Starting phenix.real_space_refine on Thu Jun 4 11:06:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r7l_53783/06_2026/9r7l_53783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r7l_53783/06_2026/9r7l_53783.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/9r7l_53783/06_2026/9r7l_53783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r7l_53783/06_2026/9r7l_53783.map" model { file = "/net/cci-nas-00/data/ceres_data/9r7l_53783/06_2026/9r7l_53783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r7l_53783/06_2026/9r7l_53783.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 336 5.16 5 C 7523 2.51 5 N 2211 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12428 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "B" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "G" Number of atoms: 263 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Conformer: "B" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} bond proxies already assigned to first conformer: 252 Chain: "H" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "I" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "J" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "K" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "L" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "M" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "N" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "O" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "P" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "Q" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "S" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "T" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "U" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "V" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "W" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "X" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "Y" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "Z" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "a" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "b" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "c" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "d" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "e" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "f" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "g" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "h" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "i" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "j" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "k" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "l" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "m" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "n" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "o" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "p" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "q" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "r" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "s" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "t" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "u" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "v" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.31, per 1000 atoms: 0.27 Number of scatterers: 12428 At special positions: 0 Unit cell: (98.904, 98.0798, 126.927, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 336 16.00 P 30 15.00 O 2328 8.00 N 2211 7.00 C 7523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=144, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 31 " distance=2.03 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 20 " distance=2.03 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 31 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 20 " distance=2.02 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 31 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 10 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS E 10 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS F 10 " - pdb=" SG CYS F 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 4 " - pdb=" SG CYS G 31 " distance=2.02 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 20 " distance=2.02 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 31 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 20 " distance=2.03 Simple disulfide: pdb=" SG CYS H 10 " - pdb=" SG CYS H 30 " distance=2.03 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 31 " distance=2.03 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 20 " distance=2.03 Simple disulfide: pdb=" SG CYS I 10 " - pdb=" SG CYS I 30 " distance=2.03 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 31 " distance=2.02 Simple disulfide: pdb=" SG CYS J 6 " - pdb=" SG CYS J 20 " distance=2.02 Simple disulfide: pdb=" SG CYS J 10 " - pdb=" SG CYS J 30 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 31 " distance=2.03 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 20 " distance=2.02 Simple disulfide: pdb=" SG CYS K 10 " - pdb=" SG CYS K 30 " distance=2.03 Simple disulfide: pdb=" SG CYS L 4 " - pdb=" SG CYS L 31 " distance=2.03 Simple disulfide: pdb=" SG CYS L 6 " - pdb=" SG CYS L 20 " distance=2.03 Simple disulfide: pdb=" SG CYS L 10 " - pdb=" SG CYS L 30 " distance=2.03 Simple disulfide: pdb=" SG CYS M 4 " - pdb=" SG CYS M 31 " distance=2.03 Simple disulfide: pdb=" SG CYS M 6 " - pdb=" SG CYS M 20 " distance=2.03 Simple disulfide: pdb=" SG CYS M 10 " - pdb=" SG CYS M 30 " distance=2.03 Simple disulfide: pdb=" SG CYS N 4 " - pdb=" SG CYS N 31 " distance=2.03 Simple disulfide: pdb=" SG CYS N 6 " - pdb=" SG CYS N 20 " distance=2.03 Simple disulfide: pdb=" SG CYS N 10 " - pdb=" SG CYS N 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 4 " - pdb=" SG CYS O 31 " distance=2.03 Simple disulfide: pdb=" SG CYS O 6 " - pdb=" SG CYS O 20 " distance=2.03 Simple disulfide: pdb=" SG CYS O 10 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS P 4 " - pdb=" SG CYS P 31 " distance=2.03 Simple disulfide: pdb=" SG CYS P 6 " - pdb=" SG CYS P 20 " distance=2.03 Simple disulfide: pdb=" SG CYS P 10 " - pdb=" SG CYS P 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 4 " - pdb=" SG CYS Q 31 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 6 " - pdb=" SG CYS Q 20 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 10 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS R 4 " - pdb=" SG CYS R 31 " distance=2.03 Simple disulfide: pdb=" SG CYS R 6 " - pdb=" SG CYS R 20 " distance=2.03 Simple disulfide: pdb=" SG CYS R 10 " - pdb=" SG CYS R 30 " distance=2.03 Simple disulfide: pdb=" SG CYS S 4 " - pdb=" SG CYS S 31 " distance=2.02 Simple disulfide: pdb=" SG CYS S 6 " - pdb=" SG CYS S 20 " distance=2.03 Simple disulfide: pdb=" SG CYS S 10 " - pdb=" SG CYS S 30 " distance=2.03 Simple disulfide: pdb=" SG CYS T 4 " - pdb=" SG CYS T 31 " distance=2.03 Simple disulfide: pdb=" SG CYS T 6 " - pdb=" SG CYS T 20 " distance=2.02 Simple disulfide: pdb=" SG CYS T 10 " - pdb=" SG CYS T 30 " distance=2.03 Simple disulfide: pdb=" SG CYS U 4 " - pdb=" SG CYS U 31 " distance=2.02 Simple disulfide: pdb=" SG CYS U 6 " - pdb=" SG CYS U 20 " distance=2.03 Simple disulfide: pdb=" SG CYS U 10 " - pdb=" SG CYS U 30 " distance=2.03 Simple disulfide: pdb=" SG CYS V 4 " - pdb=" SG CYS V 31 " distance=2.03 Simple disulfide: pdb=" SG CYS V 6 " - pdb=" SG CYS V 20 " distance=2.03 Simple disulfide: pdb=" SG CYS V 10 " - pdb=" SG CYS V 30 " distance=2.03 Simple disulfide: pdb=" SG CYS W 4 " - pdb=" SG CYS W 31 " distance=2.03 Simple disulfide: pdb=" SG CYS W 6 " - pdb=" SG CYS W 20 " distance=2.03 Simple disulfide: pdb=" SG CYS W 10 " - pdb=" SG CYS W 30 " distance=2.03 Simple disulfide: pdb=" SG CYS X 4 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 6 " - pdb=" SG CYS X 20 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 4 " - pdb=" SG CYS Y 31 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 6 " - pdb=" SG CYS Y 20 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 10 " - pdb=" SG CYS Y 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 4 " - pdb=" SG CYS Z 31 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 6 " - pdb=" SG CYS Z 20 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 10 " - pdb=" SG CYS Z 30 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 31 " distance=2.02 Simple disulfide: pdb=" SG CYS a 6 " - pdb=" SG CYS a 20 " distance=2.03 Simple disulfide: pdb=" SG CYS a 10 " - pdb=" SG CYS a 30 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 31 " distance=2.03 Simple disulfide: pdb=" SG CYS b 6 " - pdb=" SG CYS b 20 " distance=2.03 Simple disulfide: pdb=" SG CYS b 10 " - pdb=" SG CYS b 30 " distance=2.03 Simple disulfide: pdb=" SG CYS c 4 " - pdb=" SG CYS c 31 " distance=2.02 Simple disulfide: pdb=" SG CYS c 6 " - pdb=" SG CYS c 20 " distance=2.03 Simple disulfide: pdb=" SG CYS c 10 " - pdb=" SG CYS c 30 " distance=2.03 Simple disulfide: pdb=" SG CYS d 4 " - pdb=" SG CYS d 31 " distance=2.03 Simple disulfide: pdb=" SG CYS d 6 " - pdb=" SG CYS d 20 " distance=2.03 Simple disulfide: pdb=" SG CYS d 10 " - pdb=" SG CYS d 30 " distance=2.03 Simple disulfide: pdb=" SG CYS e 4 " - pdb=" SG CYS e 31 " distance=2.03 Simple disulfide: pdb=" SG CYS e 6 " - pdb=" SG CYS e 20 " distance=2.03 Simple disulfide: pdb=" SG CYS e 10 " - pdb=" SG CYS e 30 " distance=2.03 Simple disulfide: pdb=" SG CYS f 4 " - pdb=" SG CYS f 31 " distance=2.02 Simple disulfide: pdb=" SG CYS f 6 " - pdb=" SG CYS f 20 " distance=2.04 Simple disulfide: pdb=" SG CYS f 10 " - pdb=" SG CYS f 30 " distance=2.03 Simple disulfide: pdb=" SG CYS g 4 " - pdb=" SG CYS g 31 " distance=2.02 Simple disulfide: pdb=" SG CYS g 6 " - pdb=" SG CYS g 20 " distance=2.03 Simple disulfide: pdb=" SG CYS g 10 " - pdb=" SG CYS g 30 " distance=2.03 Simple disulfide: pdb=" SG CYS h 4 " - pdb=" SG CYS h 31 " distance=2.03 Simple disulfide: pdb=" SG CYS h 6 " - pdb=" SG CYS h 20 " distance=2.03 Simple disulfide: pdb=" SG CYS h 10 " - pdb=" SG CYS h 30 " distance=2.03 Simple disulfide: pdb=" SG CYS i 4 " - pdb=" SG CYS i 31 " distance=2.03 Simple disulfide: pdb=" SG CYS i 6 " - pdb=" SG CYS i 20 " distance=2.03 Simple disulfide: pdb=" SG CYS i 10 " - pdb=" SG CYS i 30 " distance=2.03 Simple disulfide: pdb=" SG CYS j 4 " - pdb=" SG CYS j 31 " distance=2.02 Simple disulfide: pdb=" SG CYS j 6 " - pdb=" SG CYS j 20 " distance=2.03 Simple disulfide: pdb=" SG CYS j 10 " - pdb=" SG CYS j 30 " distance=2.03 Simple disulfide: pdb=" SG CYS k 4 " - pdb=" SG CYS k 31 " distance=2.03 Simple disulfide: pdb=" SG CYS k 6 " - pdb=" SG CYS k 20 " distance=2.03 Simple disulfide: pdb=" SG CYS k 10 " - pdb=" SG CYS k 30 " distance=2.03 Simple disulfide: pdb=" SG CYS l 4 " - pdb=" SG CYS l 31 " distance=2.03 Simple disulfide: pdb=" SG CYS l 6 " - pdb=" SG CYS l 20 " distance=2.03 Simple disulfide: pdb=" SG CYS l 10 " - pdb=" SG CYS l 30 " distance=2.03 Simple disulfide: pdb=" SG CYS m 4 " - pdb=" SG CYS m 31 " distance=2.03 Simple disulfide: pdb=" SG CYS m 6 " - pdb=" SG CYS m 20 " distance=2.03 Simple disulfide: pdb=" SG CYS m 10 " - pdb=" SG CYS m 30 " distance=2.03 Simple disulfide: pdb=" SG CYS n 4 " - pdb=" SG CYS n 31 " distance=2.03 Simple disulfide: pdb=" SG CYS n 6 " - pdb=" SG CYS n 20 " distance=2.03 Simple disulfide: pdb=" SG CYS n 10 " - pdb=" SG CYS n 30 " distance=2.03 Simple disulfide: pdb=" SG CYS o 4 " - pdb=" SG CYS o 31 " distance=2.03 Simple disulfide: pdb=" SG CYS o 6 " - pdb=" SG CYS o 20 " distance=2.03 Simple disulfide: pdb=" SG CYS o 10 " - pdb=" SG CYS o 30 " distance=2.03 Simple disulfide: pdb=" SG CYS p 4 " - pdb=" SG CYS p 31 " distance=2.03 Simple disulfide: pdb=" SG CYS p 6 " - pdb=" SG CYS p 20 " distance=2.03 Simple disulfide: pdb=" SG CYS p 10 " - pdb=" SG CYS p 30 " distance=2.03 Simple disulfide: pdb=" SG CYS q 4 " - pdb=" SG CYS q 31 " distance=2.03 Simple disulfide: pdb=" SG CYS q 6 " - pdb=" SG CYS q 20 " distance=2.03 Simple disulfide: pdb=" SG CYS q 10 " - pdb=" SG CYS q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS r 4 " - pdb=" SG CYS r 31 " distance=2.03 Simple disulfide: pdb=" SG CYS r 6 " - pdb=" SG CYS r 20 " distance=2.03 Simple disulfide: pdb=" SG CYS r 10 " - pdb=" SG CYS r 30 " distance=2.03 Simple disulfide: pdb=" SG CYS s 4 " - pdb=" SG CYS s 31 " distance=2.02 Simple disulfide: pdb=" SG CYS s 6 " - pdb=" SG CYS s 20 " distance=2.03 Simple disulfide: pdb=" SG CYS s 10 " - pdb=" SG CYS s 30 " distance=2.03 Simple disulfide: pdb=" SG CYS t 4 " - pdb=" SG CYS t 31 " distance=2.03 Simple disulfide: pdb=" SG CYS t 6 " - pdb=" SG CYS t 20 " distance=2.03 Simple disulfide: pdb=" SG CYS t 10 " - pdb=" SG CYS t 30 " distance=2.04 Simple disulfide: pdb=" SG CYS u 4 " - pdb=" SG CYS u 31 " distance=2.03 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 20 " distance=2.03 Simple disulfide: pdb=" SG CYS u 10 " - pdb=" SG CYS u 30 " distance=2.02 Simple disulfide: pdb=" SG CYS v 4 " - pdb=" SG CYS v 31 " distance=2.03 Simple disulfide: pdb=" SG CYS v 6 " - pdb=" SG CYS v 20 " distance=2.03 Simple disulfide: pdb=" SG CYS v 10 " - pdb=" SG CYS v 30 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 575.8 milliseconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.754A pdb=" N ILE A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 21 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS A 27 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 19 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 29 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE B 29 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 19 " --> pdb=" O HIS B 27 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N HIS B 27 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 21 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR E 21 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS E 27 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR E 19 " --> pdb=" O HIS E 27 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE E 29 " --> pdb=" O TYR E 17 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER F 16 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS F 31 " --> pdb=" O SER F 16 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY I 18 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS I 31 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N SER I 16 " --> pdb=" O CYS I 31 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SER J 16 " --> pdb=" O CYS J 31 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS J 31 " --> pdb=" O SER J 16 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY J 18 " --> pdb=" O PHE J 29 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE J 29 " --> pdb=" O GLY J 18 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE M 25 " --> pdb=" O THR M 21 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR M 21 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS M 27 " --> pdb=" O THR M 19 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR M 19 " --> pdb=" O HIS M 27 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE M 29 " --> pdb=" O TYR M 17 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER N 16 " --> pdb=" O CYS N 31 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS N 31 " --> pdb=" O SER N 16 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY N 18 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR N 3 " --> pdb=" O LEU N 32 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY S 18 " --> pdb=" O PHE S 29 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N CYS S 31 " --> pdb=" O SER S 16 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER S 16 " --> pdb=" O CYS S 31 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N SER T 16 " --> pdb=" O CYS T 31 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS T 31 " --> pdb=" O SER T 16 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY T 18 " --> pdb=" O PHE T 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.760A pdb=" N THR C 3 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY C 18 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS C 31 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER C 16 " --> pdb=" O CYS C 31 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER D 16 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS D 31 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY D 18 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR G 3 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR G 21 " --> pdb=" O ILE G 25 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS G 27 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR G 19 " --> pdb=" O HIS G 27 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE G 29 " --> pdb=" O TYR G 17 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE H 29 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR H 19 " --> pdb=" O HIS H 27 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N HIS H 27 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR H 21 " --> pdb=" O ILE H 25 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE H 25 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS K 31 " --> pdb=" O SER K 16 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N SER K 16 " --> pdb=" O CYS K 31 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE L 29 " --> pdb=" O TYR L 17 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR L 19 " --> pdb=" O HIS L 27 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS L 27 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR L 21 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE L 25 " --> pdb=" O THR L 21 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE O 25 " --> pdb=" O THR O 21 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR O 21 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS O 27 " --> pdb=" O THR O 19 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR O 19 " --> pdb=" O HIS O 27 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE O 29 " --> pdb=" O TYR O 17 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE P 29 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR P 19 " --> pdb=" O HIS P 27 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS P 27 " --> pdb=" O THR P 19 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR P 21 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE P 25 " --> pdb=" O THR P 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY Q 18 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS Q 31 " --> pdb=" O SER Q 16 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER Q 16 " --> pdb=" O CYS Q 31 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER R 16 " --> pdb=" O CYS R 31 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS R 31 " --> pdb=" O SER R 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 3 through 7 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 3 through 7 current: chain 'U' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 25 through 32 current: chain 'V' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 25 through 32 current: chain 'Y' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 25 through 32 current: chain 'Z' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 25 through 32 current: chain 'c' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 25 through 32 current: chain 'd' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 25 through 31 current: chain 'g' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 25 through 32 current: chain 'h' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 25 through 32 current: chain 'k' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 25 through 32 current: chain 'l' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 25 through 31 current: chain 'o' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 25 through 32 current: chain 'p' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 25 through 32 current: chain 's' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 's' and resid 25 through 31 current: chain 't' and resid 25 through 32 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'W' and resid 3 through 7 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 3 through 7 current: chain 'W' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 25 through 32 current: chain 'X' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 25 through 31 current: chain 'a' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 25 through 32 current: chain 'b' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 25 through 32 current: chain 'e' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 25 through 32 current: chain 'f' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 25 through 32 current: chain 'i' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 25 through 31 current: chain 'j' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 25 through 32 current: chain 'm' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 25 through 32 current: chain 'n' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 25 through 31 current: chain 'q' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'q' and resid 25 through 31 current: chain 'r' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 25 through 32 current: chain 'u' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 25 through 32 current: chain 'v' and resid 25 through 32 No H-bonds generated for sheet with id=AA4 227 hydrogen bonds defined for protein. 572 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: 1.77 Time building geometry restraints manager: 1.15 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: 3891 1.34 - 1.46: 3873 1.46 - 1.58: 4539 1.58 - 1.70: 30 1.70 - 1.82: 384 Bond restraints: 12717 Sorted by residual: bond pdb=" O16 IHP C 101 " pdb=" P6 IHP C 101 " ideal model delta sigma weight residual 1.672 1.638 0.034 2.00e-02 2.50e+03 2.91e+00 bond pdb=" O32 IHP F 101 " pdb=" P2 IHP F 101 " ideal model delta sigma weight residual 1.537 1.503 0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" O15 IHP Q 101 " pdb=" P5 IHP Q 101 " ideal model delta sigma weight residual 1.675 1.641 0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" O32 IHP Q 101 " pdb=" P2 IHP Q 101 " ideal model delta sigma weight residual 1.537 1.504 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" O32 IHP C 101 " pdb=" P2 IHP C 101 " ideal model delta sigma weight residual 1.537 1.504 0.033 2.00e-02 2.50e+03 2.66e+00 ... (remaining 12712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 16783 2.13 - 4.27: 276 4.27 - 6.40: 66 6.40 - 8.53: 23 8.53 - 10.67: 13 Bond angle restraints: 17161 Sorted by residual: angle pdb=" O12 IHP L 101 " pdb=" P2 IHP L 101 " pdb=" O32 IHP L 101 " ideal model delta sigma weight residual 100.47 111.14 -10.67 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CB MET v 23 " pdb=" CG MET v 23 " pdb=" SD MET v 23 " ideal model delta sigma weight residual 112.70 122.73 -10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" O12 IHP F 101 " pdb=" P2 IHP F 101 " pdb=" O32 IHP F 101 " ideal model delta sigma weight residual 100.47 110.35 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C3 IHP L 101 " pdb=" C4 IHP L 101 " pdb=" C5 IHP L 101 " ideal model delta sigma weight residual 107.91 117.56 -9.65 3.00e+00 1.11e-01 1.04e+01 angle pdb=" O12 IHP C 101 " pdb=" P2 IHP C 101 " pdb=" O32 IHP C 101 " ideal model delta sigma weight residual 100.47 110.00 -9.53 3.00e+00 1.11e-01 1.01e+01 ... (remaining 17156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.92: 7184 30.92 - 61.85: 568 61.85 - 92.77: 31 92.77 - 123.69: 45 123.69 - 154.62: 23 Dihedral angle restraints: 7851 sinusoidal: 3335 harmonic: 4516 Sorted by residual: dihedral pdb=" CB CYS r 6 " pdb=" SG CYS r 6 " pdb=" SG CYS r 20 " pdb=" CB CYS r 20 " ideal model delta sinusoidal sigma weight residual 93.00 5.10 87.90 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS a 6 " pdb=" SG CYS a 6 " pdb=" SG CYS a 20 " pdb=" CB CYS a 20 " ideal model delta sinusoidal sigma weight residual -86.00 -166.01 80.01 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS j 6 " pdb=" SG CYS j 6 " pdb=" SG CYS j 20 " pdb=" CB CYS j 20 " ideal model delta sinusoidal sigma weight residual 93.00 13.82 79.18 1 1.00e+01 1.00e-02 7.80e+01 ... (remaining 7848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.023: 1777 1.023 - 2.046: 0 2.046 - 3.069: 0 3.069 - 4.092: 0 4.092 - 5.115: 30 Chirality restraints: 1807 Sorted by residual: chirality pdb=" C2 IHP L 101 " pdb=" C1 IHP L 101 " pdb=" C3 IHP L 101 " pdb=" O12 IHP L 101 " both_signs ideal model delta sigma weight residual False -2.52 2.60 -5.12 2.00e-01 2.50e+01 6.54e+02 chirality pdb=" C2 IHP F 101 " pdb=" C1 IHP F 101 " pdb=" C3 IHP F 101 " pdb=" O12 IHP F 101 " both_signs ideal model delta sigma weight residual False -2.52 2.54 -5.06 2.00e-01 2.50e+01 6.40e+02 chirality pdb=" C2 IHP C 101 " pdb=" C1 IHP C 101 " pdb=" C3 IHP C 101 " pdb=" O12 IHP C 101 " both_signs ideal model delta sigma weight residual False -2.52 2.52 -5.04 2.00e-01 2.50e+01 6.34e+02 ... (remaining 1804 not shown) Planarity restraints: 2114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG f 28 " -0.117 9.50e-02 1.11e+02 5.29e-02 2.44e+00 pdb=" NE ARG f 28 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG f 28 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG f 28 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG f 28 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG h 28 " 0.116 9.50e-02 1.11e+02 5.25e-02 2.18e+00 pdb=" NE ARG h 28 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG h 28 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG h 28 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG h 28 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 15 " -0.012 2.00e-02 2.50e+03 1.00e-02 2.00e+00 pdb=" CG TYR K 15 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR K 15 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR K 15 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR K 15 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR K 15 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR K 15 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 15 " -0.001 2.00e-02 2.50e+03 ... (remaining 2111 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2312 2.77 - 3.30: 10324 3.30 - 3.83: 20089 3.83 - 4.37: 24400 4.37 - 4.90: 44589 Nonbonded interactions: 101714 Sorted by model distance: nonbonded pdb=" NH2 ARG c 7 " pdb=" OE2 GLU c 14 " model vdw 2.233 3.120 nonbonded pdb=" NH1 ARG e 7 " pdb=" OE1 GLU e 14 " model vdw 2.254 3.120 nonbonded pdb=" NH1 ARG P 7 " pdb=" O24 IHP M 101 " model vdw 2.281 3.120 nonbonded pdb=" OH TYR H 17 " pdb=" NE2 HIS L 27 " model vdw 2.292 3.120 nonbonded pdb=" NH2 ARG M 7 " pdb=" OE1 GLU M 14 " model vdw 2.297 3.120 ... (remaining 101709 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 1 through 27 or resid 29 through 32)) selection = (chain 'B' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'C' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'D' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'E' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'F' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'G' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'H' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'I' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'J' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'K' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'L' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'M' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'N' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'O' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'P' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'Q' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'R' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'S' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'T' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'U' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'V' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'W' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'X' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'Y' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'Z' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'a' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'b' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'c' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'd' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'e' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'f' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'g' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'h' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'i' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'j' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'k' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'l' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'm' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'n' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'o' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'p' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'q' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'r' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 's' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 't' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'u' and (resid 1 through 27 or resid 29 through 32)) selection = (chain 'v' and (resid 1 through 27 or resid 29 through 32)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 9.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.180 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 : 0.006 0.038 12861 Z= 0.257 Angle : 0.792 10.667 17449 Z= 0.375 Chirality : 0.639 5.115 1807 Planarity : 0.004 0.053 2114 Dihedral : 23.193 154.618 4537 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.67 % Favored : 98.26 % Rotamer: Outliers : 4.74 % Allowed : 28.93 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 1441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG f 28 TYR 0.025 0.001 TYR b 17 PHE 0.013 0.002 PHE e 29 HIS 0.006 0.001 HIS U 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (12717) covalent geometry : angle 0.78898 / 0.37 (17161) SS BOND : bond 0.00406 / 0.28 ( 144) SS BOND : angle 0.96457 / 0.65 ( 288) hydrogen bonds : bond 0.14723 / 10.59 ( 227) hydrogen bonds : angle 8.79783 / 6.17 ( 572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 320 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 28 ARG cc_start: 0.7041 (mtm110) cc_final: 0.6629 (mtm-85) REVERT: o 28 ARG cc_start: 0.7950 (mpp80) cc_final: 0.7747 (mpp80) outliers start: 66 outliers final: 60 residues processed: 373 average time/residue: 0.5076 time to fit residues: 207.7202 Evaluate side-chains 377 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 317 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 26 ASN Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 19 THR Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain d residue 7 ARG Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 16 SER Chi-restraints excluded: chain f residue 10 CYS Chi-restraints excluded: chain g residue 10 CYS Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 20 CYS Chi-restraints excluded: chain h residue 16 SER Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 31 CYS Chi-restraints excluded: chain n residue 10 CYS Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain o residue 19 THR Chi-restraints excluded: chain o residue 20 CYS Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain s residue 21 THR Chi-restraints excluded: chain t residue 9 SER Chi-restraints excluded: chain t residue 16 SER Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 10 CYS Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 22 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 26 ASN ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 26 ASN e 5 HIS q 26 ASN ** s 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 27 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097813 restraints weight = 22658.549| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.87 r_work: 0.3249 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12861 Z= 0.129 Angle : 0.684 11.404 17449 Z= 0.305 Chirality : 0.055 0.587 1807 Planarity : 0.003 0.034 2114 Dihedral : 13.761 89.246 2115 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.11 % Favored : 98.82 % Rotamer: Outliers : 5.53 % Allowed : 25.13 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.19), residues: 1441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG h 28 TYR 0.027 0.001 TYR Q 15 PHE 0.011 0.002 PHE e 29 HIS 0.007 0.001 HIS U 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (12717) covalent geometry : angle 0.68550 / 0.30 (17161) SS BOND : bond 0.00229 / 0.15 ( 144) SS BOND : angle 0.61638 / 0.41 ( 288) hydrogen bonds : bond 0.03354 / 2.17 ( 227) hydrogen bonds : angle 7.27846 / 5.06 ( 572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 346 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: C 15 TYR cc_start: 0.8310 (m-80) cc_final: 0.8088 (m-10) REVERT: C 23 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8182 (mtm) REVERT: H 4 CYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8658 (m) REVERT: R 8 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8007 (ptm-80) REVERT: S 25 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8095 (mp) REVERT: U 7 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8349 (mtp85) REVERT: o 28 ARG cc_start: 0.8080 (mpp80) cc_final: 0.7773 (mpp80) REVERT: p 31 CYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7712 (m) outliers start: 77 outliers final: 36 residues processed: 381 average time/residue: 0.5611 time to fit residues: 232.5741 Evaluate side-chains 371 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 330 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain H residue 4 CYS Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 25 ILE Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 16 SER Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 10 CYS Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain k residue 32 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 10 CYS Chi-restraints excluded: chain o residue 20 CYS Chi-restraints excluded: chain p residue 31 CYS Chi-restraints excluded: chain s residue 21 THR Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 19 THR Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain v residue 9 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 0.0970 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 26 ASN n 26 ASN q 26 ASN ** s 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 27 HIS ** 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 = 0.3546 r_free = 0.3546 target = 0.113261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097576 restraints weight = 36872.435| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.52 r_work: 0.3226 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12861 Z= 0.104 Angle : 0.599 10.887 17449 Z= 0.276 Chirality : 0.050 0.433 1807 Planarity : 0.003 0.038 2114 Dihedral : 12.953 78.034 2056 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 5.31 % Allowed : 26.35 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG h 28 TYR 0.021 0.001 TYR Q 15 PHE 0.009 0.001 PHE g 29 HIS 0.006 0.001 HIS U 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (12717) covalent geometry : angle 0.60005 / 0.28 (17161) SS BOND : bond 0.00193 / 0.13 ( 144) SS BOND : angle 0.55730 / 0.38 ( 288) hydrogen bonds : bond 0.02804 / 1.79 ( 227) hydrogen bonds : angle 6.92299 / 4.79 ( 572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 349 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8638 (mtt) cc_final: 0.8383 (mtm) REVERT: C 15 TYR cc_start: 0.8364 (m-80) cc_final: 0.8137 (m-10) REVERT: C 23 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8153 (mtm) REVERT: H 4 CYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8769 (m) REVERT: J 28 ARG cc_start: 0.8294 (mmt90) cc_final: 0.7695 (mmm160) REVERT: R 8 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8126 (ptm-80) REVERT: a 23 MET cc_start: 0.8395 (mmm) cc_final: 0.8149 (mmt) REVERT: b 19 THR cc_start: 0.8181 (m) cc_final: 0.7855 (p) REVERT: f 16 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8366 (t) REVERT: t 7 ARG cc_start: 0.8153 (ptp-110) cc_final: 0.7692 (ptp-110) outliers start: 74 outliers final: 37 residues processed: 379 average time/residue: 0.5508 time to fit residues: 227.3283 Evaluate side-chains 367 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain H residue 4 CYS Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 16 SER Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 10 CYS Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain k residue 32 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain o residue 20 CYS Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain s residue 7 ARG Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain v residue 9 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 HIS ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 26 ASN n 26 ASN q 26 ASN s 27 HIS ** t 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094754 restraints weight = 22347.091| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.84 r_work: 0.3195 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12861 Z= 0.243 Angle : 0.714 12.506 17449 Z= 0.333 Chirality : 0.060 0.624 1807 Planarity : 0.004 0.037 2114 Dihedral : 13.320 83.273 2048 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 7.25 % Allowed : 25.27 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.18), residues: 1441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 28 TYR 0.031 0.001 TYR Q 15 PHE 0.013 0.002 PHE B 29 HIS 0.007 0.001 HIS U 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (12717) covalent geometry : angle 0.70879 / 0.33 (17161) SS BOND : bond 0.00456 / 0.31 ( 144) SS BOND : angle 0.95608 / 0.63 ( 288) hydrogen bonds : bond 0.03538 / 2.32 ( 227) hydrogen bonds : angle 7.33936 / 5.07 ( 572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 320 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: C 23 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: H 4 CYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8686 (m) REVERT: M 8 ARG cc_start: 0.8134 (ttt90) cc_final: 0.7805 (tpt-90) REVERT: R 8 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8058 (ptm-80) REVERT: o 23 MET cc_start: 0.8182 (mpp) cc_final: 0.7873 (mtt) REVERT: o 28 ARG cc_start: 0.8284 (mpp80) cc_final: 0.7982 (mpp80) REVERT: p 31 CYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7757 (m) outliers start: 101 outliers final: 55 residues processed: 356 average time/residue: 0.5300 time to fit residues: 205.8774 Evaluate side-chains 371 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 312 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain H residue 4 CYS Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain a residue 25 ILE Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 16 SER Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 10 CYS Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 32 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 10 CYS Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain o residue 20 CYS Chi-restraints excluded: chain p residue 31 CYS Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain s residue 19 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 19 THR Chi-restraints excluded: chain u residue 21 THR Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain v residue 9 SER Chi-restraints excluded: chain v residue 32 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 26 ASN n 26 ASN q 26 ASN ** t 27 HIS ** 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 = 0.3531 r_free = 0.3531 target = 0.112280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097347 restraints weight = 29338.795| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.18 r_work: 0.3225 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12861 Z= 0.115 Angle : 0.608 9.954 17449 Z= 0.282 Chirality : 0.050 0.466 1807 Planarity : 0.003 0.041 2114 Dihedral : 12.566 75.527 2048 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 5.38 % Allowed : 26.27 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 28 TYR 0.023 0.001 TYR Q 15 PHE 0.010 0.001 PHE S 29 HIS 0.006 0.001 HIS U 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (12717) covalent geometry : angle 0.60738 / 0.28 (17161) SS BOND : bond 0.00211 / 0.14 ( 144) SS BOND : angle 0.61540 / 0.43 ( 288) hydrogen bonds : bond 0.02777 / 1.77 ( 227) hydrogen bonds : angle 6.88016 / 4.75 ( 572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 331 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: C 15 TYR cc_start: 0.8334 (m-80) cc_final: 0.8124 (m-10) REVERT: C 23 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8113 (mtm) REVERT: H 4 CYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8739 (m) REVERT: J 28 ARG cc_start: 0.8224 (mmt90) cc_final: 0.7657 (mmm160) REVERT: M 8 ARG cc_start: 0.8075 (ttt90) cc_final: 0.7750 (tpt-90) REVERT: R 8 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8008 (ptm-80) REVERT: f 16 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8357 (t) REVERT: p 23 MET cc_start: 0.8375 (mtp) cc_final: 0.8131 (mtp) REVERT: p 31 CYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7664 (m) REVERT: u 28 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7855 (mtt90) outliers start: 75 outliers final: 41 residues processed: 360 average time/residue: 0.5024 time to fit residues: 198.6125 Evaluate side-chains 371 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain H residue 4 CYS Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 16 SER Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 10 CYS Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain k residue 32 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 10 CYS Chi-restraints excluded: chain p residue 31 CYS Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 28 ARG Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain v residue 9 SER Chi-restraints excluded: chain v residue 32 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 0.5980 chunk 89 optimal weight: 0.0020 chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 26 ASN q 26 ASN t 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096983 restraints weight = 25529.961| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.00 r_work: 0.3224 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12861 Z= 0.137 Angle : 0.610 10.638 17449 Z= 0.286 Chirality : 0.051 0.466 1807 Planarity : 0.003 0.046 2114 Dihedral : 12.329 74.243 2045 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 5.53 % Allowed : 26.49 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.19), residues: 1441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG h 28 TYR 0.025 0.001 TYR Q 15 PHE 0.011 0.001 PHE B 29 HIS 0.005 0.001 HIS U 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (12717) covalent geometry : angle 0.60930 / 0.29 (17161) SS BOND : bond 0.00266 / 0.18 ( 144) SS BOND : angle 0.66196 / 0.45 ( 288) hydrogen bonds : bond 0.02911 / 1.88 ( 227) hydrogen bonds : angle 6.89951 / 4.77 ( 572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 327 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: C 23 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8042 (mtm) REVERT: M 8 ARG cc_start: 0.8175 (ttt90) cc_final: 0.7829 (tpt-90) REVERT: R 8 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8009 (ptm-80) REVERT: U 23 MET cc_start: 0.7935 (mmm) cc_final: 0.7597 (mmm) REVERT: Y 23 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: k 23 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7304 (mpp) REVERT: o 28 ARG cc_start: 0.8318 (mpp80) cc_final: 0.8045 (mpp80) REVERT: p 23 MET cc_start: 0.8370 (mtp) cc_final: 0.8098 (mtp) REVERT: p 31 CYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7680 (m) REVERT: v 23 MET cc_start: 0.8593 (mmm) cc_final: 0.8359 (mmm) outliers start: 77 outliers final: 50 residues processed: 356 average time/residue: 0.5080 time to fit residues: 198.2203 Evaluate side-chains 375 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 10 CYS Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain i residue 8 ARG Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain k residue 23 MET Chi-restraints excluded: chain k residue 32 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 10 CYS Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain p residue 31 CYS Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 19 THR Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain v residue 9 SER Chi-restraints excluded: chain v residue 32 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 136 optimal weight: 0.0060 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 HIS ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 26 ASN q 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098054 restraints weight = 31102.473| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.28 r_work: 0.3229 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12861 Z= 0.106 Angle : 0.584 10.159 17449 Z= 0.274 Chirality : 0.047 0.399 1807 Planarity : 0.003 0.052 2114 Dihedral : 11.719 71.391 2045 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 4.59 % Allowed : 27.64 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.19), residues: 1441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG f 28 TYR 0.022 0.001 TYR Q 15 PHE 0.011 0.001 PHE f 29 HIS 0.005 0.001 HIS U 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (12717) covalent geometry : angle 0.58396 / 0.27 (17161) SS BOND : bond 0.00200 / 0.13 ( 144) SS BOND : angle 0.59306 / 0.42 ( 288) hydrogen bonds : bond 0.02691 / 1.70 ( 227) hydrogen bonds : angle 6.71792 / 4.66 ( 572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 334 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 TYR cc_start: 0.8362 (m-80) cc_final: 0.8158 (m-10) REVERT: C 23 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8053 (mtm) REVERT: J 28 ARG cc_start: 0.8228 (mmt90) cc_final: 0.7706 (mmm160) REVERT: M 8 ARG cc_start: 0.8109 (ttt90) cc_final: 0.7759 (tpt-90) REVERT: R 8 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8009 (ptm-80) REVERT: U 28 ARG cc_start: 0.7308 (mtm110) cc_final: 0.7007 (mtm-85) REVERT: Y 23 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: Z 23 MET cc_start: 0.8272 (mmm) cc_final: 0.8069 (mmt) REVERT: b 19 THR cc_start: 0.8207 (m) cc_final: 0.7896 (p) REVERT: e 28 ARG cc_start: 0.8079 (ptp-170) cc_final: 0.7868 (ptp-170) REVERT: h 14 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: p 31 CYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7665 (m) REVERT: t 7 ARG cc_start: 0.8168 (ptp-110) cc_final: 0.7749 (ptp-110) REVERT: v 23 MET cc_start: 0.8634 (mmm) cc_final: 0.8429 (mmm) outliers start: 64 outliers final: 46 residues processed: 358 average time/residue: 0.5145 time to fit residues: 201.7467 Evaluate side-chains 374 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 323 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 20 CYS Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 10 CYS Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain h residue 14 GLU Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain i residue 8 ARG Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain k residue 32 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 10 CYS Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain p residue 31 CYS Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain v residue 9 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 0.0170 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 HIS O 26 ASN ** X 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 26 ASN q 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099217 restraints weight = 25031.719| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.99 r_work: 0.3259 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12861 Z= 0.102 Angle : 0.579 10.129 17449 Z= 0.272 Chirality : 0.046 0.390 1807 Planarity : 0.003 0.056 2114 Dihedral : 11.427 69.361 2045 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 4.24 % Allowed : 28.86 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.19), residues: 1441 helix: None (None), residues: 0 sheet: -0.81 (0.65), residues: 66 loop : -1.09 (0.15), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG h 28 TYR 0.027 0.001 TYR Q 15 PHE 0.012 0.001 PHE f 29 HIS 0.004 0.001 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (12717) covalent geometry : angle 0.57802 / 0.27 (17161) SS BOND : bond 0.00201 / 0.13 ( 144) SS BOND : angle 0.61914 / 0.43 ( 288) hydrogen bonds : bond 0.02594 / 1.66 ( 227) hydrogen bonds : angle 6.63680 / 4.60 ( 572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8457 (mtt) cc_final: 0.8234 (mtm) REVERT: C 23 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8022 (mtm) REVERT: J 28 ARG cc_start: 0.8185 (mmt90) cc_final: 0.7664 (mmm160) REVERT: M 8 ARG cc_start: 0.8045 (ttt90) cc_final: 0.7707 (tpt-90) REVERT: R 8 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7899 (ptm-80) REVERT: U 28 ARG cc_start: 0.7314 (mtm110) cc_final: 0.7047 (mtm-85) REVERT: Y 23 MET cc_start: 0.8455 (mmm) cc_final: 0.8149 (mtt) REVERT: b 19 THR cc_start: 0.8156 (m) cc_final: 0.7826 (p) REVERT: b 26 ASN cc_start: 0.8046 (p0) cc_final: 0.7755 (p0) REVERT: e 28 ARG cc_start: 0.8071 (ptp-170) cc_final: 0.7866 (ptp-170) REVERT: h 14 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: p 31 CYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7616 (m) REVERT: q 8 ARG cc_start: 0.8252 (mtp85) cc_final: 0.8038 (mtp85) REVERT: u 14 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7302 (mm-30) outliers start: 59 outliers final: 45 residues processed: 349 average time/residue: 0.5160 time to fit residues: 197.3231 Evaluate side-chains 374 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 325 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 20 CYS Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain h residue 14 GLU Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 32 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain p residue 31 CYS Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 19 THR Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain v residue 9 SER Chi-restraints excluded: chain v residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 27 HIS ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 26 ASN q 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098735 restraints weight = 22117.690| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.83 r_work: 0.3260 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12861 Z= 0.127 Angle : 0.603 10.966 17449 Z= 0.285 Chirality : 0.048 0.425 1807 Planarity : 0.003 0.059 2114 Dihedral : 11.481 72.699 2044 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 4.38 % Allowed : 29.15 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.19), residues: 1441 helix: None (None), residues: 0 sheet: -0.84 (0.65), residues: 66 loop : -1.09 (0.15), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG h 28 TYR 0.028 0.001 TYR Q 15 PHE 0.013 0.001 PHE f 29 HIS 0.004 0.001 HIS u 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (12717) covalent geometry : angle 0.60161 / 0.28 (17161) SS BOND : bond 0.00249 / 0.17 ( 144) SS BOND : angle 0.69112 / 0.48 ( 288) hydrogen bonds : bond 0.02757 / 1.78 ( 227) hydrogen bonds : angle 6.70436 / 4.64 ( 572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 23 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8028 (mtm) REVERT: J 28 ARG cc_start: 0.8169 (mmt90) cc_final: 0.7666 (mmm160) REVERT: M 8 ARG cc_start: 0.8054 (ttt90) cc_final: 0.7709 (tpt-90) REVERT: R 8 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7914 (ptm-80) REVERT: V 7 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8233 (ptp90) REVERT: Y 23 MET cc_start: 0.8419 (mmm) cc_final: 0.8188 (mtt) REVERT: b 19 THR cc_start: 0.8151 (m) cc_final: 0.7816 (p) REVERT: b 26 ASN cc_start: 0.8063 (p0) cc_final: 0.7778 (p0) REVERT: o 28 ARG cc_start: 0.8237 (mpp80) cc_final: 0.7931 (mpp80) REVERT: p 31 CYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7639 (m) outliers start: 61 outliers final: 48 residues processed: 344 average time/residue: 0.4951 time to fit residues: 187.1305 Evaluate side-chains 369 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 318 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 20 CYS Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 32 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 10 CYS Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain p residue 31 CYS Chi-restraints excluded: chain r residue 2 PHE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain t residue 14 GLU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 19 THR Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain v residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 26 ASN ** X 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 26 ASN q 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094871 restraints weight = 22248.459| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.83 r_work: 0.3204 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12861 Z= 0.235 Angle : 0.708 13.294 17449 Z= 0.338 Chirality : 0.055 0.582 1807 Planarity : 0.004 0.058 2114 Dihedral : 12.118 82.053 2044 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.88 % Allowed : 29.36 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.19), residues: 1441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG f 28 TYR 0.031 0.001 TYR K 15 PHE 0.017 0.002 PHE f 29 HIS 0.005 0.001 HIS d 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (12717) covalent geometry : angle 0.69877 / 0.33 (17161) SS BOND : bond 0.00446 / 0.31 ( 144) SS BOND : angle 1.12560 / 0.76 ( 288) hydrogen bonds : bond 0.03362 / 2.21 ( 227) hydrogen bonds : angle 7.08301 / 4.89 ( 572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 316 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8096 (mtm) REVERT: M 8 ARG cc_start: 0.8234 (ttt90) cc_final: 0.7847 (tpt-90) REVERT: R 8 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8068 (ptm-80) REVERT: Y 23 MET cc_start: 0.8493 (mmm) cc_final: 0.8172 (mtt) REVERT: a 23 MET cc_start: 0.8341 (mmm) cc_final: 0.8027 (mmt) REVERT: o 28 ARG cc_start: 0.8328 (mpp80) cc_final: 0.8062 (mpp80) outliers start: 54 outliers final: 46 residues processed: 335 average time/residue: 0.5195 time to fit residues: 190.4479 Evaluate side-chains 361 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 313 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 20 CYS Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain Y residue 15 TYR Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain i residue 8 ARG Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 32 LEU Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 10 CYS Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain s residue 21 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 19 THR Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain v residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 124 optimal weight: 0.0770 chunk 126 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 27 HIS ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 26 ASN q 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097851 restraints weight = 29414.702| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.20 r_work: 0.3233 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12861 Z= 0.116 Angle : 0.613 11.006 17449 Z= 0.292 Chirality : 0.046 0.399 1807 Planarity : 0.004 0.062 2114 Dihedral : 11.604 75.465 2044 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.23 % Allowed : 30.51 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.19), residues: 1441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG f 28 TYR 0.024 0.001 TYR Q 15 PHE 0.013 0.001 PHE f 29 HIS 0.004 0.001 HIS u 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12717) covalent geometry : angle 0.60988 / 0.29 (17161) SS BOND : bond 0.00219 / 0.14 ( 144) SS BOND : angle 0.75626 / 0.53 ( 288) hydrogen bonds : bond 0.02715 / 1.73 ( 227) hydrogen bonds : angle 6.75733 / 4.68 ( 572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5200.77 seconds wall clock time: 89 minutes 25.29 seconds (5365.29 seconds total)