.32 (0.21), residues: 658 sheet: 0.49 (0.19), residues: 720 loop : -1.11 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 351 HIS 0.003 0.001 HIS B1086 PHE 0.024 0.001 PHE A 166 TYR 0.017 0.001 TYR A1065 ARG 0.004 0.000 ARG B 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 48) link_NAG-ASN : angle 2.39721 ( 144) link_BETA1-4 : bond 0.00349 ( 33) link_BETA1-4 : angle 1.63101 ( 99) hydrogen bonds : bond 0.06056 ( 1003) hydrogen bonds : angle 5.08758 ( 2748) SS BOND : bond 0.00373 ( 40) SS BOND : angle 1.61585 ( 80) covalent geometry : bond 0.00464 (25802) covalent geometry : angle 0.57889 (35109) *********************** 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 81 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8317 (t0) cc_final: 0.8065 (t0) REVERT: A 898 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.9164 (mtp) REVERT: B 1000 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7964 (tm-30) REVERT: C 988 GLU cc_start: 0.8453 (pp20) cc_final: 0.8161 (pm20) outliers start: 12 outliers final: 2 residues processed: 74 average time/residue: 1.1322 time to fit residues: 102.4258 Evaluate side-chains 61 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 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 169 optimal weight: 1.9990 chunk 241 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 268 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3747 r_free = 0.3747 target = 0.086545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.051294 restraints weight = 85229.131| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.46 r_work: 0.2707 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25923 Z= 0.154 Angle : 0.567 11.383 35432 Z= 0.282 Chirality : 0.045 0.360 4224 Planarity : 0.004 0.051 4442 Dihedral : 6.940 56.840 5011 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 0.52 % Allowed : 9.18 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3040 helix: 2.40 (0.21), residues: 657 sheet: 0.53 (0.19), residues: 716 loop : -1.07 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 PHE 0.014 0.001 PHE C 904 TYR 0.018 0.001 TYR A 419 ARG 0.002 0.000 ARG B 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 48) link_NAG-ASN : angle 2.34593 ( 144) link_BETA1-4 : bond 0.00300 ( 33) link_BETA1-4 : angle 1.62155 ( 99) hydrogen bonds : bond 0.05682 ( 1003) hydrogen bonds : angle 4.95057 ( 2748) SS BOND : bond 0.00331 ( 40) SS BOND : angle 1.44795 ( 80) covalent geometry : bond 0.00358 (25802) covalent geometry : angle 0.53858 (35109) *********************** 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 79 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 2.964 Fit side-chains revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8325 (t0) cc_final: 0.8030 (t0) REVERT: A 898 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.9165 (mtp) REVERT: B 1000 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7948 (tm-30) outliers start: 14 outliers final: 6 residues processed: 71 average time/residue: 1.2433 time to fit residues: 108.8719 Evaluate side-chains 67 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 618 VAL 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 93 optimal weight: 0.0040 chunk 119 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 223 optimal weight: 0.0170 chunk 239 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.1632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3754 r_free = 0.3754 target = 0.086911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052000 restraints weight = 85787.980| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 4.35 r_work: 0.2728 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25923 Z= 0.125 Angle : 0.546 11.213 35432 Z= 0.270 Chirality : 0.045 0.357 4224 Planarity : 0.004 0.049 4442 Dihedral : 6.453 56.644 5011 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 0.85 % Allowed : 11.00 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3040 helix: 2.51 (0.22), residues: 651 sheet: 0.56 (0.19), residues: 718 loop : -1.03 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 351 HIS 0.002 0.000 HIS B1086 PHE 0.021 0.001 PHE A 166 TYR 0.016 0.001 TYR A 449 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 48) link_NAG-ASN : angle 2.30522 ( 144) link_BETA1-4 : bond 0.00328 ( 33) link_BETA1-4 : angle 1.60174 ( 99) hydrogen bonds : bond 0.05266 ( 1003) hydrogen bonds : angle 4.82711 ( 2748) SS BOND : bond 0.00298 ( 40) SS BOND : angle 1.32567 ( 80) covalent geometry : bond 0.00285 (25802) covalent geometry : angle 0.51776 (35109) *********************** 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 89 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8336 (t0) cc_final: 0.8017 (t0) REVERT: A 898 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9136 (mtp) REVERT: B 1000 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7870 (tm-30) REVERT: C 210 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8888 (tm) outliers start: 23 outliers final: 5 residues processed: 81 average time/residue: 1.0320 time to fit residues: 103.4512 Evaluate side-chains 66 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 210 LEU 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 37 optimal weight: 6.9990 chunk 136 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN C 269 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 = 0.3721 r_free = 0.3721 target = 0.085556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050281 restraints weight = 86371.012| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.40 r_work: 0.2685 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25923 Z= 0.241 Angle : 0.626 11.118 35432 Z= 0.310 Chirality : 0.047 0.363 4224 Planarity : 0.004 0.050 4442 Dihedral : 6.504 57.975 5011 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 1.04 % Allowed : 12.85 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3040 helix: 2.42 (0.21), residues: 642 sheet: 0.34 (0.19), residues: 731 loop : -1.09 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 434 HIS 0.004 0.001 HIS B1062 PHE 0.018 0.001 PHE B1119 TYR 0.017 0.001 TYR A1065 ARG 0.004 0.000 ARG B1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 48) link_NAG-ASN : angle 2.39541 ( 144) link_BETA1-4 : bond 0.00233 ( 33) link_BETA1-4 : angle 1.70988 ( 99) hydrogen bonds : bond 0.06496 ( 1003) hydrogen bonds : angle 5.06684 ( 2748) SS BOND : bond 0.00387 ( 40) SS BOND : angle 1.60626 ( 80) covalent geometry : bond 0.00576 (25802) covalent geometry : angle 0.59843 (35109) *********************** 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 87 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.9106 (t0) cc_final: 0.8705 (m110) REVERT: A 558 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9408 (mp) REVERT: A 569 ASP cc_start: 0.8361 (t0) cc_final: 0.8121 (t0) REVERT: A 898 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.9247 (mtp) REVERT: C 108 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8389 (m) outliers start: 28 outliers final: 9 residues processed: 79 average time/residue: 1.0692 time to fit residues: 105.2909 Evaluate side-chains 71 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 898 MET 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 736 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 248 optimal weight: 30.0000 chunk 220 optimal weight: 0.1980 chunk 82 optimal weight: 5.9990 chunk 300 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 chunk 306 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3757 r_free = 0.3757 target = 0.087322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.052356 restraints weight = 85591.320| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 4.36 r_work: 0.2733 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25923 Z= 0.109 Angle : 0.557 11.358 35432 Z= 0.273 Chirality : 0.045 0.354 4224 Planarity : 0.004 0.050 4442 Dihedral : 6.101 57.508 5011 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 1.00 % Allowed : 13.77 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3040 helix: 2.49 (0.21), residues: 658 sheet: 0.61 (0.19), residues: 702 loop : -1.03 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 351 HIS 0.001 0.000 HIS B1086 PHE 0.016 0.001 PHE A 106 TYR 0.016 0.001 TYR B1065 ARG 0.003 0.000 ARG C1089 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 48) link_NAG-ASN : angle 2.27486 ( 144) link_BETA1-4 : bond 0.00392 ( 33) link_BETA1-4 : angle 1.59906 ( 99) hydrogen bonds : bond 0.05082 ( 1003) hydrogen bonds : angle 4.74826 ( 2748) SS BOND : bond 0.00332 ( 40) SS BOND : angle 1.24791 ( 80) covalent geometry : bond 0.00235 (25802) covalent geometry : angle 0.53073 (35109) *********************** 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 87 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.9117 (t0) cc_final: 0.8718 (m110) REVERT: A 569 ASP cc_start: 0.8320 (t0) cc_final: 0.8009 (t0) REVERT: A 898 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.9157 (mtp) REVERT: B 1000 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8008 (tm-30) REVERT: C 108 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8487 (m) REVERT: C 876 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8884 (tt) outliers start: 27 outliers final: 8 residues processed: 82 average time/residue: 1.0350 time to fit residues: 106.6015 Evaluate side-chains 71 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR 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 32 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 11 optimal weight: 0.0270 chunk 228 optimal weight: 0.6980 chunk 250 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3740 r_free = 0.3740 target = 0.086451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.051489 restraints weight = 86074.605| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.34 r_work: 0.2724 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1229 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= 0.163 Angle : 0.575 10.957 35432 Z= 0.282 Chirality : 0.045 0.358 4224 Planarity : 0.004 0.049 4442 Dihedral : 6.059 56.934 5011 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 1.37 % Allowed : 14.03 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3040 helix: 2.51 (0.21), residues: 654 sheet: 0.49 (0.19), residues: 721 loop : -1.04 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 884 HIS 0.003 0.001 HIS B1086 PHE 0.013 0.001 PHE B1119 TYR 0.017 0.001 TYR B 447 ARG 0.003 0.000 ARG B1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 48) link_NAG-ASN : angle 2.29870 ( 144) link_BETA1-4 : bond 0.00281 ( 33) link_BETA1-4 : angle 1.64717 ( 99) hydrogen bonds : bond 0.05592 ( 1003) hydrogen bonds : angle 4.81028 ( 2748) SS BOND : bond 0.00338 ( 40) SS BOND : angle 1.39436 ( 80) covalent geometry : bond 0.00381 (25802) covalent geometry : angle 0.54816 (35109) *********************** 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 96 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.6997 (OUTLIER) cc_final: 0.6501 (p) REVERT: A 352 ASN cc_start: 0.9119 (t0) cc_final: 0.8716 (m110) REVERT: A 389 CYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7324 (p) REVERT: A 558 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9346 (mp) REVERT: A 569 ASP cc_start: 0.8325 (t0) cc_final: 0.8034 (t0) REVERT: A 898 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.9207 (mtp) REVERT: B 1000 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8099 (tm-30) REVERT: C 108 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8507 (m) REVERT: C 876 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8929 (tt) outliers start: 37 outliers final: 16 residues processed: 88 average time/residue: 0.9335 time to fit residues: 105.1610 Evaluate side-chains 80 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 2.921 ------------------------------------------------------------------------------- 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 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET 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 453 LEU Chi-restraints excluded: chain B residue 586 THR 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 C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR 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 244 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 282 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 228 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 58 optimal weight: 0.0470 chunk 246 optimal weight: 40.0000 chunk 276 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3772 r_free = 0.3772 target = 0.087556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053048 restraints weight = 86456.787| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.28 r_work: 0.2781 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25923 Z= 0.106 Angle : 0.547 10.587 35432 Z= 0.268 Chirality : 0.044 0.351 4224 Planarity : 0.004 0.050 4442 Dihedral : 5.835 57.075 5011 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 1.18 % Allowed : 14.44 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3040 helix: 2.54 (0.21), residues: 660 sheet: 0.62 (0.19), residues: 705 loop : -0.99 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 884 HIS 0.001 0.000 HIS B1086 PHE 0.016 0.001 PHE B 454 TYR 0.015 0.001 TYR A1065 ARG 0.001 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 48) link_NAG-ASN : angle 2.23059 ( 144) link_BETA1-4 : bond 0.00378 ( 33) link_BETA1-4 : angle 1.58828 ( 99) hydrogen bonds : bond 0.04816 ( 1003) hydrogen bonds : angle 4.64362 ( 2748) SS BOND : bond 0.00256 ( 40) SS BOND : angle 1.18830 ( 80) covalent geometry : bond 0.00233 (25802) covalent geometry : angle 0.52116 (35109) *********************** 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 97 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7145 (OUTLIER) cc_final: 0.6621 (p) REVERT: A 558 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9428 (mp) REVERT: A 569 ASP cc_start: 0.8053 (t0) cc_final: 0.7737 (t0) REVERT: A 898 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9003 (mtp) REVERT: B 1000 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8149 (tm-30) REVERT: C 876 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9137 (tt) outliers start: 32 outliers final: 16 residues processed: 89 average time/residue: 1.5528 time to fit residues: 174.5980 Evaluate side-chains 78 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL 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 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 62 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 218 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3747 r_free = 0.3747 target = 0.086779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051793 restraints weight = 86229.821| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 4.33 r_work: 0.2735 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25923 Z= 0.149 Angle : 0.569 13.405 35432 Z= 0.278 Chirality : 0.045 0.354 4224 Planarity : 0.004 0.051 4442 Dihedral : 5.914 56.870 5011 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 0.85 % Allowed : 14.85 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3040 helix: 2.59 (0.21), residues: 651 sheet: 0.55 (0.19), residues: 715 loop : -1.01 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 884 HIS 0.003 0.001 HIS B1086 PHE 0.021 0.001 PHE C 375 TYR 0.018 0.001 TYR B 447 ARG 0.002 0.000 ARG B1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 48) link_NAG-ASN : angle 2.24426 ( 144) link_BETA1-4 : bond 0.00294 ( 33) link_BETA1-4 : angle 1.62219 ( 99) hydrogen bonds : bond 0.05290 ( 1003) hydrogen bonds : angle 4.71722 ( 2748) SS BOND : bond 0.00302 ( 40) SS BOND : angle 1.50304 ( 80) covalent geometry : bond 0.00349 (25802) covalent geometry : angle 0.54140 (35109) *********************** 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 84 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7059 (OUTLIER) cc_final: 0.6546 (p) REVERT: A 558 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9318 (mp) REVERT: A 569 ASP cc_start: 0.8318 (t0) cc_final: 0.8031 (t0) REVERT: A 898 MET cc_start: 0.9454 (OUTLIER) cc_final: 0.9173 (mtp) REVERT: B 1000 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8021 (tm-30) REVERT: C 876 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8939 (tt) outliers start: 23 outliers final: 16 residues processed: 80 average time/residue: 0.9466 time to fit residues: 96.0421 Evaluate side-chains 77 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 2.608 ------------------------------------------------------------------------------- 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 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 305 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 284 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3758 r_free = 0.3758 target = 0.086865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.052309 restraints weight = 86845.071| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.30 r_work: 0.2757 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25923 Z= 0.135 Angle : 0.564 12.612 35432 Z= 0.275 Chirality : 0.045 0.352 4224 Planarity : 0.004 0.051 4442 Dihedral : 5.867 56.742 5011 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.18 % Rotamer: Outliers : 1.00 % Allowed : 14.88 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3040 helix: 2.48 (0.21), residues: 663 sheet: 0.55 (0.19), residues: 714 loop : -0.99 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 351 HIS 0.003 0.001 HIS B1086 PHE 0.021 0.001 PHE C 375 TYR 0.016 0.001 TYR A1065 ARG 0.002 0.000 ARG B1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 48) link_NAG-ASN : angle 2.21374 ( 144) link_BETA1-4 : bond 0.00318 ( 33) link_BETA1-4 : angle 1.60524 ( 99) hydrogen bonds : bond 0.05232 ( 1003) hydrogen bonds : angle 4.69998 ( 2748) SS BOND : bond 0.00285 ( 40) SS BOND : angle 1.41171 ( 80) covalent geometry : bond 0.00312 (25802) covalent geometry : angle 0.53719 (35109) ********************** 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 86 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7162 (OUTLIER) cc_final: 0.6628 (p) REVERT: A 193 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7872 (ttpp) REVERT: A 558 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9401 (mp) REVERT: A 569 ASP cc_start: 0.8096 (t0) cc_final: 0.7796 (t0) REVERT: A 898 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.9004 (mtp) REVERT: B 1000 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 876 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9150 (tt) outliers start: 27 outliers final: 17 residues processed: 80 average time/residue: 1.7089 time to fit residues: 171.7218 Evaluate side-chains 80 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 5.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 193 LYS 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 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 20 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3723 r_free = 0.3723 target = 0.085604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.050375 restraints weight = 86116.867| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.41 r_work: 0.2686 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25923 Z= 0.234 Angle : 0.626 12.296 35432 Z= 0.308 Chirality : 0.047 0.357 4224 Planarity : 0.004 0.051 4442 Dihedral : 6.118 58.515 5011 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 1.07 % Allowed : 14.81 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3040 helix: 2.40 (0.21), residues: 660 sheet: 0.37 (0.19), residues: 728 loop : -1.04 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 351 HIS 0.003 0.001 HIS B1062 PHE 0.024 0.001 PHE C 375 TYR 0.017 0.001 TYR A1065 ARG 0.004 0.000 ARG B1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 48) link_NAG-ASN : angle 2.30319 ( 144) link_BETA1-4 : bond 0.00246 ( 33) link_BETA1-4 : angle 1.69838 ( 99) hydrogen bonds : bond 0.06326 ( 1003) hydrogen bonds : angle 4.94370 ( 2748) SS BOND : bond 0.00386 ( 40) SS BOND : angle 1.67567 ( 80) covalent geometry : bond 0.00556 (25802) covalent geometry : angle 0.59882 (35109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17898.24 seconds wall clock time: 316 minutes 21.10 seconds (18981.10 seconds total)