Starting phenix.real_space_refine on Thu Jun 4 10:37:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r7n_53785/06_2026/9r7n_53785.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r7n_53785/06_2026/9r7n_53785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r7n_53785/06_2026/9r7n_53785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r7n_53785/06_2026/9r7n_53785.map" model { file = "/net/cci-nas-00/data/ceres_data/9r7n_53785/06_2026/9r7n_53785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r7n_53785/06_2026/9r7n_53785.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 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 5 5.49 5 S 336 5.16 5 C 7488 2.51 5 N 2208 2.21 5 O 2228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 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: 12265 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: 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 breaks: 1 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: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.05, per 1000 atoms: 0.25 Number of scatterers: 12265 At special positions: 0 Unit cell: (97.954, 99.416, 128.656, 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 5 15.00 O 2228 8.00 N 2208 7.00 C 7488 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=2.03 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=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 31 " distance=2.03 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=2.03 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=2.03 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=2.04 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=2.03 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=2.03 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=2.03 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=2.02 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=2.03 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=2.01 Simple disulfide: pdb=" SG CYS j 4 " - pdb=" SG CYS j 31 " distance=2.03 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=2.02 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=2.02 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=2.04 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=2.03 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 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: 0.98 Conformation dependent library (CDL) restraints added in 529.8 milliseconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2880 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.509A pdb=" N CYS A 31 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER A 16 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 29 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR B 19 " --> pdb=" O HIS B 27 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS B 27 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.965A pdb=" N THR C 3 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY C 18 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS C 31 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER C 16 " --> pdb=" O CYS C 31 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE D 29 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.909A pdb=" N GLY E 18 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N CYS E 31 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N SER E 16 " --> pdb=" O CYS E 31 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER F 16 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS F 31 " --> pdb=" O SER F 16 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS I 31 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER I 16 " --> pdb=" O CYS I 31 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER J 16 " --> pdb=" O CYS J 31 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS J 31 " --> pdb=" O SER J 16 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY J 18 " --> pdb=" O PHE J 29 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE J 29 " --> pdb=" O GLY J 18 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE M 29 " --> pdb=" O TYR M 17 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER N 16 " --> pdb=" O CYS N 31 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N CYS N 31 " --> pdb=" O SER N 16 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY N 18 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY S 18 " --> pdb=" O PHE S 29 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N CYS S 31 " --> pdb=" O SER S 16 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER S 16 " --> pdb=" O CYS S 31 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER T 16 " --> pdb=" O CYS T 31 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS T 31 " --> pdb=" O SER T 16 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY T 18 " --> pdb=" O PHE T 29 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE T 29 " --> pdb=" O GLY T 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 7 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 3 through 7 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 31 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 31 current: chain 'K' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 25 through 31 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 31 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 25 through 31 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 '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 31 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, 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 31 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 25 through 31 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 31 WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 25 through 31 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=AA5 Processing sheet with id=AA6, first strand: chain 'W' and resid 3 through 7 removed outlier: 5.593A pdb=" N SER X 16 " --> pdb=" O CYS X 31 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS X 31 " --> pdb=" O SER X 16 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY X 18 " --> pdb=" O PHE X 29 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE X 29 " --> pdb=" O GLY X 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY a 18 " --> pdb=" O PHE a 29 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N CYS a 31 " --> pdb=" O SER a 16 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER a 16 " --> pdb=" O CYS a 31 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER b 16 " --> pdb=" O CYS b 31 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS b 31 " --> pdb=" O SER b 16 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY b 18 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE e 25 " --> pdb=" O THR e 21 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR e 21 " --> pdb=" O ILE e 25 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N HIS e 27 " --> pdb=" O THR e 19 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR e 19 " --> pdb=" O HIS e 27 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE e 29 " --> pdb=" O TYR e 17 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE f 29 " --> pdb=" O TYR f 17 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N THR f 19 " --> pdb=" O HIS f 27 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N HIS f 27 " --> pdb=" O THR f 19 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR f 21 " --> pdb=" O ILE f 25 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE f 25 " --> pdb=" O THR f 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG f 7 " --> pdb=" O ARG f 28 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS f 5 " --> pdb=" O CYS f 30 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE f 2 " --> pdb=" O CYS i 4 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE i 25 " --> pdb=" O THR i 21 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR i 21 " --> pdb=" O ILE i 25 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS i 27 " --> pdb=" O THR i 19 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR i 19 " --> pdb=" O HIS i 27 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE i 29 " --> pdb=" O TYR i 17 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER j 16 " --> pdb=" O CYS j 31 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS j 31 " --> pdb=" O SER j 16 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR m 3 " --> pdb=" O LEU m 32 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY m 18 " --> pdb=" O PHE m 29 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N CYS m 31 " --> pdb=" O SER m 16 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N SER m 16 " --> pdb=" O CYS m 31 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE n 29 " --> pdb=" O TYR n 17 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR n 19 " --> pdb=" O HIS n 27 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS n 27 " --> pdb=" O THR n 19 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR n 21 " --> pdb=" O ILE n 25 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE n 25 " --> pdb=" O THR n 21 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY q 18 " --> pdb=" O PHE q 29 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS q 31 " --> pdb=" O SER q 16 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N SER q 16 " --> pdb=" O CYS q 31 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER r 16 " --> pdb=" O CYS r 31 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS r 31 " --> pdb=" O SER r 16 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY r 18 " --> pdb=" O PHE r 29 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR r 3 " --> pdb=" O LEU r 32 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE u 25 " --> pdb=" O THR u 21 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR u 21 " --> pdb=" O ILE u 25 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N HIS u 27 " --> pdb=" O THR u 19 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR u 19 " --> pdb=" O HIS u 27 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE u 29 " --> pdb=" O TYR u 17 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER v 16 " --> pdb=" O CYS v 31 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS v 31 " --> pdb=" O SER v 16 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR v 3 " --> pdb=" O LEU v 32 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 744 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: 1.81 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3887 1.35 - 1.46: 3866 1.46 - 1.58: 4410 1.58 - 1.70: 0 1.70 - 1.82: 384 Bond restraints: 12547 Sorted by residual: bond pdb=" O3 PO4 E 101 " pdb=" P PO4 E 101 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" O3 PO4 B 101 " pdb=" P PO4 B 101 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" O3 PO4 S 101 " pdb=" P PO4 S 101 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" O3 PO4 O 101 " pdb=" P PO4 O 101 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" O4 PO4 J 101 " pdb=" P PO4 J 101 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.70e+00 ... (remaining 12542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16537 2.01 - 4.02: 296 4.02 - 6.03: 31 6.03 - 8.04: 9 8.04 - 10.05: 2 Bond angle restraints: 16875 Sorted by residual: angle pdb=" CB MET H 23 " pdb=" CG MET H 23 " pdb=" SD MET H 23 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA ARG L 8 " pdb=" CB ARG L 8 " pdb=" CG ARG L 8 " ideal model delta sigma weight residual 114.10 120.55 -6.45 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CG ARG E 8 " pdb=" CD ARG E 8 " pdb=" NE ARG E 8 " ideal model delta sigma weight residual 112.00 118.65 -6.65 2.20e+00 2.07e-01 9.15e+00 angle pdb=" CB ARG L 8 " pdb=" CG ARG L 8 " pdb=" CD ARG L 8 " ideal model delta sigma weight residual 111.30 118.03 -6.73 2.30e+00 1.89e-01 8.55e+00 angle pdb=" CA CYS r 6 " pdb=" CB CYS r 6 " pdb=" SG CYS r 6 " ideal model delta sigma weight residual 114.40 121.11 -6.71 2.30e+00 1.89e-01 8.52e+00 ... (remaining 16870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6253 17.69 - 35.38: 1027 35.38 - 53.07: 294 53.07 - 70.76: 46 70.76 - 88.44: 11 Dihedral angle restraints: 7631 sinusoidal: 3120 harmonic: 4511 Sorted by residual: 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 -86.00 2.44 -88.44 1 1.00e+01 1.00e-02 9.34e+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 -174.00 88.00 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS h 10 " pdb=" SG CYS h 10 " pdb=" SG CYS h 30 " pdb=" CB CYS h 30 " ideal model delta sinusoidal sigma weight residual -86.00 -170.83 84.83 1 1.00e+01 1.00e-02 8.74e+01 ... (remaining 7628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1143 0.033 - 0.066: 433 0.066 - 0.099: 132 0.099 - 0.132: 63 0.132 - 0.165: 5 Chirality restraints: 1776 Sorted by residual: chirality pdb=" CA VAL R 22 " pdb=" N VAL R 22 " pdb=" C VAL R 22 " pdb=" CB VAL R 22 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CB VAL E 22 " pdb=" CA VAL E 22 " pdb=" CG1 VAL E 22 " pdb=" CG2 VAL E 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA VAL E 22 " pdb=" N VAL E 22 " pdb=" C VAL E 22 " pdb=" CB VAL E 22 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1773 not shown) Planarity restraints: 2111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 8 " -0.153 9.50e-02 1.11e+02 6.92e-02 3.96e+00 pdb=" NE ARG E 8 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 8 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG E 8 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 8 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR Q 13 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C THR Q 13 " -0.033 2.00e-02 2.50e+03 pdb=" O THR Q 13 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU Q 14 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 15 " 0.012 2.00e-02 2.50e+03 1.31e-02 3.44e+00 pdb=" CG TYR P 15 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR P 15 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR P 15 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR P 15 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR P 15 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR P 15 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR P 15 " -0.001 2.00e-02 2.50e+03 ... (remaining 2108 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 297 2.67 - 3.23: 10802 3.23 - 3.79: 17711 3.79 - 4.34: 24246 4.34 - 4.90: 42681 Nonbonded interactions: 95737 Sorted by model distance: nonbonded pdb=" OG1 THR Q 21 " pdb=" OG1 THR R 21 " model vdw 2.115 3.040 nonbonded pdb=" O ARG a 8 " pdb=" NH2 ARG a 28 " model vdw 2.235 3.120 nonbonded pdb=" O ARG t 8 " pdb=" NH1 ARG t 28 " model vdw 2.264 3.120 nonbonded pdb=" O ARG B 8 " pdb=" NE ARG B 8 " model vdw 2.289 3.120 nonbonded pdb=" OG1 THR Y 13 " pdb=" OE1 GLU Y 14 " model vdw 2.294 3.040 ... (remaining 95732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 32) selection = chain 'C' selection = chain 'D' selection = (chain 'E' and resid 1 through 32) selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = (chain 'J' and resid 1 through 32) selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = (chain 'O' and resid 1 through 32) selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = (chain 'S' and resid 1 through 32) selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.340 Find NCS groups from input model: 0.240 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12691 Z= 0.195 Angle : 0.687 10.048 17163 Z= 0.393 Chirality : 0.041 0.165 1776 Planarity : 0.004 0.069 2111 Dihedral : 17.263 81.830 4319 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.36 % Allowed : 31.03 % Favored : 68.61 % 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: -1.83 (0.21), residues: 1439 helix: None (None), residues: 0 sheet: -1.18 (0.16), residues: 810 loop : -1.04 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 8 TYR 0.032 0.001 TYR P 15 PHE 0.030 0.002 PHE k 29 HIS 0.008 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (12547) covalent geometry : angle 0.68018 / 0.39 (16875) SS BOND : bond 0.00320 / 0.22 ( 144) SS BOND : angle 1.00711 / 0.67 ( 288) hydrogen bonds : bond 0.18789 / 13.05 ( 294) hydrogen bonds : angle 9.26264 / 6.51 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 375 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 ILE cc_start: 0.7580 (mm) cc_final: 0.7124 (tt) REVERT: P 11 TYR cc_start: 0.5559 (m-10) cc_final: 0.5293 (m-10) REVERT: P 14 GLU cc_start: 0.5652 (pm20) cc_final: 0.5157 (pm20) REVERT: T 14 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7096 (mt-10) REVERT: a 14 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6575 (tt0) REVERT: e 14 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7117 (mt-10) REVERT: n 23 MET cc_start: 0.8124 (mtt) cc_final: 0.7478 (mtt) REVERT: v 11 TYR cc_start: 0.7541 (m-10) cc_final: 0.7326 (m-80) outliers start: 5 outliers final: 5 residues processed: 376 average time/residue: 0.1316 time to fit residues: 67.3594 Evaluate side-chains 362 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 357 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain R residue 15 TYR Chi-restraints excluded: chain j residue 11 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN J 26 ASN ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 5 HIS t 27 HIS ** v 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 = 0.4000 r_free = 0.4000 target = 0.133971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.118559 restraints weight = 24022.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.122077 restraints weight = 12122.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.124372 restraints weight = 7347.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.125894 restraints weight = 4995.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.126939 restraints weight = 3699.439| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12691 Z= 0.158 Angle : 0.549 6.755 17163 Z= 0.307 Chirality : 0.040 0.146 1776 Planarity : 0.003 0.034 2111 Dihedral : 6.550 69.800 1830 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.74 % Allowed : 25.93 % Favored : 69.32 % 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: -1.75 (0.21), residues: 1439 helix: None (None), residues: 0 sheet: -1.13 (0.17), residues: 828 loop : -0.96 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 8 TYR 0.021 0.001 TYR L 11 PHE 0.017 0.002 PHE k 29 HIS 0.006 0.001 HIS m 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (12547) covalent geometry : angle 0.54027 / 0.30 (16875) SS BOND : bond 0.00319 / 0.22 ( 144) SS BOND : angle 0.93664 / 0.60 ( 288) hydrogen bonds : bond 0.03583 / 2.44 ( 294) hydrogen bonds : angle 7.66057 / 5.34 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 379 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.6529 (ptp-110) cc_final: 0.6326 (ptp-170) REVERT: H 7 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7884 (ptp90) REVERT: K 28 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7387 (mmm160) REVERT: N 22 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9059 (p) REVERT: P 14 GLU cc_start: 0.5757 (pm20) cc_final: 0.5524 (pm20) REVERT: T 14 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6920 (mt-10) REVERT: U 23 MET cc_start: 0.6968 (mtt) cc_final: 0.6700 (mtt) REVERT: n 23 MET cc_start: 0.8356 (mtt) cc_final: 0.7796 (mtt) REVERT: t 28 ARG cc_start: 0.7196 (mtp180) cc_final: 0.6791 (ptt180) REVERT: v 11 TYR cc_start: 0.7388 (m-10) cc_final: 0.7071 (m-80) outliers start: 66 outliers final: 40 residues processed: 420 average time/residue: 0.1267 time to fit residues: 72.5459 Evaluate side-chains 393 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 351 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain H residue 7 ARG Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 15 TYR Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain c residue 5 HIS Chi-restraints excluded: chain c residue 27 HIS Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain e residue 30 CYS Chi-restraints excluded: chain f residue 9 SER Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain j residue 11 TYR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain v residue 13 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 134 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN N 26 ASN ** v 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.134690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.120050 restraints weight = 23417.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.123555 restraints weight = 11804.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.125813 restraints weight = 7155.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.127342 restraints weight = 4870.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.128384 restraints weight = 3596.818| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12691 Z= 0.124 Angle : 0.516 7.090 17163 Z= 0.285 Chirality : 0.039 0.134 1776 Planarity : 0.003 0.029 2111 Dihedral : 6.171 64.303 1828 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.60 % Allowed : 26.58 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.21), residues: 1439 helix: None (None), residues: 0 sheet: -1.10 (0.17), residues: 822 loop : -0.90 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 8 TYR 0.019 0.001 TYR P 17 PHE 0.019 0.002 PHE l 29 HIS 0.007 0.001 HIS m 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (12547) covalent geometry : angle 0.51071 / 0.28 (16875) SS BOND : bond 0.00252 / 0.17 ( 144) SS BOND : angle 0.75273 / 0.48 ( 288) hydrogen bonds : bond 0.03122 / 2.09 ( 294) hydrogen bonds : angle 7.29961 / 5.08 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 377 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 ILE cc_start: 0.8120 (mm) cc_final: 0.7700 (tt) REVERT: H 7 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7742 (ptp90) REVERT: J 8 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7413 (ttm110) REVERT: J 15 TYR cc_start: 0.7743 (t80) cc_final: 0.7480 (t80) REVERT: J 21 THR cc_start: 0.9349 (m) cc_final: 0.9081 (p) REVERT: K 28 ARG cc_start: 0.7556 (mmm-85) cc_final: 0.7324 (mmm160) REVERT: N 22 VAL cc_start: 0.9283 (OUTLIER) cc_final: 0.9058 (m) REVERT: P 14 GLU cc_start: 0.5848 (pm20) cc_final: 0.5628 (pm20) REVERT: U 23 MET cc_start: 0.7246 (mtt) cc_final: 0.7012 (mtt) REVERT: V 28 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7592 (mmm160) REVERT: l 23 MET cc_start: 0.6992 (mtt) cc_final: 0.6694 (mtt) REVERT: r 15 TYR cc_start: 0.6868 (t80) cc_final: 0.6334 (t80) REVERT: t 28 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6847 (ptt180) outliers start: 64 outliers final: 50 residues processed: 417 average time/residue: 0.1327 time to fit residues: 74.9358 Evaluate side-chains 413 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 361 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 ARG Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain R residue 15 TYR Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain b residue 10 CYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 5 HIS Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain e residue 30 CYS Chi-restraints excluded: chain f residue 9 SER Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain i residue 11 TYR Chi-restraints excluded: chain j residue 9 SER Chi-restraints excluded: chain j residue 11 TYR Chi-restraints excluded: chain k residue 10 CYS Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 9 SER Chi-restraints excluded: chain t residue 10 CYS Chi-restraints excluded: chain v residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN O 27 HIS S 26 ASN f 5 HIS ** v 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.129184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.113542 restraints weight = 24169.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.116995 restraints weight = 12437.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.119262 restraints weight = 7662.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.120779 restraints weight = 5287.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.121755 restraints weight = 3946.736| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12691 Z= 0.245 Angle : 0.606 7.327 17163 Z= 0.336 Chirality : 0.041 0.145 1776 Planarity : 0.003 0.035 2111 Dihedral : 6.824 58.945 1828 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.32 % Allowed : 26.15 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.21), residues: 1439 helix: None (None), residues: 0 sheet: -1.16 (0.17), residues: 810 loop : -1.14 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 8 TYR 0.017 0.002 TYR e 15 PHE 0.021 0.003 PHE q 29 HIS 0.009 0.002 HIS m 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 (12547) covalent geometry : angle 0.59493 / 0.33 (16875) SS BOND : bond 0.00481 / 0.32 ( 144) SS BOND : angle 1.07187 / 0.70 ( 288) hydrogen bonds : bond 0.03599 / 2.43 ( 294) hydrogen bonds : angle 7.63289 / 5.30 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 363 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.6630 (ptp-110) cc_final: 0.6323 (ptp-170) REVERT: E 22 VAL cc_start: 0.9119 (t) cc_final: 0.8917 (m) REVERT: F 32 LEU cc_start: 0.8518 (tp) cc_final: 0.8099 (tt) REVERT: H 7 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8036 (ptp90) REVERT: I 16 SER cc_start: 0.9085 (m) cc_final: 0.8559 (p) REVERT: J 8 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7639 (ttp80) REVERT: J 15 TYR cc_start: 0.7826 (t80) cc_final: 0.7625 (t80) REVERT: J 21 THR cc_start: 0.9351 (m) cc_final: 0.9077 (p) REVERT: K 14 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7235 (mm-30) REVERT: N 22 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.8988 (p) REVERT: N 28 ARG cc_start: 0.8587 (mmp-170) cc_final: 0.8365 (mmp-170) REVERT: P 14 GLU cc_start: 0.6029 (pm20) cc_final: 0.5802 (pm20) REVERT: V 28 ARG cc_start: 0.8273 (mmm160) cc_final: 0.7600 (mmm160) REVERT: Z 5 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6704 (m170) REVERT: Z 28 ARG cc_start: 0.6652 (mmt90) cc_final: 0.6368 (mtm-85) REVERT: b 15 TYR cc_start: 0.7935 (t80) cc_final: 0.7665 (t80) REVERT: d 5 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7271 (t-90) REVERT: f 32 LEU cc_start: 0.9339 (tt) cc_final: 0.9122 (tt) REVERT: l 23 MET cc_start: 0.7296 (mtt) cc_final: 0.7067 (mtt) REVERT: n 23 MET cc_start: 0.8673 (mtt) cc_final: 0.8231 (mtt) outliers start: 88 outliers final: 70 residues processed: 427 average time/residue: 0.1315 time to fit residues: 75.7336 Evaluate side-chains 417 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 343 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 ARG Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 22 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 5 HIS Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain b residue 10 CYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 5 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain d residue 5 HIS Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain e residue 30 CYS Chi-restraints excluded: chain f residue 10 CYS Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain h residue 10 CYS Chi-restraints excluded: chain i residue 30 CYS Chi-restraints excluded: chain j residue 9 SER Chi-restraints excluded: chain j residue 11 TYR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 10 CYS Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain o residue 10 CYS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 9 SER Chi-restraints excluded: chain t residue 10 CYS Chi-restraints excluded: chain u residue 16 SER Chi-restraints excluded: chain v residue 13 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS ** v 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112578 restraints weight = 22429.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115918 restraints weight = 11803.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.118115 restraints weight = 7346.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.119603 restraints weight = 5098.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120639 restraints weight = 3807.769| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12691 Z= 0.134 Angle : 0.530 6.139 17163 Z= 0.293 Chirality : 0.039 0.128 1776 Planarity : 0.003 0.029 2111 Dihedral : 6.187 64.103 1826 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.53 % Allowed : 27.30 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.21), residues: 1439 helix: None (None), residues: 0 sheet: -1.10 (0.17), residues: 816 loop : -0.98 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG t 28 TYR 0.015 0.001 TYR d 15 PHE 0.014 0.002 PHE k 29 HIS 0.007 0.001 HIS m 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (12547) covalent geometry : angle 0.52492 / 0.29 (16875) SS BOND : bond 0.00297 / 0.20 ( 144) SS BOND : angle 0.78076 / 0.51 ( 288) hydrogen bonds : bond 0.02997 / 2.03 ( 294) hydrogen bonds : angle 7.28525 / 5.08 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 378 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 MET cc_start: 0.8664 (mtt) cc_final: 0.8351 (mtm) REVERT: C 23 MET cc_start: 0.7220 (mmt) cc_final: 0.6860 (mmt) REVERT: D 25 ILE cc_start: 0.7623 (mt) cc_final: 0.7374 (pt) REVERT: F 32 LEU cc_start: 0.8269 (tp) cc_final: 0.7981 (tt) REVERT: H 7 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8135 (ptp90) REVERT: I 16 SER cc_start: 0.9030 (m) cc_final: 0.8520 (p) REVERT: J 8 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7712 (ttp80) REVERT: J 21 THR cc_start: 0.9426 (m) cc_final: 0.9163 (p) REVERT: N 22 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9001 (p) REVERT: N 28 ARG cc_start: 0.8549 (mmp-170) cc_final: 0.8338 (mmp-170) REVERT: P 28 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.7969 (mmm160) REVERT: b 15 TYR cc_start: 0.7835 (t80) cc_final: 0.7602 (t80) REVERT: c 28 ARG cc_start: 0.6943 (ptp90) cc_final: 0.6592 (ptt-90) REVERT: d 5 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7410 (t-90) REVERT: e 15 TYR cc_start: 0.7843 (t80) cc_final: 0.7486 (t80) REVERT: f 8 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8007 (mtm110) REVERT: k 23 MET cc_start: 0.8093 (mpp) cc_final: 0.7759 (mpp) REVERT: m 5 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.5745 (m90) REVERT: n 9 SER cc_start: 0.8086 (p) cc_final: 0.7758 (p) REVERT: n 23 MET cc_start: 0.8653 (mtt) cc_final: 0.8346 (mtt) REVERT: o 30 CYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5690 (p) REVERT: t 28 ARG cc_start: 0.7329 (mtm110) cc_final: 0.6981 (ptt180) outliers start: 77 outliers final: 65 residues processed: 427 average time/residue: 0.1303 time to fit residues: 75.8646 Evaluate side-chains 430 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 359 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 ARG Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain R residue 15 TYR Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 22 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain b residue 10 CYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain c residue 5 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 30 CYS Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain d residue 5 HIS Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain f residue 8 ARG Chi-restraints excluded: chain f residue 10 CYS Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain i residue 11 TYR Chi-restraints excluded: chain j residue 9 SER Chi-restraints excluded: chain j residue 11 TYR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 10 CYS Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain m residue 5 HIS Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 30 CYS Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 10 CYS Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain v residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 HIS ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS ** v 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.128183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114711 restraints weight = 22380.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.117629 restraints weight = 12521.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.119545 restraints weight = 8072.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120899 restraints weight = 5790.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.121821 restraints weight = 4376.439| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12691 Z= 0.113 Angle : 0.515 7.882 17163 Z= 0.283 Chirality : 0.038 0.131 1776 Planarity : 0.003 0.030 2111 Dihedral : 5.994 66.358 1826 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.89 % Allowed : 27.37 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.21), residues: 1439 helix: None (None), residues: 0 sheet: -1.08 (0.17), residues: 792 loop : -0.98 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 28 TYR 0.023 0.001 TYR r 15 PHE 0.014 0.002 PHE I 2 HIS 0.007 0.001 HIS m 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (12547) covalent geometry : angle 0.51181 / 0.28 (16875) SS BOND : bond 0.00277 / 0.19 ( 144) SS BOND : angle 0.69492 / 0.45 ( 288) hydrogen bonds : bond 0.02816 / 1.91 ( 294) hydrogen bonds : angle 7.07352 / 4.93 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 379 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 MET cc_start: 0.8674 (mtt) cc_final: 0.8467 (mtm) REVERT: C 23 MET cc_start: 0.7212 (mmt) cc_final: 0.6818 (mmt) REVERT: F 32 LEU cc_start: 0.8179 (tp) cc_final: 0.7835 (tt) REVERT: H 7 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8137 (ptp90) REVERT: I 16 SER cc_start: 0.9015 (m) cc_final: 0.8477 (p) REVERT: J 8 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7571 (ttp80) REVERT: J 15 TYR cc_start: 0.7623 (t80) cc_final: 0.7285 (t80) REVERT: N 22 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9089 (p) REVERT: Z 5 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.6709 (m170) REVERT: c 28 ARG cc_start: 0.6877 (ptp90) cc_final: 0.6632 (ptt-90) REVERT: d 5 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7336 (t-90) REVERT: f 8 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7965 (mtm110) REVERT: n 23 MET cc_start: 0.8631 (mtt) cc_final: 0.8392 (mtt) REVERT: o 17 TYR cc_start: 0.8444 (m-80) cc_final: 0.7834 (m-10) REVERT: o 30 CYS cc_start: 0.5968 (OUTLIER) cc_final: 0.5532 (p) outliers start: 82 outliers final: 68 residues processed: 428 average time/residue: 0.1315 time to fit residues: 76.9564 Evaluate side-chains 431 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 357 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 ARG Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 22 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 5 HIS Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain b residue 10 CYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain c residue 5 HIS Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 30 CYS Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain d residue 5 HIS Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain f residue 8 ARG Chi-restraints excluded: chain f residue 10 CYS Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain h residue 10 CYS Chi-restraints excluded: chain j residue 11 TYR Chi-restraints excluded: chain k residue 10 CYS Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain o residue 10 CYS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 30 CYS Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 9 SER Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 9 SER Chi-restraints excluded: chain t residue 10 CYS Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 16 SER Chi-restraints excluded: chain v residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 32 optimal weight: 0.0570 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 56 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 HIS ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS m 5 HIS ** v 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 = 0.3864 r_free = 0.3864 target = 0.129335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114715 restraints weight = 22180.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.118084 restraints weight = 11600.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120285 restraints weight = 7173.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.121711 restraints weight = 4945.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.122789 restraints weight = 3715.020| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12691 Z= 0.132 Angle : 0.536 8.069 17163 Z= 0.293 Chirality : 0.038 0.130 1776 Planarity : 0.004 0.148 2111 Dihedral : 5.993 64.346 1826 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 6.47 % Allowed : 27.73 % Favored : 65.80 % 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: -1.64 (0.21), residues: 1439 helix: None (None), residues: 0 sheet: -1.06 (0.17), residues: 792 loop : -0.91 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG n 28 TYR 0.018 0.001 TYR C 15 PHE 0.014 0.002 PHE q 29 HIS 0.007 0.001 HIS m 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (12547) covalent geometry : angle 0.53062 / 0.29 (16875) SS BOND : bond 0.00272 / 0.18 ( 144) SS BOND : angle 0.76916 / 0.51 ( 288) hydrogen bonds : bond 0.02885 / 1.95 ( 294) hydrogen bonds : angle 7.06181 / 4.91 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 373 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 MET cc_start: 0.7176 (mmt) cc_final: 0.6662 (mmt) REVERT: F 32 LEU cc_start: 0.8335 (tp) cc_final: 0.7989 (tt) REVERT: H 7 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8190 (ptp90) REVERT: I 16 SER cc_start: 0.9093 (m) cc_final: 0.8524 (p) REVERT: J 8 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7581 (ttp80) REVERT: J 15 TYR cc_start: 0.7667 (t80) cc_final: 0.7449 (t80) REVERT: N 22 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9090 (p) REVERT: P 28 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7785 (mmm160) REVERT: Z 5 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6721 (m170) REVERT: c 28 ARG cc_start: 0.6951 (ptp90) cc_final: 0.6618 (ptt-90) REVERT: d 5 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7282 (t-90) REVERT: f 8 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8046 (mtm110) REVERT: n 23 MET cc_start: 0.8660 (mtt) cc_final: 0.8291 (mtt) REVERT: o 17 TYR cc_start: 0.8492 (m-80) cc_final: 0.7862 (m-10) REVERT: o 30 CYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5672 (p) REVERT: r 15 TYR cc_start: 0.6855 (t80) cc_final: 0.6316 (t80) outliers start: 90 outliers final: 74 residues processed: 433 average time/residue: 0.1310 time to fit residues: 76.9887 Evaluate side-chains 437 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 357 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 ARG Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 22 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 5 HIS Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain b residue 10 CYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain c residue 5 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 30 CYS Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain d residue 5 HIS Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain f residue 8 ARG Chi-restraints excluded: chain f residue 10 CYS Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain h residue 10 CYS Chi-restraints excluded: chain i residue 30 CYS Chi-restraints excluded: chain j residue 11 TYR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 10 CYS Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain o residue 10 CYS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 30 CYS Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 10 CYS Chi-restraints excluded: chain u residue 10 CYS Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 16 SER Chi-restraints excluded: chain v residue 13 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS E 27 HIS ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN e 5 HIS f 5 HIS ** v 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 = 0.3843 r_free = 0.3843 target = 0.127641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112875 restraints weight = 22265.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.116214 restraints weight = 11804.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.118401 restraints weight = 7370.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.119892 restraints weight = 5117.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.120868 restraints weight = 3829.310| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12691 Z= 0.159 Angle : 0.571 9.119 17163 Z= 0.311 Chirality : 0.039 0.132 1776 Planarity : 0.004 0.107 2111 Dihedral : 6.091 62.983 1826 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 6.75 % Allowed : 27.08 % Favored : 66.16 % 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: -1.66 (0.21), residues: 1439 helix: None (None), residues: 0 sheet: -1.09 (0.17), residues: 792 loop : -0.91 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG n 28 TYR 0.020 0.001 TYR Y 15 PHE 0.018 0.002 PHE e 29 HIS 0.008 0.001 HIS m 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (12547) covalent geometry : angle 0.56479 / 0.31 (16875) SS BOND : bond 0.00335 / 0.22 ( 144) SS BOND : angle 0.85850 / 0.57 ( 288) hydrogen bonds : bond 0.03004 / 2.02 ( 294) hydrogen bonds : angle 7.18567 / 5.01 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 368 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 MET cc_start: 0.8600 (mtt) cc_final: 0.8170 (mtm) REVERT: C 23 MET cc_start: 0.7220 (mmt) cc_final: 0.6798 (mmt) REVERT: F 32 LEU cc_start: 0.8384 (tp) cc_final: 0.8053 (tt) REVERT: H 7 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8179 (ptp90) REVERT: I 16 SER cc_start: 0.8586 (m) cc_final: 0.8162 (p) REVERT: J 8 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7591 (ttp80) REVERT: N 22 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9092 (p) REVERT: P 15 TYR cc_start: 0.7437 (t80) cc_final: 0.7192 (t80) REVERT: P 28 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7888 (mmm160) REVERT: Z 5 HIS cc_start: 0.7232 (OUTLIER) cc_final: 0.6693 (m170) REVERT: c 28 ARG cc_start: 0.7006 (ptp90) cc_final: 0.6675 (ptt-90) REVERT: d 5 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7256 (t-90) REVERT: n 23 MET cc_start: 0.8670 (mtt) cc_final: 0.8347 (mtt) REVERT: o 30 CYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5921 (p) REVERT: r 15 TYR cc_start: 0.6703 (t80) cc_final: 0.6248 (t80) outliers start: 94 outliers final: 80 residues processed: 432 average time/residue: 0.1306 time to fit residues: 77.7719 Evaluate side-chains 440 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 355 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 ARG Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain Q residue 20 CYS Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 22 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 5 HIS Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain b residue 10 CYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain c residue 5 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 30 CYS Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain d residue 5 HIS Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain f residue 10 CYS Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain h residue 10 CYS Chi-restraints excluded: chain i residue 30 CYS Chi-restraints excluded: chain j residue 11 TYR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 10 CYS Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain o residue 10 CYS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 30 CYS Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 9 SER Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 10 CYS Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 16 SER Chi-restraints excluded: chain u residue 30 CYS Chi-restraints excluded: chain v residue 13 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS J 26 ASN K 5 HIS ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS n 5 HIS ** v 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 = 0.3817 r_free = 0.3817 target = 0.125780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.111861 restraints weight = 22254.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.114804 restraints weight = 12575.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.116779 restraints weight = 8166.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.118115 restraints weight = 5826.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.119066 restraints weight = 4463.412| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12691 Z= 0.214 Angle : 0.613 9.791 17163 Z= 0.336 Chirality : 0.041 0.150 1776 Planarity : 0.004 0.086 2111 Dihedral : 6.528 66.728 1826 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 6.97 % Allowed : 27.08 % Favored : 65.95 % 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: -1.75 (0.20), residues: 1439 helix: None (None), residues: 0 sheet: -1.56 (0.31), residues: 264 loop : -1.14 (0.16), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG n 28 TYR 0.018 0.001 TYR d 15 PHE 0.021 0.002 PHE k 29 HIS 0.012 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (12547) covalent geometry : angle 0.60366 / 0.33 (16875) SS BOND : bond 0.00430 / 0.28 ( 144) SS BOND : angle 1.00647 / 0.66 ( 288) hydrogen bonds : bond 0.03337 / 2.24 ( 294) hydrogen bonds : angle 7.33386 / 5.10 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 356 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 MET cc_start: 0.8621 (mtt) cc_final: 0.8199 (mtm) REVERT: C 23 MET cc_start: 0.7316 (mmt) cc_final: 0.6900 (mmt) REVERT: F 32 LEU cc_start: 0.8256 (tp) cc_final: 0.7787 (tt) REVERT: H 7 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8307 (ptp90) REVERT: I 16 SER cc_start: 0.8695 (m) cc_final: 0.8304 (p) REVERT: J 8 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7610 (ttp80) REVERT: J 15 TYR cc_start: 0.7385 (t80) cc_final: 0.7104 (t80) REVERT: N 22 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9099 (p) REVERT: U 23 MET cc_start: 0.5961 (ptp) cc_final: 0.5735 (ptp) REVERT: Z 5 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6715 (m170) REVERT: o 30 CYS cc_start: 0.6540 (OUTLIER) cc_final: 0.5986 (p) REVERT: v 8 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7227 (mtp85) outliers start: 97 outliers final: 86 residues processed: 419 average time/residue: 0.1263 time to fit residues: 73.1344 Evaluate side-chains 438 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 347 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 ARG Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain Q residue 20 CYS Chi-restraints excluded: chain R residue 15 TYR Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 22 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 5 HIS Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 10 CYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain c residue 5 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 30 CYS Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain d residue 5 HIS Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 30 CYS Chi-restraints excluded: chain f residue 10 CYS Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain h residue 10 CYS Chi-restraints excluded: chain i residue 30 CYS Chi-restraints excluded: chain j residue 11 TYR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 10 CYS Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain o residue 10 CYS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 30 CYS Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 9 SER Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 10 CYS Chi-restraints excluded: chain u residue 10 CYS Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 16 SER Chi-restraints excluded: chain u residue 30 CYS Chi-restraints excluded: chain v residue 8 ARG Chi-restraints excluded: chain v residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 132 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS E 27 HIS J 26 ASN ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS ** v 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.127449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.113510 restraints weight = 22473.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.116481 restraints weight = 12625.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.118419 restraints weight = 8173.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.119787 restraints weight = 5905.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120765 restraints weight = 4504.428| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12691 Z= 0.139 Angle : 0.586 12.606 17163 Z= 0.317 Chirality : 0.039 0.137 1776 Planarity : 0.003 0.065 2111 Dihedral : 6.411 73.506 1826 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 6.54 % Allowed : 27.66 % Favored : 65.80 % 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 (0.20), residues: 1439 helix: None (None), residues: 0 sheet: -1.55 (0.31), residues: 264 loop : -1.12 (0.16), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 28 TYR 0.019 0.001 TYR Y 15 PHE 0.016 0.002 PHE k 29 HIS 0.007 0.001 HIS m 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12547) covalent geometry : angle 0.57881 / 0.31 (16875) SS BOND : bond 0.00299 / 0.20 ( 144) SS BOND : angle 0.91211 / 0.56 ( 288) hydrogen bonds : bond 0.03008 / 2.05 ( 294) hydrogen bonds : angle 7.17165 / 4.99 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 358 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.6568 (mtp-110) cc_final: 0.6356 (mtm-85) REVERT: C 23 MET cc_start: 0.7150 (mmt) cc_final: 0.6750 (mmt) REVERT: E 25 ILE cc_start: 0.8467 (mm) cc_final: 0.7872 (tt) REVERT: E 28 ARG cc_start: 0.7834 (mpp80) cc_final: 0.7393 (mpp80) REVERT: H 7 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8190 (ptp90) REVERT: I 16 SER cc_start: 0.8633 (m) cc_final: 0.8113 (p) REVERT: J 8 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7646 (ttp80) REVERT: J 15 TYR cc_start: 0.7276 (t80) cc_final: 0.7036 (t80) REVERT: L 25 ILE cc_start: 0.7903 (mm) cc_final: 0.7674 (mt) REVERT: N 22 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9101 (p) REVERT: P 11 TYR cc_start: 0.4840 (m-10) cc_final: 0.4480 (m-10) REVERT: P 14 GLU cc_start: 0.5853 (pm20) cc_final: 0.5510 (pm20) REVERT: U 23 MET cc_start: 0.5701 (ptp) cc_final: 0.5354 (ptp) REVERT: Y 2 PHE cc_start: 0.7483 (m-80) cc_final: 0.7221 (m-10) REVERT: Z 5 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6711 (m170) REVERT: b 23 MET cc_start: 0.8088 (mpp) cc_final: 0.7734 (mpp) REVERT: d 5 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7366 (t-90) REVERT: f 8 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7977 (mtm110) REVERT: n 8 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7404 (mtm-85) REVERT: o 30 CYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5768 (p) REVERT: v 8 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7122 (mtp85) outliers start: 91 outliers final: 82 residues processed: 419 average time/residue: 0.1280 time to fit residues: 74.0265 Evaluate side-chains 440 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 351 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 ARG Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain Q residue 20 CYS Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 15 TYR Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 5 HIS Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 10 CYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain c residue 5 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 30 CYS Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain d residue 5 HIS Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain f residue 8 ARG Chi-restraints excluded: chain f residue 10 CYS Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain h residue 10 CYS Chi-restraints excluded: chain i residue 30 CYS Chi-restraints excluded: chain j residue 11 TYR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 10 CYS Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain n residue 19 THR Chi-restraints excluded: chain n residue 20 CYS Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain o residue 10 CYS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 30 CYS Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 9 SER Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 10 CYS Chi-restraints excluded: chain u residue 10 CYS Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 16 SER Chi-restraints excluded: chain u residue 30 CYS Chi-restraints excluded: chain v residue 8 ARG Chi-restraints excluded: chain v residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 HIS H 26 ASN L 26 ASN N 26 ASN Q 5 HIS e 5 HIS ** v 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.129457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.114670 restraints weight = 22214.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.117990 restraints weight = 11816.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.120165 restraints weight = 7385.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.121630 restraints weight = 5146.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.122655 restraints weight = 3877.954| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12691 Z= 0.113 Angle : 0.567 12.272 17163 Z= 0.305 Chirality : 0.039 0.128 1776 Planarity : 0.003 0.054 2111 Dihedral : 6.203 74.081 1826 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.68 % Allowed : 28.30 % Favored : 66.02 % 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: -1.60 (0.20), residues: 1439 helix: None (None), residues: 0 sheet: -1.46 (0.31), residues: 264 loop : -1.03 (0.16), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 8 TYR 0.021 0.001 TYR e 15 PHE 0.015 0.001 PHE q 29 HIS 0.007 0.001 HIS m 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (12547) covalent geometry : angle 0.56322 / 0.30 (16875) SS BOND : bond 0.00249 / 0.17 ( 144) SS BOND : angle 0.73782 / 0.46 ( 288) hydrogen bonds : bond 0.02796 / 1.91 ( 294) hydrogen bonds : angle 6.99169 / 4.86 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.49 seconds wall clock time: 40 minutes 21.16 seconds (2421.16 seconds total)