Starting phenix.real_space_refine on Tue Aug 26 03:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnp_27576/08_2025/8dnp_27576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnp_27576/08_2025/8dnp_27576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dnp_27576/08_2025/8dnp_27576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnp_27576/08_2025/8dnp_27576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dnp_27576/08_2025/8dnp_27576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnp_27576/08_2025/8dnp_27576.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.071 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 Fe 24 7.16 5 S 168 5.16 5 C 21264 2.51 5 N 5952 2.21 5 O 6528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33936 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "U" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.10, per 1000 atoms: 0.24 Number of scatterers: 33936 At special positions: 0 Unit cell: (135.89, 135.89, 135.89, 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) Fe 24 26.01 S 168 16.00 O 6528 8.00 N 5952 7.00 C 21264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.11 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 14 through 42 Processing helix chain 'A' and resid 49 through 77 Processing helix chain 'A' and resid 96 through 125 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'A' and resid 164 through 175 Processing helix chain 'B' and resid 14 through 42 Processing helix chain 'B' and resid 49 through 77 Processing helix chain 'B' and resid 96 through 125 Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 138 through 160 Processing helix chain 'B' and resid 164 through 175 Processing helix chain 'C' and resid 14 through 42 Processing helix chain 'C' and resid 49 through 77 Processing helix chain 'C' and resid 96 through 125 Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'D' and resid 14 through 42 Processing helix chain 'D' and resid 49 through 77 Processing helix chain 'D' and resid 96 through 125 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 138 through 160 Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'E' and resid 14 through 42 Processing helix chain 'E' and resid 49 through 77 Processing helix chain 'E' and resid 96 through 125 Processing helix chain 'E' and resid 127 through 138 Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'F' and resid 14 through 42 Processing helix chain 'F' and resid 49 through 77 Processing helix chain 'F' and resid 96 through 125 Processing helix chain 'F' and resid 127 through 138 Processing helix chain 'F' and resid 138 through 160 Processing helix chain 'F' and resid 164 through 175 Processing helix chain 'G' and resid 14 through 42 Processing helix chain 'G' and resid 49 through 77 Processing helix chain 'G' and resid 96 through 125 Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 138 through 160 Processing helix chain 'G' and resid 164 through 175 Processing helix chain 'H' and resid 14 through 42 Processing helix chain 'H' and resid 49 through 77 Processing helix chain 'H' and resid 96 through 125 Processing helix chain 'H' and resid 127 through 138 Processing helix chain 'H' and resid 138 through 160 Processing helix chain 'H' and resid 164 through 175 Processing helix chain 'I' and resid 14 through 42 Processing helix chain 'I' and resid 49 through 77 Processing helix chain 'I' and resid 96 through 125 Processing helix chain 'I' and resid 127 through 138 Processing helix chain 'I' and resid 138 through 160 Processing helix chain 'I' and resid 164 through 175 Processing helix chain 'J' and resid 14 through 42 Processing helix chain 'J' and resid 49 through 77 Processing helix chain 'J' and resid 96 through 125 Processing helix chain 'J' and resid 127 through 138 Processing helix chain 'J' and resid 138 through 160 Processing helix chain 'J' and resid 164 through 175 Processing helix chain 'K' and resid 14 through 42 Processing helix chain 'K' and resid 49 through 77 Processing helix chain 'K' and resid 96 through 125 Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 138 through 160 Processing helix chain 'K' and resid 164 through 175 Processing helix chain 'L' and resid 14 through 42 Processing helix chain 'L' and resid 49 through 77 Processing helix chain 'L' and resid 96 through 125 Processing helix chain 'L' and resid 127 through 138 Processing helix chain 'L' and resid 138 through 160 Processing helix chain 'L' and resid 164 through 175 Processing helix chain 'M' and resid 14 through 42 Processing helix chain 'M' and resid 49 through 77 Processing helix chain 'M' and resid 96 through 125 Processing helix chain 'M' and resid 127 through 138 Processing helix chain 'M' and resid 138 through 160 Processing helix chain 'M' and resid 164 through 175 Processing helix chain 'N' and resid 14 through 42 Processing helix chain 'N' and resid 49 through 77 Processing helix chain 'N' and resid 96 through 125 Processing helix chain 'N' and resid 127 through 138 Processing helix chain 'N' and resid 138 through 160 Processing helix chain 'N' and resid 164 through 175 Processing helix chain 'O' and resid 14 through 42 Processing helix chain 'O' and resid 49 through 77 Processing helix chain 'O' and resid 96 through 125 Processing helix chain 'O' and resid 127 through 138 Processing helix chain 'O' and resid 138 through 160 Processing helix chain 'O' and resid 164 through 175 Processing helix chain 'P' and resid 14 through 42 Processing helix chain 'P' and resid 49 through 77 Processing helix chain 'P' and resid 96 through 125 Processing helix chain 'P' and resid 127 through 138 Processing helix chain 'P' and resid 138 through 160 Processing helix chain 'P' and resid 164 through 175 Processing helix chain 'Q' and resid 14 through 42 Processing helix chain 'Q' and resid 49 through 77 Processing helix chain 'Q' and resid 96 through 125 Processing helix chain 'Q' and resid 127 through 138 Processing helix chain 'Q' and resid 138 through 160 Processing helix chain 'Q' and resid 164 through 175 Processing helix chain 'R' and resid 14 through 42 Processing helix chain 'R' and resid 49 through 77 Processing helix chain 'R' and resid 96 through 125 Processing helix chain 'R' and resid 127 through 138 Processing helix chain 'R' and resid 138 through 160 Processing helix chain 'R' and resid 164 through 175 Processing helix chain 'S' and resid 14 through 42 Processing helix chain 'S' and resid 49 through 77 Processing helix chain 'S' and resid 96 through 125 Processing helix chain 'S' and resid 127 through 138 Processing helix chain 'S' and resid 138 through 160 Processing helix chain 'S' and resid 164 through 175 Processing helix chain 'T' and resid 14 through 42 Processing helix chain 'T' and resid 49 through 77 Processing helix chain 'T' and resid 96 through 125 Processing helix chain 'T' and resid 127 through 138 Processing helix chain 'T' and resid 138 through 160 Processing helix chain 'T' and resid 164 through 175 Processing helix chain 'U' and resid 14 through 42 Processing helix chain 'U' and resid 49 through 77 Processing helix chain 'U' and resid 96 through 125 Processing helix chain 'U' and resid 127 through 138 Processing helix chain 'U' and resid 138 through 160 Processing helix chain 'U' and resid 164 through 175 Processing helix chain 'V' and resid 14 through 42 Processing helix chain 'V' and resid 49 through 77 Processing helix chain 'V' and resid 96 through 125 Processing helix chain 'V' and resid 127 through 138 Processing helix chain 'V' and resid 138 through 160 Processing helix chain 'V' and resid 164 through 175 Processing helix chain 'W' and resid 14 through 42 Processing helix chain 'W' and resid 49 through 77 Processing helix chain 'W' and resid 96 through 125 Processing helix chain 'W' and resid 127 through 138 Processing helix chain 'W' and resid 138 through 160 Processing helix chain 'W' and resid 164 through 175 Processing helix chain 'X' and resid 14 through 42 Processing helix chain 'X' and resid 49 through 77 Processing helix chain 'X' and resid 96 through 125 Processing helix chain 'X' and resid 127 through 138 Processing helix chain 'X' and resid 138 through 160 Processing helix chain 'X' and resid 164 through 175 2664 hydrogen bonds defined for protein. 7992 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: 7.32 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11176 1.33 - 1.45: 6003 1.45 - 1.57: 17165 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34608 Sorted by residual: bond pdb=" CA LYS X 125 " pdb=" C LYS X 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.60e+00 bond pdb=" CA LYS T 125 " pdb=" C LYS T 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.45e+00 bond pdb=" CA LYS N 125 " pdb=" C LYS N 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.45e+00 bond pdb=" CA LYS G 125 " pdb=" C LYS G 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.41e+00 bond pdb=" CA LYS C 125 " pdb=" C LYS C 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.34e+00 ... (remaining 34603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 42612 1.75 - 3.50: 2988 3.50 - 5.25: 648 5.25 - 6.99: 312 6.99 - 8.74: 48 Bond angle restraints: 46608 Sorted by residual: angle pdb=" N HIS S 58 " pdb=" CA HIS S 58 " pdb=" C HIS S 58 " ideal model delta sigma weight residual 112.23 104.11 8.12 1.26e+00 6.30e-01 4.15e+01 angle pdb=" N HIS X 58 " pdb=" CA HIS X 58 " pdb=" C HIS X 58 " ideal model delta sigma weight residual 112.23 104.12 8.11 1.26e+00 6.30e-01 4.14e+01 angle pdb=" N HIS U 58 " pdb=" CA HIS U 58 " pdb=" C HIS U 58 " ideal model delta sigma weight residual 112.23 104.13 8.10 1.26e+00 6.30e-01 4.13e+01 angle pdb=" N HIS Q 58 " pdb=" CA HIS Q 58 " pdb=" C HIS Q 58 " ideal model delta sigma weight residual 112.23 104.13 8.10 1.26e+00 6.30e-01 4.13e+01 angle pdb=" N HIS K 58 " pdb=" CA HIS K 58 " pdb=" C HIS K 58 " ideal model delta sigma weight residual 112.23 104.13 8.10 1.26e+00 6.30e-01 4.13e+01 ... (remaining 46603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.85: 18035 12.85 - 25.71: 2077 25.71 - 38.56: 552 38.56 - 51.41: 144 51.41 - 64.27: 120 Dihedral angle restraints: 20928 sinusoidal: 8688 harmonic: 12240 Sorted by residual: dihedral pdb=" CA ALA T 161 " pdb=" C ALA T 161 " pdb=" N PRO T 162 " pdb=" CA PRO T 162 " ideal model delta harmonic sigma weight residual 0.00 28.57 -28.57 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ALA B 161 " pdb=" C ALA B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta harmonic sigma weight residual 0.00 28.56 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ALA H 161 " pdb=" C ALA H 161 " pdb=" N PRO H 162 " pdb=" CA PRO H 162 " ideal model delta harmonic sigma weight residual 0.00 28.54 -28.54 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 20925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3541 0.073 - 0.146: 982 0.146 - 0.218: 301 0.218 - 0.291: 48 0.291 - 0.364: 24 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA TYR D 40 " pdb=" N TYR D 40 " pdb=" C TYR D 40 " pdb=" CB TYR D 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA TYR E 40 " pdb=" N TYR E 40 " pdb=" C TYR E 40 " pdb=" CB TYR E 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA TYR C 40 " pdb=" N TYR C 40 " pdb=" C TYR C 40 " pdb=" CB TYR C 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 4893 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Q 57 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C LEU Q 57 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU Q 57 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS Q 58 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 57 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C LEU F 57 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU F 57 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS F 58 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 57 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C LEU P 57 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU P 57 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS P 58 " 0.010 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 92 2.39 - 3.02: 20017 3.02 - 3.65: 56090 3.65 - 4.27: 93571 4.27 - 4.90: 144378 Nonbonded interactions: 314148 Sorted by model distance: nonbonded pdb=" OE1 GLU A 28 " pdb="FE FE A 201 " model vdw 1.768 2.260 nonbonded pdb=" OE1 GLU B 28 " pdb="FE FE B 201 " model vdw 1.789 2.260 nonbonded pdb=" OE1 GLU V 28 " pdb="FE FE V 201 " model vdw 1.962 2.260 nonbonded pdb=" OE1 GLU J 28 " pdb="FE FE J 201 " model vdw 1.962 2.260 nonbonded pdb=" OE1 GLU D 28 " pdb="FE FE D 201 " model vdw 1.962 2.260 ... (remaining 314143 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: 0.11 Found NCS groups: ncs_group { reference = 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' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 32.030 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.010 0.039 34608 Z= 0.779 Angle : 1.160 8.744 46608 Z= 0.818 Chirality : 0.078 0.364 4896 Planarity : 0.004 0.018 6144 Dihedral : 12.976 64.268 13008 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.31 % Allowed : 3.27 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.12), residues: 4080 helix: 0.66 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -0.74 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG W 44 TYR 0.018 0.002 TYR L 40 PHE 0.007 0.002 PHE Q 42 TRP 0.003 0.002 TRP V 94 HIS 0.005 0.002 HIS M 174 Details of bonding type rmsd covalent geometry : bond 0.01032 (34608) covalent geometry : angle 1.15984 (46608) hydrogen bonds : bond 0.17840 ( 2664) hydrogen bonds : angle 5.76606 ( 7992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1654 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1606 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7970 (mm-30) REVERT: B 63 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8016 (mm-30) REVERT: B 102 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7386 (mt-10) REVERT: C 63 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7603 (mm-30) REVERT: C 88 LYS cc_start: 0.8138 (pttt) cc_final: 0.7855 (pttt) REVERT: C 102 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7347 (mt-10) REVERT: D 63 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7835 (mm-30) REVERT: E 63 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7559 (mm-30) REVERT: F 63 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7712 (mm-30) REVERT: F 71 MET cc_start: 0.8380 (mtp) cc_final: 0.8105 (mtp) REVERT: G 63 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7622 (mm-30) REVERT: H 63 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7537 (mm-30) REVERT: H 88 LYS cc_start: 0.7860 (pttt) cc_final: 0.7604 (pttt) REVERT: I 33 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.6538 (t80) REVERT: I 63 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7619 (mm-30) REVERT: J 63 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7851 (mm-30) REVERT: K 63 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7519 (mm-30) REVERT: K 76 GLN cc_start: 0.8068 (mt0) cc_final: 0.7782 (mt0) REVERT: L 63 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7717 (mm-30) REVERT: L 71 MET cc_start: 0.8350 (mtp) cc_final: 0.8135 (mtp) REVERT: L 168 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7622 (mt-10) REVERT: M 63 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7569 (mm-30) REVERT: N 63 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7561 (mm-30) REVERT: O 33 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.6396 (t80) REVERT: O 63 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7617 (mm-30) REVERT: P 63 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7834 (mm-30) REVERT: Q 63 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7605 (mm-30) REVERT: R 63 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7703 (mm-30) REVERT: S 63 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7636 (mm-30) REVERT: T 63 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7524 (mm-30) REVERT: U 63 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7645 (mm-30) REVERT: U 140 ASN cc_start: 0.8121 (t0) cc_final: 0.7906 (t0) REVERT: V 63 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7879 (mm-30) REVERT: V 151 ASP cc_start: 0.7940 (m-30) cc_final: 0.7674 (m-30) REVERT: W 63 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7607 (mm-30) REVERT: W 76 GLN cc_start: 0.8005 (mt0) cc_final: 0.7747 (mt0) REVERT: X 63 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7708 (mm-30) REVERT: X 71 MET cc_start: 0.8348 (mtp) cc_final: 0.8126 (mtp) outliers start: 48 outliers final: 25 residues processed: 1651 average time/residue: 0.7756 time to fit residues: 1497.8825 Evaluate side-chains 1290 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 1263 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain I residue 33 TYR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain K residue 103 CYS Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain O residue 33 TYR Chi-restraints excluded: chain O residue 103 CYS Chi-restraints excluded: chain P residue 103 CYS Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain U residue 103 CYS Chi-restraints excluded: chain V residue 103 CYS Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 103 CYS Chi-restraints excluded: chain X residue 103 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 99 ASN A 110 ASN A 174 HIS B 99 ASN B 119 HIS B 174 HIS C 84 GLN C 99 ASN C 113 GLN C 119 HIS C 174 HIS ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS D 174 HIS E 99 ASN E 174 HIS F 61 HIS F 84 GLN F 119 HIS F 174 HIS G 11 GLN G 59 GLN G 99 ASN G 174 HIS H 61 HIS H 84 GLN H 113 GLN H 119 HIS H 174 HIS I 76 GLN I 99 ASN I 174 HIS J 119 HIS J 174 HIS K 99 ASN K 174 HIS L 84 GLN L 119 HIS L 174 HIS M 59 GLN M 61 HIS M 174 HIS N 84 GLN N 174 HIS O 84 GLN O 99 ASN O 174 HIS ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 GLN P 119 HIS P 174 HIS Q 76 GLN Q 174 HIS R 84 GLN R 119 HIS R 174 HIS S 59 GLN S 76 GLN S 174 HIS T 61 HIS T 84 GLN T 113 GLN T 119 HIS T 174 HIS U 99 ASN U 174 HIS V 84 GLN V 119 HIS V 174 HIS W 14 HIS W 59 GLN W 174 HIS X 84 GLN X 119 HIS X 174 HIS Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.138325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.130694 restraints weight = 35035.204| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 0.78 r_work: 0.3236 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 34608 Z= 0.117 Angle : 0.502 6.792 46608 Z= 0.272 Chirality : 0.037 0.141 4896 Planarity : 0.003 0.017 6144 Dihedral : 4.644 65.734 4519 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.19 % Allowed : 13.75 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.75 (0.13), residues: 4080 helix: 2.91 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.67 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 157 TYR 0.018 0.002 TYR N 138 PHE 0.010 0.001 PHE M 42 TRP 0.007 0.001 TRP B 94 HIS 0.004 0.001 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00234 (34608) covalent geometry : angle 0.50227 (46608) hydrogen bonds : bond 0.04280 ( 2664) hydrogen bonds : angle 3.45577 ( 7992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1308 time to evaluate : 1.370 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: A 33 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.6635 (t80) REVERT: A 40 TYR cc_start: 0.8546 (m-80) cc_final: 0.7944 (m-80) REVERT: A 64 ARG cc_start: 0.7781 (ttp-170) cc_final: 0.7326 (tmm-80) REVERT: A 84 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8273 (mm-40) REVERT: A 117 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 120 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7718 (tmtp) REVERT: B 16 ASP cc_start: 0.8418 (m-30) cc_final: 0.8176 (m-30) REVERT: B 40 TYR cc_start: 0.8553 (m-80) cc_final: 0.7993 (m-80) REVERT: B 64 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7676 (tpp-160) REVERT: B 68 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8084 (mt-10) REVERT: B 120 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7883 (tmtp) REVERT: B 157 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7743 (mtt-85) REVERT: C 23 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7925 (mtm110) REVERT: C 40 TYR cc_start: 0.8519 (m-80) cc_final: 0.7938 (m-80) REVERT: C 63 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7899 (mm-30) REVERT: C 68 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8042 (mt-10) REVERT: C 84 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8264 (mm-40) REVERT: C 88 LYS cc_start: 0.8314 (pttt) cc_final: 0.8000 (pttt) REVERT: C 157 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7817 (mtt-85) REVERT: D 23 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7929 (mtm110) REVERT: D 40 TYR cc_start: 0.8478 (m-80) cc_final: 0.7691 (m-80) REVERT: D 63 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7839 (mm-30) REVERT: D 68 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8085 (mt-10) REVERT: D 69 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7971 (tppt) REVERT: D 85 ASP cc_start: 0.8371 (m-30) cc_final: 0.8154 (m-30) REVERT: D 102 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7895 (mt-10) REVERT: D 126 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8219 (m-40) REVERT: D 157 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7675 (mtt-85) REVERT: E 64 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.7641 (ttm110) REVERT: E 96 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8043 (p) REVERT: E 120 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7617 (tptp) REVERT: F 16 ASP cc_start: 0.8326 (m-30) cc_final: 0.8125 (m-30) REVERT: F 40 TYR cc_start: 0.8416 (m-80) cc_final: 0.7578 (m-80) REVERT: F 92 ASP cc_start: 0.7236 (p0) cc_final: 0.6989 (OUTLIER) REVERT: F 120 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7969 (tmtt) REVERT: F 157 ARG cc_start: 0.8024 (mtt-85) cc_final: 0.7752 (mtt-85) REVERT: G 66 HIS cc_start: 0.8872 (m170) cc_final: 0.8636 (m170) REVERT: G 69 LYS cc_start: 0.8262 (ttpt) cc_final: 0.8030 (tppt) REVERT: G 120 LYS cc_start: 0.8192 (tttt) cc_final: 0.7704 (tmtp) REVERT: H 110 ASN cc_start: 0.7901 (m-40) cc_final: 0.7607 (m110) REVERT: I 68 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8114 (mt-10) REVERT: I 93 ASP cc_start: 0.6892 (t70) cc_final: 0.6678 (t70) REVERT: I 96 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8036 (p) REVERT: I 120 LYS cc_start: 0.8185 (tttm) cc_final: 0.7767 (tptp) REVERT: I 155 ASN cc_start: 0.8800 (m-40) cc_final: 0.8576 (m-40) REVERT: J 16 ASP cc_start: 0.8276 (m-30) cc_final: 0.8053 (m-30) REVERT: J 23 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7967 (mtm110) REVERT: J 40 TYR cc_start: 0.8497 (m-80) cc_final: 0.7749 (m-80) REVERT: J 87 LYS cc_start: 0.8086 (mttm) cc_final: 0.7884 (mptm) REVERT: K 40 TYR cc_start: 0.8448 (m-80) cc_final: 0.7699 (m-80) REVERT: K 68 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8305 (mt-10) REVERT: K 69 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8052 (tttt) REVERT: K 96 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8015 (p) REVERT: K 117 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7870 (mt-10) REVERT: L 64 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7640 (ttp-110) REVERT: L 84 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8225 (mm-40) REVERT: L 120 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7968 (tmtt) REVERT: L 157 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7682 (mtt-85) REVERT: M 66 HIS cc_start: 0.8860 (m170) cc_final: 0.8613 (m170) REVERT: M 96 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.7980 (p) REVERT: M 120 LYS cc_start: 0.8245 (tmtp) cc_final: 0.7765 (tmtp) REVERT: N 40 TYR cc_start: 0.8448 (m-80) cc_final: 0.7597 (m-80) REVERT: N 50 LYS cc_start: 0.8146 (mttm) cc_final: 0.7885 (mmtm) REVERT: N 84 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8201 (mm-40) REVERT: N 102 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7960 (mt-10) REVERT: N 120 LYS cc_start: 0.8242 (tmtp) cc_final: 0.7796 (tmtp) REVERT: N 157 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7697 (mtt-85) REVERT: O 68 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8165 (mt-10) REVERT: O 84 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8245 (mm-40) REVERT: O 120 LYS cc_start: 0.8333 (tmtt) cc_final: 0.7928 (tmtp) REVERT: O 155 ASN cc_start: 0.8809 (m-40) cc_final: 0.8574 (m-40) REVERT: P 16 ASP cc_start: 0.8418 (m-30) cc_final: 0.8216 (m-30) REVERT: P 23 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7847 (mtm110) REVERT: P 40 TYR cc_start: 0.8499 (m-80) cc_final: 0.7751 (m-80) REVERT: P 63 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7761 (mm-30) REVERT: P 92 ASP cc_start: 0.7401 (p0) cc_final: 0.7167 (p0) REVERT: P 102 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7903 (mt-10) REVERT: P 120 LYS cc_start: 0.7984 (ttpt) cc_final: 0.7749 (tmtp) REVERT: P 126 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8213 (m-40) REVERT: P 127 ASP cc_start: 0.8854 (t0) cc_final: 0.8641 (t0) REVERT: P 157 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7755 (mtt-85) REVERT: Q 68 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8337 (mt-10) REVERT: Q 96 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8019 (p) REVERT: Q 110 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7554 (m110) REVERT: Q 126 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8099 (m-40) REVERT: R 16 ASP cc_start: 0.8290 (m-30) cc_final: 0.8067 (m-30) REVERT: R 40 TYR cc_start: 0.8426 (m-80) cc_final: 0.7577 (m-80) REVERT: R 54 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7750 (tptt) REVERT: R 63 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7851 (mm-30) REVERT: R 64 ARG cc_start: 0.8119 (tpp-160) cc_final: 0.7823 (tpp-160) REVERT: R 68 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8261 (mt-10) REVERT: R 84 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8234 (mm-40) REVERT: R 120 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7891 (tmtt) REVERT: S 96 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8035 (p) REVERT: S 110 ASN cc_start: 0.7899 (m-40) cc_final: 0.7647 (m110) REVERT: T 15 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7127 (mm-40) REVERT: T 40 TYR cc_start: 0.8465 (m-80) cc_final: 0.7600 (m-80) REVERT: T 92 ASP cc_start: 0.7337 (p0) cc_final: 0.7133 (OUTLIER) REVERT: T 102 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7869 (mt-10) REVERT: T 120 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7617 (tmtp) REVERT: T 157 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.7665 (mtt-85) REVERT: U 16 ASP cc_start: 0.8429 (m-30) cc_final: 0.8228 (m-30) REVERT: U 68 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8158 (mt-10) REVERT: U 102 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8022 (mt-10) REVERT: U 120 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7671 (tttt) REVERT: U 155 ASN cc_start: 0.8790 (m-40) cc_final: 0.8550 (m-40) REVERT: U 157 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7594 (mtt-85) REVERT: V 16 ASP cc_start: 0.8265 (m-30) cc_final: 0.8047 (m-30) REVERT: V 40 TYR cc_start: 0.8473 (m-80) cc_final: 0.7741 (m-80) REVERT: V 63 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7813 (mm-30) REVERT: V 69 LYS cc_start: 0.8335 (ttpt) cc_final: 0.8019 (tppt) REVERT: V 96 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7999 (p) REVERT: V 120 LYS cc_start: 0.8086 (tmtp) cc_final: 0.7828 (tmtt) REVERT: V 126 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8203 (m-40) REVERT: W 120 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7767 (tmtp) REVERT: X 84 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8238 (mm-40) REVERT: X 102 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7843 (mt-10) REVERT: X 157 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7701 (mtt-85) outliers start: 117 outliers final: 31 residues processed: 1337 average time/residue: 0.8029 time to fit residues: 1253.4390 Evaluate side-chains 1243 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1193 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 110 ASN Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 286 optimal weight: 0.9980 chunk 381 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 168 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 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 110 ASN A 119 HIS A 140 ASN B 84 GLN B 110 ASN B 140 ASN C 110 ASN C 113 GLN C 140 ASN D 14 HIS D 110 ASN D 140 ASN E 110 ASN E 113 GLN F 15 GLN F 84 GLN F 113 GLN F 140 ASN F 155 ASN G 11 GLN G 59 GLN G 110 ASN G 119 HIS G 140 ASN H 84 GLN H 113 GLN H 140 ASN H 155 ASN I 76 GLN I 110 ASN I 140 ASN J 15 GLN J 84 GLN J 99 ASN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 140 ASN L 110 ASN L 113 GLN L 140 ASN L 155 ASN M 59 GLN M 119 HIS M 140 ASN N 119 HIS N 140 ASN N 155 ASN O 76 GLN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN R 110 ASN R 140 ASN R 155 ASN S 59 GLN S 119 HIS T 84 GLN T 113 GLN T 140 ASN T 155 ASN U 110 ASN U 140 ASN V 84 GLN V 110 ASN V 113 GLN W 110 ASN W 113 GLN X 99 ASN X 110 ASN X 140 ASN X 155 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.134506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.126524 restraints weight = 34462.521| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 0.78 r_work: 0.3181 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34608 Z= 0.142 Angle : 0.533 6.624 46608 Z= 0.284 Chirality : 0.039 0.142 4896 Planarity : 0.003 0.021 6144 Dihedral : 4.235 70.927 4491 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.17 % Allowed : 15.52 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.39 (0.13), residues: 4080 helix: 3.27 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.23 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 157 TYR 0.018 0.002 TYR H 138 PHE 0.012 0.002 PHE H 42 TRP 0.007 0.002 TRP B 94 HIS 0.005 0.001 HIS U 66 Details of bonding type rmsd covalent geometry : bond 0.00306 (34608) covalent geometry : angle 0.53298 (46608) hydrogen bonds : bond 0.04524 ( 2664) hydrogen bonds : angle 3.39388 ( 7992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 1191 time to evaluate : 1.247 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8046 (tppt) REVERT: A 84 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8286 (mm-40) REVERT: A 120 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7980 (tmtp) REVERT: A 127 ASP cc_start: 0.8785 (t0) cc_final: 0.8547 (t0) REVERT: B 16 ASP cc_start: 0.8530 (m-30) cc_final: 0.8295 (m-30) REVERT: B 40 TYR cc_start: 0.8649 (m-80) cc_final: 0.7759 (m-80) REVERT: B 64 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7670 (tpp-160) REVERT: B 120 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7813 (tmtp) REVERT: C 16 ASP cc_start: 0.8481 (m-30) cc_final: 0.8269 (m-30) REVERT: C 40 TYR cc_start: 0.8632 (m-80) cc_final: 0.7707 (m-80) REVERT: C 84 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8269 (mm-40) REVERT: C 120 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7755 (tptp) REVERT: D 40 TYR cc_start: 0.8602 (m-80) cc_final: 0.7667 (m-80) REVERT: D 63 GLU cc_start: 0.8677 (mm-30) cc_final: 0.7962 (mm-30) REVERT: D 64 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7673 (tpp-160) REVERT: D 69 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8089 (tppt) REVERT: D 84 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8223 (mm-40) REVERT: D 125 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7591 (mptp) REVERT: D 126 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: E 64 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7626 (ttm110) REVERT: E 69 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8156 (tppt) REVERT: E 84 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8257 (mm-40) REVERT: E 96 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8080 (p) REVERT: E 120 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7652 (tptp) REVERT: F 16 ASP cc_start: 0.8463 (m-30) cc_final: 0.8246 (m-30) REVERT: F 40 TYR cc_start: 0.8552 (m-80) cc_final: 0.7678 (m-80) REVERT: F 84 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8201 (mm-40) REVERT: F 120 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7929 (tmtp) REVERT: G 40 TYR cc_start: 0.8571 (m-80) cc_final: 0.7653 (m-80) REVERT: G 69 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8166 (tppt) REVERT: G 102 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8063 (mt-10) REVERT: G 127 ASP cc_start: 0.8622 (t0) cc_final: 0.8409 (t0) REVERT: G 157 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7883 (mtt-85) REVERT: H 23 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7916 (mtm110) REVERT: H 84 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8242 (mm-40) REVERT: H 110 ASN cc_start: 0.7978 (m-40) cc_final: 0.7653 (m110) REVERT: H 120 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7821 (tptp) REVERT: I 40 TYR cc_start: 0.8652 (m-80) cc_final: 0.7845 (m-80) REVERT: I 68 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8095 (mt-10) REVERT: I 84 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8242 (mm-40) REVERT: I 96 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8059 (p) REVERT: I 120 LYS cc_start: 0.8102 (tttm) cc_final: 0.7698 (tptp) REVERT: I 125 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7914 (mptp) REVERT: I 127 ASP cc_start: 0.8640 (t0) cc_final: 0.8438 (t0) REVERT: J 16 ASP cc_start: 0.8368 (m-30) cc_final: 0.8135 (m-30) REVERT: J 40 TYR cc_start: 0.8587 (m-80) cc_final: 0.7651 (m-80) REVERT: J 63 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8076 (mm-30) REVERT: J 64 ARG cc_start: 0.8173 (tpp-160) cc_final: 0.7920 (tpp-160) REVERT: J 84 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8306 (mm110) REVERT: K 40 TYR cc_start: 0.8554 (m-80) cc_final: 0.7618 (m-80) REVERT: K 64 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7656 (ttm110) REVERT: K 69 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8172 (tppt) REVERT: K 96 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8033 (p) REVERT: K 120 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7750 (tptp) REVERT: L 15 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7500 (mm-40) REVERT: L 64 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7614 (ttp-110) REVERT: L 84 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8276 (mm-40) REVERT: L 120 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7942 (tmtt) REVERT: M 59 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8205 (mm110) REVERT: M 84 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8259 (mm-40) REVERT: M 96 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8034 (p) REVERT: M 125 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7848 (mptp) REVERT: N 84 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8215 (mm-40) REVERT: O 15 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7419 (mm-40) REVERT: O 40 TYR cc_start: 0.8644 (m-80) cc_final: 0.7845 (m-80) REVERT: O 68 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8172 (mt-10) REVERT: O 84 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8153 (mm110) REVERT: O 96 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8089 (p) REVERT: P 15 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7402 (mm-40) REVERT: P 40 TYR cc_start: 0.8595 (m-80) cc_final: 0.7640 (m-80) REVERT: P 64 ARG cc_start: 0.8002 (ttm170) cc_final: 0.7767 (tpp-160) REVERT: P 69 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8091 (tppt) REVERT: P 84 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8229 (mm110) REVERT: P 120 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7806 (tmtp) REVERT: P 126 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8219 (m-40) REVERT: Q 96 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8063 (p) REVERT: Q 120 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7873 (tptp) REVERT: Q 126 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8119 (m-40) REVERT: R 23 ARG cc_start: 0.8185 (mtm110) cc_final: 0.7950 (mtm110) REVERT: R 64 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.7918 (tpp-160) REVERT: R 68 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8210 (mt-10) REVERT: R 69 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8040 (tppt) REVERT: R 84 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8220 (mm-40) REVERT: R 120 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7928 (tmtt) REVERT: S 40 TYR cc_start: 0.8569 (m-80) cc_final: 0.7654 (m-80) REVERT: S 59 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8177 (mm110) REVERT: S 68 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8182 (mt-10) REVERT: S 96 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8093 (p) REVERT: S 110 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7664 (m-40) REVERT: S 117 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: S 120 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7879 (tptp) REVERT: T 40 TYR cc_start: 0.8559 (m-80) cc_final: 0.7632 (m-80) REVERT: U 16 ASP cc_start: 0.8435 (m-30) cc_final: 0.8210 (m-30) REVERT: U 40 TYR cc_start: 0.8647 (m-80) cc_final: 0.7681 (m-80) REVERT: U 68 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8168 (mt-10) REVERT: U 84 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8192 (mm-40) REVERT: U 102 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7601 (mt-10) REVERT: U 120 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7902 (tmtp) REVERT: U 157 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7702 (mtt-85) REVERT: V 40 TYR cc_start: 0.8581 (m-80) cc_final: 0.7636 (m-80) REVERT: V 64 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7695 (tpp-160) REVERT: V 68 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8271 (mt-10) REVERT: V 69 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8114 (tppt) REVERT: V 96 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8066 (p) REVERT: V 120 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7853 (tmtt) REVERT: V 126 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8194 (m-40) REVERT: W 64 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7586 (tpp-160) REVERT: W 92 ASP cc_start: 0.7111 (p0) cc_final: 0.6842 (p0) REVERT: W 127 ASP cc_start: 0.8703 (t0) cc_final: 0.8479 (t0) REVERT: X 15 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7500 (mm-40) REVERT: X 64 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7815 (tpp-160) REVERT: X 84 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8269 (mm110) outliers start: 153 outliers final: 50 residues processed: 1244 average time/residue: 0.7755 time to fit residues: 1121.3268 Evaluate side-chains 1173 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1087 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain M residue 59 GLN Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 59 GLN Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 244 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 384 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 113 GLN A 140 ASN B 110 ASN B 140 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN E 110 ASN E 113 GLN E 140 ASN F 113 GLN F 140 ASN G 110 ASN G 140 ASN H 113 GLN H 140 ASN I 110 ASN I 119 HIS I 140 ASN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 110 ASN L 113 GLN M 140 ASN N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN P 140 ASN Q 59 GLN R 110 ASN R 140 ASN T 84 GLN T 113 GLN T 140 ASN U 110 ASN U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 110 ASN W 113 GLN W 140 ASN X 110 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.133907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.126500 restraints weight = 34276.703| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 0.71 r_work: 0.3183 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 34608 Z= 0.186 Angle : 0.587 6.830 46608 Z= 0.307 Chirality : 0.041 0.150 4896 Planarity : 0.003 0.026 6144 Dihedral : 4.304 72.876 4491 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 4.87 % Allowed : 17.59 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.49 (0.13), residues: 4080 helix: 3.28 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.59 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 157 TYR 0.022 0.002 TYR U 40 PHE 0.013 0.002 PHE R 42 TRP 0.007 0.002 TRP I 94 HIS 0.006 0.001 HIS S 58 Details of bonding type rmsd covalent geometry : bond 0.00414 (34608) covalent geometry : angle 0.58742 (46608) hydrogen bonds : bond 0.04911 ( 2664) hydrogen bonds : angle 3.48733 ( 7992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 1155 time to evaluate : 1.093 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8087 (tppt) REVERT: A 84 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8271 (mm-40) REVERT: A 120 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7993 (tmtp) REVERT: B 120 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7790 (tmtp) REVERT: B 157 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7931 (mtt-85) REVERT: C 64 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7774 (ttm170) REVERT: C 84 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8283 (mm-40) REVERT: C 120 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7787 (tptp) REVERT: C 157 ARG cc_start: 0.8390 (mtt-85) cc_final: 0.7895 (mtt-85) REVERT: D 84 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8252 (mm-40) REVERT: E 14 HIS cc_start: 0.8839 (t-90) cc_final: 0.8631 (t70) REVERT: E 64 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7622 (ttm110) REVERT: E 69 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8157 (tppt) REVERT: E 84 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8224 (mm-40) REVERT: E 96 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8075 (p) REVERT: E 120 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7623 (tptp) REVERT: F 120 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7579 (tmtp) REVERT: G 64 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7661 (ttm170) REVERT: G 69 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8137 (tppt) REVERT: G 120 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7779 (tptp) REVERT: H 110 ASN cc_start: 0.8035 (m-40) cc_final: 0.7701 (m110) REVERT: H 120 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7779 (tptp) REVERT: I 40 TYR cc_start: 0.8625 (m-80) cc_final: 0.7705 (m-80) REVERT: I 84 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8191 (mm-40) REVERT: I 96 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8077 (p) REVERT: I 120 LYS cc_start: 0.8060 (tttm) cc_final: 0.7684 (tptp) REVERT: J 64 ARG cc_start: 0.8072 (tpp-160) cc_final: 0.7840 (tpp-160) REVERT: J 84 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8304 (mm110) REVERT: K 64 ARG cc_start: 0.7892 (ttm110) cc_final: 0.7648 (ttm110) REVERT: K 69 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8151 (tppt) REVERT: K 96 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8052 (p) REVERT: K 120 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7715 (tptp) REVERT: L 15 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7533 (mm-40) REVERT: L 64 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7682 (ttp-110) REVERT: L 84 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8294 (mm-40) REVERT: L 120 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7693 (tmtp) REVERT: L 125 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7896 (mptp) REVERT: M 84 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8180 (mm110) REVERT: M 92 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7056 (p0) REVERT: M 96 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8052 (p) REVERT: M 125 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7708 (mptp) REVERT: N 84 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8240 (mm-40) REVERT: N 92 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7108 (p0) REVERT: O 15 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7440 (mm-40) REVERT: O 84 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8262 (mm-40) REVERT: O 96 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8093 (p) REVERT: P 64 ARG cc_start: 0.7913 (ttm170) cc_final: 0.7708 (tpp-160) REVERT: P 69 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8129 (tppt) REVERT: P 84 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8241 (mm-40) REVERT: P 120 LYS cc_start: 0.8042 (ttpt) cc_final: 0.7805 (tmtp) REVERT: Q 96 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8055 (p) REVERT: Q 120 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7872 (tptp) REVERT: Q 126 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8079 (m-40) REVERT: R 64 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7906 (tpp-160) REVERT: R 120 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7598 (tmtp) REVERT: R 127 ASP cc_start: 0.8783 (t0) cc_final: 0.8563 (t0) REVERT: S 40 TYR cc_start: 0.8625 (m-80) cc_final: 0.7771 (m-80) REVERT: S 64 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7663 (ttm170) REVERT: S 96 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8091 (p) REVERT: S 120 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7871 (tptp) REVERT: S 127 ASP cc_start: 0.8660 (t0) cc_final: 0.8398 (t0) REVERT: T 120 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7998 (tmtp) REVERT: U 15 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7506 (mm-40) REVERT: U 84 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8225 (mm-40) REVERT: U 102 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7561 (mt-10) REVERT: U 120 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7925 (tmtp) REVERT: U 157 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7670 (mtt-85) REVERT: V 64 ARG cc_start: 0.8041 (tpp-160) cc_final: 0.7402 (ttt-90) REVERT: V 69 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8136 (tppt) REVERT: V 96 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.8068 (p) REVERT: V 120 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7815 (tptp) REVERT: V 126 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8222 (m-40) REVERT: V 127 ASP cc_start: 0.8708 (t0) cc_final: 0.8507 (t0) REVERT: W 15 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7547 (mm-40) REVERT: W 84 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8211 (mm110) REVERT: W 92 ASP cc_start: 0.7263 (p0) cc_final: 0.6998 (p0) REVERT: W 120 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7780 (tptp) REVERT: X 64 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7795 (tpp-160) REVERT: X 84 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8298 (mm110) REVERT: X 120 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7797 (tptp) outliers start: 179 outliers final: 86 residues processed: 1204 average time/residue: 0.7419 time to fit residues: 1037.6231 Evaluate side-chains 1203 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1080 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 117 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 64 ARG Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 50 LYS Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 114 SER Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 120 LYS Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 301 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 315 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 113 GLN A 140 ASN B 84 GLN B 110 ASN B 140 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN E 110 ASN E 113 GLN E 140 ASN F 84 GLN F 113 GLN F 140 ASN G 110 ASN G 140 ASN H 84 GLN H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN L 110 ASN L 113 GLN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN P 126 ASN P 140 ASN R 84 GLN R 110 ASN R 140 ASN T 84 GLN T 113 GLN T 140 ASN U 110 ASN U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 110 ASN W 113 GLN X 110 ASN X 140 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.135084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.127662 restraints weight = 34544.250| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 0.72 r_work: 0.3196 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34608 Z= 0.154 Angle : 0.544 6.276 46608 Z= 0.286 Chirality : 0.039 0.143 4896 Planarity : 0.003 0.024 6144 Dihedral : 4.245 72.692 4491 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.68 % Allowed : 18.06 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.84 (0.13), residues: 4080 helix: 3.49 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.88 (0.29), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 157 TYR 0.018 0.002 TYR O 40 PHE 0.012 0.002 PHE W 42 TRP 0.007 0.002 TRP B 94 HIS 0.004 0.001 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00337 (34608) covalent geometry : angle 0.54401 (46608) hydrogen bonds : bond 0.04512 ( 2664) hydrogen bonds : angle 3.36407 ( 7992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1131 time to evaluate : 0.877 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: A 40 TYR cc_start: 0.8597 (m-80) cc_final: 0.7705 (m-80) REVERT: A 69 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8062 (tppt) REVERT: A 84 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8225 (mm110) REVERT: A 120 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7957 (tmtp) REVERT: B 40 TYR cc_start: 0.8579 (m-80) cc_final: 0.7592 (m-80) REVERT: B 64 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7717 (tpp-160) REVERT: B 68 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8107 (mt-10) REVERT: B 120 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7783 (tmtp) REVERT: C 40 TYR cc_start: 0.8592 (m-80) cc_final: 0.7613 (m-80) REVERT: C 68 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 84 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8330 (mm-40) REVERT: C 120 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7772 (tptp) REVERT: C 157 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.7895 (mtt-85) REVERT: D 40 TYR cc_start: 0.8595 (m-80) cc_final: 0.7603 (m-80) REVERT: D 68 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8099 (mt-10) REVERT: D 84 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8356 (mm-40) REVERT: D 120 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7926 (tmtt) REVERT: D 125 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7706 (mptp) REVERT: D 157 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.8221 (mtt-85) REVERT: E 40 TYR cc_start: 0.8581 (m-80) cc_final: 0.7620 (m-80) REVERT: E 64 ARG cc_start: 0.7864 (ttp-170) cc_final: 0.7574 (ttm110) REVERT: E 69 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8144 (tppt) REVERT: E 84 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8229 (mm-40) REVERT: E 96 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.8068 (p) REVERT: E 120 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7619 (tptp) REVERT: E 127 ASP cc_start: 0.8605 (t0) cc_final: 0.8355 (t0) REVERT: F 40 TYR cc_start: 0.8559 (m-80) cc_final: 0.7626 (m-80) REVERT: F 84 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8214 (mm-40) REVERT: F 120 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8006 (tmtp) REVERT: G 40 TYR cc_start: 0.8595 (m-80) cc_final: 0.7649 (m-80) REVERT: G 64 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7642 (ttm170) REVERT: G 69 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8165 (tppt) REVERT: G 120 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7751 (tptp) REVERT: G 157 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7954 (mtt-85) REVERT: H 40 TYR cc_start: 0.8589 (m-80) cc_final: 0.7630 (m-80) REVERT: H 68 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8080 (mt-10) REVERT: H 84 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8300 (mm-40) REVERT: H 110 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7675 (m110) REVERT: H 120 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7928 (tmtp) REVERT: I 40 TYR cc_start: 0.8568 (m-80) cc_final: 0.7607 (m-80) REVERT: I 84 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8219 (mm-40) REVERT: I 96 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8064 (p) REVERT: I 120 LYS cc_start: 0.8058 (tttm) cc_final: 0.7683 (tptp) REVERT: J 40 TYR cc_start: 0.8582 (m-80) cc_final: 0.7600 (m-80) REVERT: J 64 ARG cc_start: 0.8047 (tpp-160) cc_final: 0.7779 (tpp-160) REVERT: J 84 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8306 (mm110) REVERT: J 120 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7881 (tmtt) REVERT: K 40 TYR cc_start: 0.8561 (m-80) cc_final: 0.7586 (m-80) REVERT: K 64 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7633 (ttm110) REVERT: K 69 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8172 (tppt) REVERT: K 96 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8042 (p) REVERT: K 120 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7699 (tptp) REVERT: L 15 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7536 (mm-40) REVERT: L 40 TYR cc_start: 0.8594 (m-80) cc_final: 0.7598 (m-80) REVERT: L 64 ARG cc_start: 0.7919 (ttp-170) cc_final: 0.7680 (ttp-110) REVERT: L 84 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8280 (mm-40) REVERT: L 120 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.8004 (tmtp) REVERT: M 40 TYR cc_start: 0.8581 (m-80) cc_final: 0.7628 (m-80) REVERT: M 68 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8118 (mt-10) REVERT: M 84 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8213 (mm110) REVERT: M 96 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8040 (p) REVERT: M 125 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7706 (mptp) REVERT: N 40 TYR cc_start: 0.8586 (m-80) cc_final: 0.7630 (m-80) REVERT: N 84 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8319 (mm-40) REVERT: N 92 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7103 (p0) REVERT: O 15 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7439 (mm-40) REVERT: O 40 TYR cc_start: 0.8586 (m-80) cc_final: 0.7613 (m-80) REVERT: O 68 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8070 (mt-10) REVERT: O 84 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8253 (mm110) REVERT: O 96 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8078 (p) REVERT: O 120 LYS cc_start: 0.8152 (tmtp) cc_final: 0.7917 (tmtp) REVERT: P 40 TYR cc_start: 0.8615 (m-80) cc_final: 0.7628 (m-80) REVERT: P 64 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7692 (tpp-160) REVERT: P 69 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8121 (tppt) REVERT: P 84 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8230 (mm-40) REVERT: P 93 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.6906 (t70) REVERT: P 120 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7811 (tmtp) REVERT: Q 40 TYR cc_start: 0.8567 (m-80) cc_final: 0.7611 (m-80) REVERT: Q 84 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8258 (mm-40) REVERT: Q 92 ASP cc_start: 0.7357 (p0) cc_final: 0.6902 (p0) REVERT: Q 120 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7811 (tptp) REVERT: Q 126 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8050 (m-40) REVERT: R 40 TYR cc_start: 0.8571 (m-80) cc_final: 0.7611 (m-80) REVERT: R 64 ARG cc_start: 0.8106 (tpp-160) cc_final: 0.7899 (tpp-160) REVERT: R 69 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8098 (tppt) REVERT: R 84 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8266 (mm-40) REVERT: R 120 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7939 (tmtp) REVERT: S 40 TYR cc_start: 0.8574 (m-80) cc_final: 0.7633 (m-80) REVERT: S 84 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8270 (mm-40) REVERT: S 96 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8085 (p) REVERT: S 120 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7853 (tptp) REVERT: T 40 TYR cc_start: 0.8568 (m-80) cc_final: 0.7607 (m-80) REVERT: T 120 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7787 (tptp) REVERT: U 15 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7506 (mm-40) REVERT: U 40 TYR cc_start: 0.8599 (m-80) cc_final: 0.7585 (m-80) REVERT: U 68 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8038 (mt-10) REVERT: U 84 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8205 (mm-40) REVERT: U 102 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7552 (mt-10) REVERT: U 120 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7728 (tptp) REVERT: U 157 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7663 (mtt-85) REVERT: V 40 TYR cc_start: 0.8571 (m-80) cc_final: 0.7593 (m-80) REVERT: V 64 ARG cc_start: 0.8042 (tpp-160) cc_final: 0.7406 (ttt-90) REVERT: V 69 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8135 (tppt) REVERT: V 96 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8052 (p) REVERT: V 120 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7812 (tptp) REVERT: V 126 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8216 (m-40) REVERT: W 15 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7550 (mm-40) REVERT: W 40 TYR cc_start: 0.8576 (m-80) cc_final: 0.7605 (m-80) REVERT: W 68 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8121 (mt-10) REVERT: W 84 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8311 (mm-40) REVERT: W 120 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7754 (tptp) REVERT: X 40 TYR cc_start: 0.8597 (m-80) cc_final: 0.7662 (m-80) REVERT: X 64 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7788 (tpp-160) REVERT: X 84 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8339 (mm110) REVERT: X 120 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7782 (tptp) outliers start: 172 outliers final: 91 residues processed: 1179 average time/residue: 0.7221 time to fit residues: 990.1473 Evaluate side-chains 1211 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1082 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain T residue 168 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 114 SER Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 120 LYS Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 368 optimal weight: 0.5980 chunk 280 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 323 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 140 ASN B 84 GLN B 110 ASN B 140 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 113 GLN E 140 ASN F 113 GLN F 140 ASN G 110 ASN G 126 ASN G 140 ASN H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 110 ASN L 113 GLN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN Q 15 GLN R 110 ASN R 140 ASN T 84 GLN T 113 GLN T 140 ASN U 110 ASN U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 110 ASN W 113 GLN W 126 ASN X 110 ASN X 140 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.136010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.128598 restraints weight = 34334.030| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.71 r_work: 0.3212 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34608 Z= 0.125 Angle : 0.507 5.802 46608 Z= 0.269 Chirality : 0.038 0.135 4896 Planarity : 0.003 0.023 6144 Dihedral : 4.136 71.459 4491 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.87 % Allowed : 18.14 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.19 (0.13), residues: 4080 helix: 3.74 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.99 (0.29), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 157 TYR 0.016 0.002 TYR W 138 PHE 0.011 0.001 PHE X 42 TRP 0.007 0.002 TRP H 94 HIS 0.004 0.001 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00267 (34608) covalent geometry : angle 0.50670 (46608) hydrogen bonds : bond 0.04101 ( 2664) hydrogen bonds : angle 3.23884 ( 7992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 1157 time to evaluate : 1.325 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 40 TYR cc_start: 0.8547 (m-80) cc_final: 0.7826 (m-80) REVERT: A 66 HIS cc_start: 0.9087 (m170) cc_final: 0.8873 (m170) REVERT: A 69 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8104 (tppt) REVERT: A 84 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8257 (mm-40) REVERT: A 120 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7965 (tmtp) REVERT: B 40 TYR cc_start: 0.8545 (m-80) cc_final: 0.7832 (m-80) REVERT: B 120 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7774 (tmtp) REVERT: B 157 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8229 (mtt-85) REVERT: C 40 TYR cc_start: 0.8516 (m-80) cc_final: 0.7821 (m-80) REVERT: C 84 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8310 (mm110) REVERT: C 102 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 120 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7933 (tmtp) REVERT: C 157 ARG cc_start: 0.8336 (mtt-85) cc_final: 0.7956 (mtt-85) REVERT: D 40 TYR cc_start: 0.8544 (m-80) cc_final: 0.7802 (m-80) REVERT: D 84 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8295 (mm-40) REVERT: D 120 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7923 (tmtt) REVERT: D 125 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7870 (mptp) REVERT: D 126 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8213 (m-40) REVERT: E 40 TYR cc_start: 0.8527 (m-80) cc_final: 0.7822 (m-80) REVERT: E 64 ARG cc_start: 0.7880 (ttp-170) cc_final: 0.7590 (ttm110) REVERT: E 69 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8169 (tppt) REVERT: E 84 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8247 (mm-40) REVERT: E 96 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8056 (p) REVERT: E 120 LYS cc_start: 0.7959 (ttpt) cc_final: 0.7615 (tptp) REVERT: F 40 TYR cc_start: 0.8492 (m-80) cc_final: 0.7664 (m-80) REVERT: F 84 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8246 (mm-40) REVERT: F 120 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7905 (tmtp) REVERT: G 40 TYR cc_start: 0.8503 (m-80) cc_final: 0.7767 (m-80) REVERT: G 69 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8156 (tppt) REVERT: G 120 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7757 (tptp) REVERT: G 125 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7868 (mptp) REVERT: G 157 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.8153 (mtt-85) REVERT: H 23 ARG cc_start: 0.8184 (mtm110) cc_final: 0.7924 (mtm110) REVERT: H 40 TYR cc_start: 0.8485 (m-80) cc_final: 0.7796 (m-80) REVERT: H 84 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8335 (mm-40) REVERT: H 110 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7633 (m110) REVERT: H 120 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7916 (tmtp) REVERT: I 40 TYR cc_start: 0.8508 (m-80) cc_final: 0.7816 (m-80) REVERT: I 84 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8252 (mm-40) REVERT: I 96 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8044 (p) REVERT: I 120 LYS cc_start: 0.8061 (tttm) cc_final: 0.7678 (tptp) REVERT: J 40 TYR cc_start: 0.8526 (m-80) cc_final: 0.7811 (m-80) REVERT: J 64 ARG cc_start: 0.8067 (tpp-160) cc_final: 0.7804 (tpp-160) REVERT: J 84 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8316 (mm110) REVERT: J 120 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7785 (tptp) REVERT: K 40 TYR cc_start: 0.8514 (m-80) cc_final: 0.7793 (m-80) REVERT: K 64 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7608 (ttm110) REVERT: K 69 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8156 (tppt) REVERT: K 96 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8014 (p) REVERT: K 120 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7672 (tptp) REVERT: L 15 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7533 (mm-40) REVERT: L 40 TYR cc_start: 0.8542 (m-80) cc_final: 0.7805 (m-80) REVERT: L 64 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7649 (ttp-110) REVERT: L 84 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8293 (mm-40) REVERT: L 120 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7932 (tmtt) REVERT: L 126 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8194 (m-40) REVERT: M 40 TYR cc_start: 0.8491 (m-80) cc_final: 0.7781 (m-80) REVERT: M 84 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8220 (mm110) REVERT: M 92 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7186 (p0) REVERT: M 96 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8020 (p) REVERT: M 125 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7603 (mptp) REVERT: N 40 TYR cc_start: 0.8505 (m-80) cc_final: 0.7795 (m-80) REVERT: N 84 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8229 (mm-40) REVERT: N 92 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7151 (p0) REVERT: N 157 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7716 (mtt-85) REVERT: O 40 TYR cc_start: 0.8515 (m-80) cc_final: 0.7806 (m-80) REVERT: O 84 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8265 (mm-40) REVERT: O 96 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8064 (p) REVERT: O 157 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.7870 (mtt-85) REVERT: P 40 TYR cc_start: 0.8543 (m-80) cc_final: 0.7818 (m-80) REVERT: P 64 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7630 (tpp-160) REVERT: P 68 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8270 (mt-10) REVERT: P 69 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8113 (tppt) REVERT: P 84 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8259 (mm-40) REVERT: P 93 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6908 (t70) REVERT: P 120 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7761 (tmtp) REVERT: P 126 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8208 (m-40) REVERT: Q 40 TYR cc_start: 0.8513 (m-80) cc_final: 0.7786 (m-80) REVERT: Q 84 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8316 (mm-40) REVERT: Q 110 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7723 (m-40) REVERT: Q 120 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7804 (tptp) REVERT: Q 126 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8017 (m-40) REVERT: Q 127 ASP cc_start: 0.8576 (t0) cc_final: 0.8362 (t0) REVERT: R 40 TYR cc_start: 0.8494 (m-80) cc_final: 0.7798 (m-80) REVERT: R 64 ARG cc_start: 0.8125 (tpp-160) cc_final: 0.7919 (tpp-160) REVERT: R 69 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8078 (tppt) REVERT: R 84 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8277 (mm-40) REVERT: R 120 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7938 (tmtp) REVERT: S 40 TYR cc_start: 0.8508 (m-80) cc_final: 0.7787 (m-80) REVERT: S 84 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8330 (mm-40) REVERT: S 110 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7729 (m-40) REVERT: S 120 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7792 (tptp) REVERT: T 40 TYR cc_start: 0.8506 (m-80) cc_final: 0.7675 (m-80) REVERT: T 54 LYS cc_start: 0.8293 (tmtt) cc_final: 0.8086 (tmtt) REVERT: T 84 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8242 (mm-40) REVERT: T 120 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7768 (tptp) REVERT: U 15 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7529 (mm-40) REVERT: U 40 TYR cc_start: 0.8550 (m-80) cc_final: 0.7816 (m-80) REVERT: U 84 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8264 (mm-40) REVERT: U 102 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7568 (mt-10) REVERT: U 120 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7726 (tptp) REVERT: U 157 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7654 (mtt-85) REVERT: V 40 TYR cc_start: 0.8514 (m-80) cc_final: 0.7790 (m-80) REVERT: V 64 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.7663 (tpp-160) REVERT: V 69 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8134 (tppt) REVERT: V 96 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8029 (p) REVERT: V 120 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7809 (tptp) REVERT: V 127 ASP cc_start: 0.8645 (t0) cc_final: 0.8439 (t0) REVERT: W 15 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7543 (mm-40) REVERT: W 40 TYR cc_start: 0.8524 (m-80) cc_final: 0.7805 (m-80) REVERT: W 84 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8316 (mm-40) REVERT: W 92 ASP cc_start: 0.7424 (p0) cc_final: 0.6935 (p0) REVERT: W 120 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7723 (tptp) REVERT: W 157 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.8099 (mpt-90) REVERT: X 40 TYR cc_start: 0.8513 (m-80) cc_final: 0.7825 (m-80) REVERT: X 64 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.7690 (tpp-160) REVERT: X 84 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8347 (mm110) REVERT: X 120 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7753 (tptp) outliers start: 179 outliers final: 99 residues processed: 1218 average time/residue: 0.6915 time to fit residues: 981.1326 Evaluate side-chains 1249 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1108 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 110 ASN Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain T residue 168 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 114 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 154 THR Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 46 ASP Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 114 SER Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 120 LYS Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 163 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 334 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 393 optimal weight: 4.9990 chunk 403 optimal weight: 0.0670 chunk 41 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 264 optimal weight: 0.5980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 140 ASN B 58 HIS B 59 GLN B 110 ASN B 140 ASN C 58 HIS C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 140 ASN F 113 GLN F 140 ASN G 110 ASN G 140 ASN H 58 HIS H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 110 ASN J 126 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN L 110 ASN L 113 GLN L 140 ASN M 140 ASN N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 HIS P 110 ASN P 140 ASN R 110 ASN R 140 ASN T 113 GLN T 140 ASN U 110 ASN U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 110 ASN W 113 GLN W 140 ASN X 110 ASN X 126 ASN X 140 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.129253 restraints weight = 34503.559| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 0.73 r_work: 0.3219 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34608 Z= 0.117 Angle : 0.497 6.184 46608 Z= 0.264 Chirality : 0.037 0.130 4896 Planarity : 0.003 0.024 6144 Dihedral : 4.073 70.364 4491 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.58 % Allowed : 18.82 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.40 (0.13), residues: 4080 helix: 3.89 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 2.02 (0.29), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 157 TYR 0.015 0.002 TYR W 138 PHE 0.011 0.001 PHE X 42 TRP 0.007 0.001 TRP H 94 HIS 0.003 0.001 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00248 (34608) covalent geometry : angle 0.49724 (46608) hydrogen bonds : bond 0.03916 ( 2664) hydrogen bonds : angle 3.17927 ( 7992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1155 time to evaluate : 1.230 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 40 TYR cc_start: 0.8521 (m-80) cc_final: 0.7814 (m-80) REVERT: A 69 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8098 (tppt) REVERT: A 84 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8247 (mm-40) REVERT: A 120 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7985 (tmtp) REVERT: B 40 TYR cc_start: 0.8472 (m-80) cc_final: 0.7771 (m-80) REVERT: B 120 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7785 (tmtp) REVERT: B 157 ARG cc_start: 0.8389 (mtt-85) cc_final: 0.8181 (mtt-85) REVERT: C 40 TYR cc_start: 0.8485 (m-80) cc_final: 0.7792 (m-80) REVERT: C 84 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8326 (mm-40) REVERT: C 120 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7914 (tmtp) REVERT: D 40 TYR cc_start: 0.8504 (m-80) cc_final: 0.7791 (m-80) REVERT: D 54 LYS cc_start: 0.8350 (tmtt) cc_final: 0.7972 (tptt) REVERT: D 84 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8288 (mm-40) REVERT: D 120 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7769 (tptp) REVERT: D 125 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7945 (mptp) REVERT: D 126 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8201 (m-40) REVERT: D 157 ARG cc_start: 0.8378 (mtt-85) cc_final: 0.8066 (mtt-85) REVERT: E 40 TYR cc_start: 0.8472 (m-80) cc_final: 0.7775 (m-80) REVERT: E 64 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7577 (ttm110) REVERT: E 69 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8168 (tppt) REVERT: E 84 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8262 (mm-40) REVERT: E 96 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8046 (p) REVERT: E 120 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7612 (tptp) REVERT: F 40 TYR cc_start: 0.8449 (m-80) cc_final: 0.7750 (m-80) REVERT: F 84 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8260 (mm-40) REVERT: F 120 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7898 (tmtp) REVERT: F 157 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.7982 (mtt-85) REVERT: G 40 TYR cc_start: 0.8480 (m-80) cc_final: 0.7776 (m-80) REVERT: G 54 LYS cc_start: 0.8315 (tmtt) cc_final: 0.7933 (tptt) REVERT: G 69 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8155 (tppt) REVERT: G 85 ASP cc_start: 0.8339 (m-30) cc_final: 0.8132 (m-30) REVERT: G 120 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7754 (tptp) REVERT: G 125 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7891 (mptp) REVERT: G 157 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.8135 (mtt-85) REVERT: H 40 TYR cc_start: 0.8464 (m-80) cc_final: 0.7782 (m-80) REVERT: H 84 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8299 (mm-40) REVERT: H 110 ASN cc_start: 0.7871 (m-40) cc_final: 0.7583 (m110) REVERT: H 120 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7905 (tmtp) REVERT: I 40 TYR cc_start: 0.8468 (m-80) cc_final: 0.7808 (m-80) REVERT: I 84 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8251 (mm-40) REVERT: I 96 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8047 (p) REVERT: I 120 LYS cc_start: 0.8049 (tttm) cc_final: 0.7672 (tptp) REVERT: I 125 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7971 (mptp) REVERT: J 40 TYR cc_start: 0.8491 (m-80) cc_final: 0.7791 (m-80) REVERT: J 64 ARG cc_start: 0.8058 (tpp-160) cc_final: 0.7775 (tpp-160) REVERT: J 84 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8286 (mm-40) REVERT: J 120 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7763 (tptp) REVERT: J 157 ARG cc_start: 0.8366 (mtt-85) cc_final: 0.7199 (mtt90) REVERT: K 40 TYR cc_start: 0.8451 (m-80) cc_final: 0.7761 (m-80) REVERT: K 64 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7587 (ttm110) REVERT: K 69 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8158 (tppt) REVERT: K 96 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.7892 (p) REVERT: K 120 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7681 (tptp) REVERT: L 15 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7484 (mm-40) REVERT: L 40 TYR cc_start: 0.8492 (m-80) cc_final: 0.7767 (m-80) REVERT: L 84 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8308 (mm-40) REVERT: L 120 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7932 (tmtt) REVERT: M 40 TYR cc_start: 0.8441 (m-80) cc_final: 0.7751 (m-80) REVERT: M 84 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8221 (mm110) REVERT: M 96 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8069 (p) REVERT: M 125 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7674 (mptp) REVERT: N 40 TYR cc_start: 0.8455 (m-80) cc_final: 0.7769 (m-80) REVERT: N 84 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8264 (mm-40) REVERT: N 92 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7152 (p0) REVERT: N 157 ARG cc_start: 0.8055 (mtt-85) cc_final: 0.7706 (mpt-90) REVERT: O 40 TYR cc_start: 0.8475 (m-80) cc_final: 0.7806 (m-80) REVERT: O 84 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8247 (mm-40) REVERT: O 96 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8103 (p) REVERT: P 40 TYR cc_start: 0.8496 (m-80) cc_final: 0.7782 (m-80) REVERT: P 68 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8247 (mt-10) REVERT: P 69 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8122 (tppt) REVERT: P 84 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8270 (mm-40) REVERT: P 92 ASP cc_start: 0.7587 (p0) cc_final: 0.7325 (p0) REVERT: P 102 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7953 (mt-10) REVERT: P 120 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7774 (tmtp) REVERT: P 126 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8204 (m-40) REVERT: P 157 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7935 (mtt-85) REVERT: Q 40 TYR cc_start: 0.8474 (m-80) cc_final: 0.7766 (m-80) REVERT: Q 84 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8304 (mm-40) REVERT: Q 110 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7626 (m-40) REVERT: Q 120 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7759 (tptp) REVERT: Q 126 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8032 (m-40) REVERT: Q 127 ASP cc_start: 0.8575 (t0) cc_final: 0.8327 (t0) REVERT: R 40 TYR cc_start: 0.8452 (m-80) cc_final: 0.7771 (m-80) REVERT: R 64 ARG cc_start: 0.8118 (tpp-160) cc_final: 0.7904 (tpp-160) REVERT: R 69 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8098 (tppt) REVERT: R 84 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8310 (mm-40) REVERT: R 120 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7771 (tptp) REVERT: S 40 TYR cc_start: 0.8475 (m-80) cc_final: 0.7749 (m-80) REVERT: S 84 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8295 (mm-40) REVERT: S 96 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8067 (p) REVERT: S 110 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7646 (m-40) REVERT: S 120 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7792 (tptp) REVERT: T 40 TYR cc_start: 0.8456 (m-80) cc_final: 0.7742 (m-80) REVERT: T 120 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7880 (tmtp) REVERT: T 157 ARG cc_start: 0.8360 (mtt-85) cc_final: 0.7993 (mtt-85) REVERT: U 15 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7535 (mm-40) REVERT: U 40 TYR cc_start: 0.8481 (m-80) cc_final: 0.7779 (m-80) REVERT: U 84 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8258 (mm-40) REVERT: U 102 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7539 (mt-10) REVERT: U 120 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7725 (tptp) REVERT: U 157 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.7635 (mtt-85) REVERT: V 40 TYR cc_start: 0.8473 (m-80) cc_final: 0.7774 (m-80) REVERT: V 69 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8132 (tppt) REVERT: V 96 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8049 (p) REVERT: V 120 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7816 (tptp) REVERT: W 15 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7505 (mm-40) REVERT: W 40 TYR cc_start: 0.8469 (m-80) cc_final: 0.7771 (m-80) REVERT: W 84 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8281 (mm-40) REVERT: W 92 ASP cc_start: 0.7488 (p0) cc_final: 0.7089 (p0) REVERT: W 120 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7726 (tptp) REVERT: W 157 ARG cc_start: 0.8347 (mtt-85) cc_final: 0.8106 (mpt-90) REVERT: X 40 TYR cc_start: 0.8456 (m-80) cc_final: 0.7783 (m-80) REVERT: X 84 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8346 (mm110) REVERT: X 120 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7754 (tptp) REVERT: X 157 ARG cc_start: 0.8044 (mtt-85) cc_final: 0.7752 (mtt-85) outliers start: 168 outliers final: 107 residues processed: 1221 average time/residue: 0.6706 time to fit residues: 953.5768 Evaluate side-chains 1239 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1092 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 110 ASN Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain T residue 154 THR Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain T residue 168 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 114 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 114 SER Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 154 THR Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 120 LYS Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 318 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 346 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 396 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 387 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 110 ASN A 140 ASN B 110 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 113 GLN E 140 ASN F 113 GLN F 140 ASN G 110 ASN G 140 ASN H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 66 HIS J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 126 ASN K 140 ASN L 66 HIS L 110 ASN L 126 ASN L 140 ASN M 66 HIS M 140 ASN N 76 GLN N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 HIS P 110 ASN P 140 ASN Q 140 ASN R 110 ASN R 140 ASN S 140 ASN T 84 GLN T 113 GLN T 140 ASN U 110 ASN U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 110 ASN W 113 GLN W 126 ASN W 140 ASN X 66 HIS X 110 ASN X 140 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.137713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.130302 restraints weight = 34292.285| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 0.72 r_work: 0.3232 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34608 Z= 0.111 Angle : 0.491 6.332 46608 Z= 0.262 Chirality : 0.036 0.127 4896 Planarity : 0.003 0.023 6144 Dihedral : 4.018 69.363 4491 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.19 % Allowed : 19.50 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.56 (0.13), residues: 4080 helix: 4.01 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 2.02 (0.29), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 157 TYR 0.014 0.002 TYR O 40 PHE 0.011 0.001 PHE S 42 TRP 0.008 0.001 TRP H 94 HIS 0.009 0.001 HIS X 66 Details of bonding type rmsd covalent geometry : bond 0.00235 (34608) covalent geometry : angle 0.49138 (46608) hydrogen bonds : bond 0.03751 ( 2664) hydrogen bonds : angle 3.13268 ( 7992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1149 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8408 (m-80) cc_final: 0.7702 (m-80) REVERT: A 69 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8119 (tppt) REVERT: A 84 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8251 (mm-40) REVERT: A 120 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7907 (tmtp) REVERT: A 157 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7879 (mtt-85) REVERT: B 40 TYR cc_start: 0.8386 (m-80) cc_final: 0.7691 (m-80) REVERT: B 120 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7676 (tptp) REVERT: C 40 TYR cc_start: 0.8424 (m-80) cc_final: 0.7708 (m-80) REVERT: C 84 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8333 (mm-40) REVERT: C 102 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7724 (mt-10) REVERT: C 120 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7915 (tmtp) REVERT: C 157 ARG cc_start: 0.8312 (mtt-85) cc_final: 0.7943 (mtt-85) REVERT: D 40 TYR cc_start: 0.8416 (m-80) cc_final: 0.7672 (m-80) REVERT: D 84 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8290 (mm-40) REVERT: D 120 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7730 (tptp) REVERT: D 125 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7942 (mptp) REVERT: D 126 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8198 (m-40) REVERT: E 40 TYR cc_start: 0.8409 (m-80) cc_final: 0.7685 (m-80) REVERT: E 64 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7542 (ttm110) REVERT: E 69 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8161 (tppt) REVERT: E 84 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8258 (mm-40) REVERT: E 96 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8043 (p) REVERT: E 120 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7602 (tptp) REVERT: E 157 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.8007 (mtt-85) REVERT: F 40 TYR cc_start: 0.8400 (m-80) cc_final: 0.7681 (m-80) REVERT: F 84 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8268 (mm-40) REVERT: F 120 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7902 (tmtp) REVERT: F 157 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7932 (mtt-85) REVERT: G 40 TYR cc_start: 0.8415 (m-80) cc_final: 0.7679 (m-80) REVERT: G 69 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8153 (tppt) REVERT: G 120 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7727 (tptp) REVERT: G 125 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7945 (mptp) REVERT: G 157 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.8102 (mtt-85) REVERT: H 40 TYR cc_start: 0.8416 (m-80) cc_final: 0.7706 (m-80) REVERT: H 84 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8298 (mm-40) REVERT: H 110 ASN cc_start: 0.7838 (m-40) cc_final: 0.7543 (m110) REVERT: H 120 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7867 (tmtp) REVERT: I 40 TYR cc_start: 0.8404 (m-80) cc_final: 0.7724 (m-80) REVERT: I 84 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8265 (mm-40) REVERT: I 96 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7973 (p) REVERT: I 120 LYS cc_start: 0.8037 (tttm) cc_final: 0.7672 (tptp) REVERT: I 125 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7986 (mptp) REVERT: J 40 TYR cc_start: 0.8405 (m-80) cc_final: 0.7677 (m-80) REVERT: J 54 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7928 (tptt) REVERT: J 64 ARG cc_start: 0.8018 (tpp-160) cc_final: 0.7784 (tpp-160) REVERT: J 84 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8273 (mm-40) REVERT: J 120 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7743 (tptp) REVERT: J 126 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8216 (m-40) REVERT: K 40 TYR cc_start: 0.8389 (m-80) cc_final: 0.7666 (m-80) REVERT: K 64 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7572 (ttm110) REVERT: K 69 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8154 (tppt) REVERT: K 96 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7921 (p) REVERT: K 120 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7671 (tptp) REVERT: L 15 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7476 (mm-40) REVERT: L 40 TYR cc_start: 0.8409 (m-80) cc_final: 0.7666 (m-80) REVERT: L 84 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8269 (mm-40) REVERT: L 120 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7797 (tptp) REVERT: L 157 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7975 (mtt-85) REVERT: M 40 TYR cc_start: 0.8382 (m-80) cc_final: 0.7653 (m-80) REVERT: M 84 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8228 (mm110) REVERT: M 96 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.7944 (p) REVERT: M 125 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7705 (mptp) REVERT: N 40 TYR cc_start: 0.8396 (m-80) cc_final: 0.7683 (m-80) REVERT: N 84 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8290 (mm-40) REVERT: N 92 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7205 (p0) REVERT: O 40 TYR cc_start: 0.8417 (m-80) cc_final: 0.7738 (m-80) REVERT: O 54 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7979 (tptt) REVERT: O 84 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8249 (mm-40) REVERT: O 96 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8095 (p) REVERT: P 40 TYR cc_start: 0.8422 (m-80) cc_final: 0.7687 (m-80) REVERT: P 69 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8107 (tppt) REVERT: P 84 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8291 (mm110) REVERT: P 92 ASP cc_start: 0.7563 (p0) cc_final: 0.7299 (p0) REVERT: P 102 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7813 (mt-10) REVERT: P 120 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7625 (tptp) REVERT: P 157 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7782 (mtt-85) REVERT: Q 40 TYR cc_start: 0.8406 (m-80) cc_final: 0.7678 (m-80) REVERT: Q 84 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8288 (mm-40) REVERT: Q 110 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7602 (m-40) REVERT: Q 120 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7770 (tptp) REVERT: Q 126 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8007 (m-40) REVERT: Q 127 ASP cc_start: 0.8527 (t0) cc_final: 0.8261 (t0) REVERT: R 40 TYR cc_start: 0.8392 (m-80) cc_final: 0.7689 (m-80) REVERT: R 64 ARG cc_start: 0.8083 (tpp-160) cc_final: 0.7866 (tpp-160) REVERT: R 69 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8119 (tppt) REVERT: R 84 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8308 (mm-40) REVERT: R 120 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7752 (tptp) REVERT: R 157 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7947 (mtt-85) REVERT: S 40 TYR cc_start: 0.8419 (m-80) cc_final: 0.7701 (m-80) REVERT: S 84 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8282 (mm-40) REVERT: S 92 ASP cc_start: 0.7511 (p0) cc_final: 0.7140 (p0) REVERT: S 96 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.7944 (p) REVERT: S 110 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7626 (m-40) REVERT: S 120 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7794 (tptp) REVERT: T 40 TYR cc_start: 0.8406 (m-80) cc_final: 0.7679 (m-80) REVERT: T 84 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8233 (mm-40) REVERT: T 120 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7897 (tmtp) REVERT: T 157 ARG cc_start: 0.8260 (mtt-85) cc_final: 0.7923 (mtt-85) REVERT: U 15 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7502 (mm-40) REVERT: U 40 TYR cc_start: 0.8415 (m-80) cc_final: 0.7726 (m-80) REVERT: U 84 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8243 (mm-40) REVERT: U 102 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7536 (mt-10) REVERT: U 120 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7678 (tptp) REVERT: U 157 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7622 (mtt-85) REVERT: V 40 TYR cc_start: 0.8411 (m-80) cc_final: 0.7689 (m-80) REVERT: V 69 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8128 (tppt) REVERT: V 96 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.8048 (p) REVERT: V 120 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7808 (tptp) REVERT: V 126 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8203 (m-40) REVERT: V 127 ASP cc_start: 0.8713 (t0) cc_final: 0.8467 (t0) REVERT: V 158 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7474 (tppp) REVERT: W 15 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7531 (mm-40) REVERT: W 40 TYR cc_start: 0.8391 (m-80) cc_final: 0.7652 (m-80) REVERT: W 84 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8280 (mm-40) REVERT: W 92 ASP cc_start: 0.7481 (p0) cc_final: 0.7113 (p0) REVERT: W 120 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7414 (tptp) REVERT: W 157 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.8069 (mtt-85) REVERT: X 40 TYR cc_start: 0.8386 (m-80) cc_final: 0.7678 (m-80) REVERT: X 54 LYS cc_start: 0.8174 (tmtt) cc_final: 0.7915 (tptt) REVERT: X 84 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8312 (mm-40) REVERT: X 120 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7721 (tptp) REVERT: X 157 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7711 (mpt-90) outliers start: 154 outliers final: 95 residues processed: 1213 average time/residue: 0.6871 time to fit residues: 974.9558 Evaluate side-chains 1246 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1108 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 126 ASN Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 110 ASN Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain T residue 154 THR Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain T residue 168 GLU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 114 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 154 THR Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain V residue 158 LYS Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 154 THR Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 120 LYS Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 195 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 306 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 110 ASN A 140 ASN B 59 GLN B 66 HIS B 110 ASN B 140 ASN C 110 ASN C 140 ASN D 66 HIS D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 110 ASN E 140 ASN F 59 GLN F 66 HIS F 113 GLN F 140 ASN G 66 HIS G 110 ASN G 140 ASN H 140 ASN I 110 ASN I 140 ASN J 66 HIS J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 66 HIS L 110 ASN L 140 ASN M 66 HIS M 140 ASN N 66 HIS N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 GLN P 110 ASN P 140 ASN Q 140 ASN R 66 HIS R 110 ASN R 140 ASN T 113 GLN T 140 ASN U 110 ASN U 140 ASN V 66 HIS V 84 GLN V 110 ASN V 140 ASN W 66 HIS W 110 ASN W 113 GLN W 140 ASN X 66 HIS X 110 ASN X 126 ASN X 140 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.136120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.128682 restraints weight = 34142.496| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 0.72 r_work: 0.3214 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34608 Z= 0.146 Angle : 0.550 6.197 46608 Z= 0.289 Chirality : 0.039 0.137 4896 Planarity : 0.003 0.044 6144 Dihedral : 4.116 71.896 4491 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.47 % Allowed : 19.93 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.39 (0.13), residues: 4080 helix: 3.88 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 2.02 (0.29), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 157 TYR 0.017 0.002 TYR O 40 PHE 0.012 0.002 PHE V 42 TRP 0.006 0.002 TRP H 94 HIS 0.012 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00320 (34608) covalent geometry : angle 0.54956 (46608) hydrogen bonds : bond 0.04231 ( 2664) hydrogen bonds : angle 3.26218 ( 7992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1126 time to evaluate : 0.853 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 40 TYR cc_start: 0.8568 (m-80) cc_final: 0.7585 (m-80) REVERT: A 68 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 69 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8067 (tppt) REVERT: A 84 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8236 (mm-40) REVERT: A 120 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7952 (tmtp) REVERT: B 40 TYR cc_start: 0.8521 (m-80) cc_final: 0.7786 (m-80) REVERT: B 64 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7642 (tpp-160) REVERT: B 68 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 102 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7663 (mm-30) REVERT: B 120 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7808 (tmtp) REVERT: B 157 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8084 (mpt-90) REVERT: C 40 TYR cc_start: 0.8543 (m-80) cc_final: 0.7576 (m-80) REVERT: C 84 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8329 (mm-40) REVERT: C 120 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7916 (tmtp) REVERT: D 40 TYR cc_start: 0.8550 (m-80) cc_final: 0.7600 (m-80) REVERT: D 54 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7984 (tptt) REVERT: D 84 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8295 (mm-40) REVERT: D 120 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7777 (tptp) REVERT: D 125 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7956 (mptp) REVERT: D 126 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8220 (m-40) REVERT: D 157 ARG cc_start: 0.8411 (mtt-85) cc_final: 0.8023 (mtt-85) REVERT: D 158 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7701 (tppp) REVERT: E 40 TYR cc_start: 0.8536 (m-80) cc_final: 0.7598 (m-80) REVERT: E 64 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7536 (ttm110) REVERT: E 69 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8133 (tppt) REVERT: E 84 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8230 (mm-40) REVERT: E 96 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.7966 (p) REVERT: E 120 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7621 (tptp) REVERT: F 40 TYR cc_start: 0.8513 (m-80) cc_final: 0.7581 (m-80) REVERT: F 84 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8240 (mm-40) REVERT: F 120 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7901 (tmtp) REVERT: F 127 ASP cc_start: 0.8762 (t0) cc_final: 0.8514 (t0) REVERT: F 157 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.7976 (mtt-85) REVERT: G 40 TYR cc_start: 0.8535 (m-80) cc_final: 0.7590 (m-80) REVERT: G 54 LYS cc_start: 0.8200 (tmtt) cc_final: 0.7987 (tptt) REVERT: G 69 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8147 (tppt) REVERT: G 120 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7752 (tptp) REVERT: G 125 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7866 (mptp) REVERT: G 158 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7677 (tppp) REVERT: H 40 TYR cc_start: 0.8546 (m-80) cc_final: 0.7610 (m-80) REVERT: H 110 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7559 (m-40) REVERT: H 120 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7913 (tmtp) REVERT: I 40 TYR cc_start: 0.8545 (m-80) cc_final: 0.7726 (m-80) REVERT: I 84 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8195 (mm-40) REVERT: I 96 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.7970 (p) REVERT: I 120 LYS cc_start: 0.8065 (tttm) cc_final: 0.7685 (tptp) REVERT: J 23 ARG cc_start: 0.8114 (mtm110) cc_final: 0.7902 (mtm110) REVERT: J 40 TYR cc_start: 0.8540 (m-80) cc_final: 0.7577 (m-80) REVERT: J 64 ARG cc_start: 0.8003 (tpp-160) cc_final: 0.7775 (tpp-160) REVERT: J 84 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8315 (mm110) REVERT: J 120 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7782 (tptp) REVERT: J 157 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.7220 (mtt90) REVERT: K 40 TYR cc_start: 0.8522 (m-80) cc_final: 0.7576 (m-80) REVERT: K 64 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7604 (ttm110) REVERT: K 69 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8174 (tppt) REVERT: K 96 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7937 (p) REVERT: K 120 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7702 (tptp) REVERT: L 15 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7548 (mm-40) REVERT: L 40 TYR cc_start: 0.8553 (m-80) cc_final: 0.7574 (m-80) REVERT: L 84 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8223 (mm-40) REVERT: L 120 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7929 (tmtt) REVERT: M 40 TYR cc_start: 0.8528 (m-80) cc_final: 0.7583 (m-80) REVERT: M 84 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8289 (mm-40) REVERT: M 96 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.7949 (p) REVERT: M 120 LYS cc_start: 0.8228 (tmtp) cc_final: 0.7562 (tmtp) REVERT: M 125 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7723 (mptp) REVERT: N 40 TYR cc_start: 0.8538 (m-80) cc_final: 0.7595 (m-80) REVERT: N 84 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8299 (mm-40) REVERT: N 92 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7286 (p0) REVERT: N 157 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7716 (mtt-85) REVERT: O 40 TYR cc_start: 0.8557 (m-80) cc_final: 0.7716 (m-80) REVERT: O 84 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8253 (mm-40) REVERT: O 96 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8088 (p) REVERT: O 157 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.8163 (mpt-90) REVERT: P 23 ARG cc_start: 0.8114 (mtm110) cc_final: 0.7885 (mtm110) REVERT: P 40 TYR cc_start: 0.8554 (m-80) cc_final: 0.7594 (m-80) REVERT: P 64 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7596 (tpp-160) REVERT: P 69 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8122 (tppt) REVERT: P 84 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8261 (mm-40) REVERT: P 92 ASP cc_start: 0.7631 (p0) cc_final: 0.7353 (p0) REVERT: P 120 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7800 (tmtp) REVERT: Q 40 TYR cc_start: 0.8533 (m-80) cc_final: 0.7591 (m-80) REVERT: Q 84 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8298 (mm-40) REVERT: Q 110 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7647 (m-40) REVERT: Q 120 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7788 (tptp) REVERT: Q 126 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8019 (m-40) REVERT: Q 127 ASP cc_start: 0.8613 (t0) cc_final: 0.8366 (t0) REVERT: R 40 TYR cc_start: 0.8527 (m-80) cc_final: 0.7586 (m-80) REVERT: R 64 ARG cc_start: 0.8076 (tpp-160) cc_final: 0.7861 (tpp-160) REVERT: R 69 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8101 (tppt) REVERT: R 84 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8240 (mm-40) REVERT: R 120 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7887 (tmtp) REVERT: S 40 TYR cc_start: 0.8532 (m-80) cc_final: 0.7601 (m-80) REVERT: S 84 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8270 (mm-40) REVERT: S 92 ASP cc_start: 0.7541 (p0) cc_final: 0.7182 (p0) REVERT: S 110 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7691 (m-40) REVERT: S 120 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7796 (tptp) REVERT: S 157 ARG cc_start: 0.8377 (mtt-85) cc_final: 0.8150 (mpt-90) REVERT: T 40 TYR cc_start: 0.8531 (m-80) cc_final: 0.7591 (m-80) REVERT: T 120 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7694 (tmtp) REVERT: T 157 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.7958 (mtt-85) REVERT: U 15 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7536 (mm-40) REVERT: U 40 TYR cc_start: 0.8538 (m-80) cc_final: 0.7683 (m-80) REVERT: U 84 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8203 (mm-40) REVERT: U 102 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7499 (mt-10) REVERT: U 120 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7719 (tptp) REVERT: U 157 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7622 (mtt-85) REVERT: V 40 TYR cc_start: 0.8543 (m-80) cc_final: 0.7592 (m-80) REVERT: V 69 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8136 (tppt) REVERT: V 96 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7906 (p) REVERT: V 120 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7817 (tptp) REVERT: V 126 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8216 (m-40) REVERT: W 15 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7598 (mm-40) REVERT: W 40 TYR cc_start: 0.8540 (m-80) cc_final: 0.7575 (m-80) REVERT: W 84 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8272 (mm-40) REVERT: W 92 ASP cc_start: 0.7548 (p0) cc_final: 0.7187 (p0) REVERT: W 120 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7706 (tptp) REVERT: X 40 TYR cc_start: 0.8548 (m-80) cc_final: 0.7631 (m-80) REVERT: X 64 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7639 (tpp-160) REVERT: X 84 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8336 (mm-40) REVERT: X 120 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7756 (tptp) outliers start: 164 outliers final: 111 residues processed: 1197 average time/residue: 0.6758 time to fit residues: 942.5228 Evaluate side-chains 1218 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1066 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 158 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 110 ASN Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain T residue 154 THR Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain T residue 168 GLU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 114 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 154 THR Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 114 SER Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain V residue 158 LYS Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 154 THR Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 120 LYS Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 121 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 377 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 140 ASN B 66 HIS B 84 GLN B 110 ASN C 110 ASN C 140 ASN D 66 HIS D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 66 HIS E 110 ASN E 113 GLN E 140 ASN F 66 HIS F 113 GLN F 140 ASN G 66 HIS G 110 ASN G 140 ASN H 84 GLN H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 110 ASN J 126 ASN J 140 ASN K 84 GLN K 110 ASN K 126 ASN K 140 ASN L 66 HIS L 110 ASN L 113 GLN L 126 ASN L 140 ASN M 140 ASN N 66 HIS N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 GLN P 110 ASN P 140 ASN Q 140 ASN R 66 HIS R 110 ASN R 140 ASN T 84 GLN T 113 GLN T 140 ASN U 110 ASN U 140 ASN V 66 HIS V 84 GLN V 110 ASN V 140 ASN W 66 HIS W 110 ASN W 113 GLN W 126 ASN W 140 ASN X 110 ASN X 140 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.136153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.128682 restraints weight = 34424.050| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.73 r_work: 0.3212 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34608 Z= 0.148 Angle : 0.556 6.118 46608 Z= 0.293 Chirality : 0.039 0.137 4896 Planarity : 0.003 0.045 6144 Dihedral : 4.129 72.590 4491 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.30 % Allowed : 20.15 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.38 (0.13), residues: 4080 helix: 3.87 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 2.05 (0.29), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 157 TYR 0.017 0.002 TYR O 40 PHE 0.012 0.002 PHE V 42 TRP 0.006 0.002 TRP B 94 HIS 0.014 0.001 HIS L 66 Details of bonding type rmsd covalent geometry : bond 0.00325 (34608) covalent geometry : angle 0.55648 (46608) hydrogen bonds : bond 0.04248 ( 2664) hydrogen bonds : angle 3.27256 ( 7992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1080 time to evaluate : 0.940 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: A 40 TYR cc_start: 0.8558 (m-80) cc_final: 0.7591 (m-80) REVERT: A 69 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8074 (tppt) REVERT: A 84 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8236 (mm-40) REVERT: A 120 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7961 (tmtp) REVERT: B 40 TYR cc_start: 0.8538 (m-80) cc_final: 0.7779 (m-80) REVERT: B 64 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7634 (tpp-160) REVERT: B 120 LYS cc_start: 0.8039 (ttpt) cc_final: 0.7814 (tmtp) REVERT: B 157 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8114 (mpt-90) REVERT: C 40 TYR cc_start: 0.8552 (m-80) cc_final: 0.7810 (m-80) REVERT: C 84 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8319 (mm-40) REVERT: C 120 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7922 (tmtp) REVERT: D 40 TYR cc_start: 0.8560 (m-80) cc_final: 0.7717 (m-80) REVERT: D 54 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7980 (tptt) REVERT: D 84 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8239 (mm-40) REVERT: D 120 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7773 (tptp) REVERT: D 125 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7952 (mptp) REVERT: D 126 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8217 (m-40) REVERT: D 157 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.8001 (mtt-85) REVERT: E 40 TYR cc_start: 0.8541 (m-80) cc_final: 0.7603 (m-80) REVERT: E 64 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7545 (ttm110) REVERT: E 69 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8167 (tppt) REVERT: E 84 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8216 (mm-40) REVERT: E 96 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.8036 (p) REVERT: E 120 LYS cc_start: 0.7984 (ttpt) cc_final: 0.7625 (tptp) REVERT: F 40 TYR cc_start: 0.8523 (m-80) cc_final: 0.7581 (m-80) REVERT: F 84 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8245 (mm-40) REVERT: F 92 ASP cc_start: 0.7356 (p0) cc_final: 0.7012 (p0) REVERT: F 120 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7915 (tmtp) REVERT: F 157 ARG cc_start: 0.8323 (mtt-85) cc_final: 0.7955 (mtt-85) REVERT: G 40 TYR cc_start: 0.8542 (m-80) cc_final: 0.7600 (m-80) REVERT: G 54 LYS cc_start: 0.8232 (tmtt) cc_final: 0.8021 (tptt) REVERT: G 69 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8150 (tppt) REVERT: G 120 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7761 (tptp) REVERT: G 125 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7798 (mptp) REVERT: G 157 ARG cc_start: 0.8320 (mtt-85) cc_final: 0.7944 (mtt-85) REVERT: H 40 TYR cc_start: 0.8550 (m-80) cc_final: 0.7608 (m-80) REVERT: H 110 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7599 (m110) REVERT: H 120 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7909 (tmtp) REVERT: I 40 TYR cc_start: 0.8525 (m-80) cc_final: 0.7691 (m-80) REVERT: I 84 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8198 (mm-40) REVERT: I 96 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.7979 (p) REVERT: I 120 LYS cc_start: 0.8059 (tttm) cc_final: 0.7687 (tptp) REVERT: J 40 TYR cc_start: 0.8557 (m-80) cc_final: 0.7589 (m-80) REVERT: J 64 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7709 (tpp-160) REVERT: J 84 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8359 (mm110) REVERT: J 120 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7774 (tptp) REVERT: J 157 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.8176 (mpt-90) REVERT: K 40 TYR cc_start: 0.8531 (m-80) cc_final: 0.7579 (m-80) REVERT: K 64 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7605 (ttm110) REVERT: K 69 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8158 (tppt) REVERT: K 96 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7942 (p) REVERT: K 120 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7698 (tptp) REVERT: L 15 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7567 (mm-40) REVERT: L 40 TYR cc_start: 0.8556 (m-80) cc_final: 0.7580 (m-80) REVERT: L 84 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8223 (mm-40) REVERT: L 92 ASP cc_start: 0.7513 (p0) cc_final: 0.7186 (p0) REVERT: L 120 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7949 (tmtt) REVERT: M 40 TYR cc_start: 0.8536 (m-80) cc_final: 0.7587 (m-80) REVERT: M 84 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8295 (mm-40) REVERT: M 96 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.7957 (p) REVERT: M 120 LYS cc_start: 0.8196 (tmtp) cc_final: 0.7788 (tptp) REVERT: N 40 TYR cc_start: 0.8532 (m-80) cc_final: 0.7583 (m-80) REVERT: N 84 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8236 (mm110) REVERT: O 40 TYR cc_start: 0.8540 (m-80) cc_final: 0.7681 (m-80) REVERT: O 84 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8249 (mm-40) REVERT: O 96 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7990 (p) REVERT: O 125 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8054 (mptp) REVERT: O 157 ARG cc_start: 0.8397 (mtt-85) cc_final: 0.8156 (mpt-90) REVERT: P 40 TYR cc_start: 0.8574 (m-80) cc_final: 0.7605 (m-80) REVERT: P 64 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7630 (tpp-160) REVERT: P 69 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8114 (tppt) REVERT: P 84 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8294 (mm-40) REVERT: P 92 ASP cc_start: 0.7658 (p0) cc_final: 0.7386 (p0) REVERT: P 120 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7789 (tmtp) REVERT: P 157 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.8027 (mpt-90) REVERT: Q 40 TYR cc_start: 0.8538 (m-80) cc_final: 0.7592 (m-80) REVERT: Q 84 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8291 (mm-40) REVERT: Q 120 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7789 (tptp) REVERT: Q 126 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8056 (m-40) REVERT: R 40 TYR cc_start: 0.8530 (m-80) cc_final: 0.7588 (m-80) REVERT: R 64 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.7778 (tpp-160) REVERT: R 69 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8097 (tppt) REVERT: R 84 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8270 (mm-40) REVERT: R 120 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7889 (tmtp) REVERT: R 157 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7959 (mtt-85) REVERT: S 40 TYR cc_start: 0.8542 (m-80) cc_final: 0.7711 (m-80) REVERT: S 84 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8268 (mm-40) REVERT: S 92 ASP cc_start: 0.7543 (p0) cc_final: 0.7189 (p0) REVERT: S 110 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7696 (m-40) REVERT: S 120 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7804 (tptp) REVERT: S 157 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8144 (mpt-90) REVERT: T 40 TYR cc_start: 0.8533 (m-80) cc_final: 0.7587 (m-80) REVERT: T 84 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8230 (mm-40) REVERT: T 92 ASP cc_start: 0.7313 (p0) cc_final: 0.7003 (p0) REVERT: T 120 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8040 (tmtp) REVERT: T 157 ARG cc_start: 0.8364 (mtt-85) cc_final: 0.8059 (mtt-85) REVERT: U 15 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7570 (mm-40) REVERT: U 40 TYR cc_start: 0.8546 (m-80) cc_final: 0.7695 (m-80) REVERT: U 84 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8207 (mm-40) REVERT: U 102 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7496 (mt-10) REVERT: U 120 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7713 (tptp) REVERT: U 157 ARG cc_start: 0.7987 (mtt-85) cc_final: 0.7621 (mtt-85) REVERT: V 40 TYR cc_start: 0.8551 (m-80) cc_final: 0.7589 (m-80) REVERT: V 69 LYS cc_start: 0.8365 (ttpt) cc_final: 0.8128 (tppt) REVERT: V 96 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7903 (p) REVERT: V 120 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7824 (tptp) REVERT: V 126 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8218 (m-40) REVERT: V 127 ASP cc_start: 0.8716 (t0) cc_final: 0.8464 (t0) REVERT: W 15 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7579 (mm-40) REVERT: W 40 TYR cc_start: 0.8545 (m-80) cc_final: 0.7702 (m-80) REVERT: W 84 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8264 (mm-40) REVERT: W 120 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7716 (tptp) REVERT: X 40 TYR cc_start: 0.8549 (m-80) cc_final: 0.7609 (m-80) REVERT: X 64 ARG cc_start: 0.7887 (tpp-160) cc_final: 0.7628 (tpp-160) REVERT: X 84 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8327 (mm-40) REVERT: X 120 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7754 (tptp) outliers start: 158 outliers final: 109 residues processed: 1147 average time/residue: 0.7024 time to fit residues: 936.9258 Evaluate side-chains 1216 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1069 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain T residue 154 THR Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain T residue 168 GLU Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 114 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 154 THR Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 114 SER Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain V residue 158 LYS Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 154 THR Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 120 LYS Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 183 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 387 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 379 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 269 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 140 ASN B 110 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 140 ASN F 113 GLN F 140 ASN G 110 ASN G 140 ASN H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 140 ASN L 66 HIS L 110 ASN L 113 GLN L 140 ASN M 140 ASN N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 GLN P 110 ASN P 140 ASN Q 140 ASN R 110 ASN R 140 ASN T 113 GLN T 140 ASN U 110 ASN U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 110 ASN W 113 GLN W 140 ASN X 110 ASN X 126 ASN X 140 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.137793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.130435 restraints weight = 34151.539| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.72 r_work: 0.3232 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34608 Z= 0.122 Angle : 0.521 6.353 46608 Z= 0.278 Chirality : 0.037 0.130 4896 Planarity : 0.003 0.041 6144 Dihedral : 4.065 70.933 4491 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.14 % Allowed : 20.53 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.57 (0.13), residues: 4080 helix: 4.01 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 2.08 (0.29), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 157 TYR 0.014 0.002 TYR O 40 PHE 0.012 0.001 PHE X 42 TRP 0.007 0.002 TRP R 94 HIS 0.016 0.001 HIS L 66 Details of bonding type rmsd covalent geometry : bond 0.00263 (34608) covalent geometry : angle 0.52145 (46608) hydrogen bonds : bond 0.03877 ( 2664) hydrogen bonds : angle 3.18121 ( 7992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15610.64 seconds wall clock time: 265 minutes 53.00 seconds (15953.00 seconds total)