Starting phenix.real_space_refine on Mon Mar 25 19:43:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/03_2024/8f53_28859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/03_2024/8f53_28859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/03_2024/8f53_28859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/03_2024/8f53_28859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/03_2024/8f53_28859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/03_2024/8f53_28859.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.062 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 S 180 5.16 5 C 15780 2.51 5 N 3840 2.21 5 O 4800 1.98 5 H 26460 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51060 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "F" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "K" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "J1" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Od" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Tc" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Ba" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "B" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "L" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "V" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Z" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Id" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Nh" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Sl" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Xp" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Yb" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "H" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "M" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "W" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Ca" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "He" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Mi" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Rm" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Wq" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Ae" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "I" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "X" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Bb" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Gf" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Lj" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Qn" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Vr" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Zt" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "E" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "O" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Y" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Dc" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Fg" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Kk" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Po" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Us" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Hu" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "P" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Gv" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Q" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Fw" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "R" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Ex" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "S" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Dy" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "T" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "Cz" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "0" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Chain: "2" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 851 Classifications: {'peptide': 54} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 53} Time building chain proxies: 20.58, per 1000 atoms: 0.40 Number of scatterers: 51060 At special positions: 0 Unit cell: (133.56, 133.56, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 O 4800 8.00 N 3840 7.00 C 15780 6.00 H 26460 1.00 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 - 3.50 Amino acid : False - 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: 38.37 Conformation dependent library (CDL) restraints added in 4.8 seconds 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 0 sheets defined 90.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 Processing helix chain 'A' and resid 16 through 32 Processing helix chain 'A' and resid 34 through 52 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 16 through 32 Processing helix chain 'F' and resid 34 through 52 Processing helix chain 'K' and resid 2 through 14 Processing helix chain 'K' and resid 16 through 32 Processing helix chain 'K' and resid 34 through 52 Processing helix chain 'U' and resid 2 through 14 Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 34 through 52 Processing helix chain 'J1' and resid 2 through 14 Processing helix chain 'J1' and resid 16 through 31 Processing helix chain 'J1' and resid 34 through 52 Processing helix chain 'Od' and resid 2 through 14 Processing helix chain 'Od' and resid 16 through 32 Processing helix chain 'Od' and resid 34 through 52 Processing helix chain 'Tc' and resid 2 through 14 Processing helix chain 'Tc' and resid 16 through 32 Processing helix chain 'Tc' and resid 34 through 52 Processing helix chain 'Ba' and resid 2 through 14 Processing helix chain 'Ba' and resid 16 through 32 Processing helix chain 'Ba' and resid 34 through 52 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 16 through 32 Processing helix chain 'B' and resid 34 through 52 Processing helix chain 'G' and resid 2 through 14 Processing helix chain 'G' and resid 16 through 32 Processing helix chain 'G' and resid 34 through 52 Processing helix chain 'L' and resid 2 through 14 Processing helix chain 'L' and resid 16 through 32 Processing helix chain 'L' and resid 34 through 52 Processing helix chain 'V' and resid 2 through 14 Processing helix chain 'V' and resid 16 through 32 Processing helix chain 'V' and resid 34 through 52 Processing helix chain 'Z' and resid 4 through 14 Processing helix chain 'Z' and resid 16 through 31 Processing helix chain 'Z' and resid 34 through 52 removed outlier: 3.512A pdb=" N ASN Z 50 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) Processing helix chain 'Id' and resid 2 through 14 Processing helix chain 'Id' and resid 16 through 32 Processing helix chain 'Id' and resid 34 through 52 Processing helix chain 'Nh' and resid 2 through 14 Processing helix chain 'Nh' and resid 16 through 32 Processing helix chain 'Nh' and resid 34 through 52 Processing helix chain 'Sl' and resid 2 through 14 Processing helix chain 'Sl' and resid 16 through 32 Processing helix chain 'Sl' and resid 34 through 52 Processing helix chain 'Xp' and resid 2 through 14 Processing helix chain 'Xp' and resid 16 through 31 Processing helix chain 'Xp' and resid 34 through 52 Processing helix chain 'Yb' and resid 2 through 14 Processing helix chain 'Yb' and resid 16 through 32 Processing helix chain 'Yb' and resid 34 through 52 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 34 through 52 Processing helix chain 'H' and resid 2 through 14 Processing helix chain 'H' and resid 16 through 31 Processing helix chain 'H' and resid 34 through 52 Processing helix chain 'M' and resid 2 through 14 Processing helix chain 'M' and resid 16 through 32 Processing helix chain 'M' and resid 34 through 52 Processing helix chain 'W' and resid 2 through 14 Processing helix chain 'W' and resid 16 through 32 Processing helix chain 'W' and resid 34 through 52 Processing helix chain 'Ca' and resid 2 through 14 Processing helix chain 'Ca' and resid 16 through 32 Processing helix chain 'Ca' and resid 34 through 52 Processing helix chain 'He' and resid 2 through 14 Processing helix chain 'He' and resid 16 through 32 Processing helix chain 'He' and resid 34 through 52 Processing helix chain 'Mi' and resid 2 through 14 Processing helix chain 'Mi' and resid 16 through 32 Processing helix chain 'Mi' and resid 34 through 52 Processing helix chain 'Rm' and resid 2 through 14 Processing helix chain 'Rm' and resid 16 through 32 Processing helix chain 'Rm' and resid 34 through 52 Processing helix chain 'Wq' and resid 2 through 14 Processing helix chain 'Wq' and resid 16 through 31 Processing helix chain 'Wq' and resid 34 through 52 Processing helix chain 'Ae' and resid 2 through 14 Processing helix chain 'Ae' and resid 16 through 31 Processing helix chain 'Ae' and resid 34 through 52 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 16 through 32 Processing helix chain 'D' and resid 34 through 52 Processing helix chain 'I' and resid 2 through 14 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 34 through 52 Processing helix chain 'N' and resid 2 through 14 Processing helix chain 'N' and resid 16 through 31 Processing helix chain 'N' and resid 34 through 52 Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 16 through 32 Processing helix chain 'X' and resid 34 through 52 Processing helix chain 'Bb' and resid 2 through 14 Processing helix chain 'Bb' and resid 16 through 32 Processing helix chain 'Bb' and resid 34 through 52 Processing helix chain 'Gf' and resid 2 through 14 Processing helix chain 'Gf' and resid 16 through 32 Processing helix chain 'Gf' and resid 34 through 52 Processing helix chain 'Lj' and resid 2 through 14 Processing helix chain 'Lj' and resid 16 through 31 Processing helix chain 'Lj' and resid 34 through 52 Processing helix chain 'Qn' and resid 2 through 14 Processing helix chain 'Qn' and resid 16 through 31 Processing helix chain 'Qn' and resid 34 through 52 Processing helix chain 'Vr' and resid 2 through 14 Processing helix chain 'Vr' and resid 16 through 32 Processing helix chain 'Vr' and resid 34 through 52 Processing helix chain 'Zt' and resid 2 through 14 Processing helix chain 'Zt' and resid 16 through 32 Processing helix chain 'Zt' and resid 34 through 52 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 16 through 32 Processing helix chain 'E' and resid 34 through 52 Processing helix chain 'J' and resid 2 through 14 Processing helix chain 'J' and resid 16 through 32 removed outlier: 3.543A pdb=" N GLY J 32 " --> pdb=" O VAL J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 52 Processing helix chain 'O' and resid 2 through 14 Processing helix chain 'O' and resid 16 through 32 Processing helix chain 'O' and resid 34 through 52 Processing helix chain 'Y' and resid 2 through 14 Processing helix chain 'Y' and resid 16 through 32 Processing helix chain 'Y' and resid 34 through 52 Processing helix chain 'Dc' and resid 2 through 14 Processing helix chain 'Dc' and resid 16 through 31 Processing helix chain 'Dc' and resid 34 through 52 Processing helix chain 'Fg' and resid 2 through 14 Processing helix chain 'Fg' and resid 16 through 32 Processing helix chain 'Fg' and resid 34 through 52 Processing helix chain 'Kk' and resid 2 through 14 Processing helix chain 'Kk' and resid 16 through 32 Processing helix chain 'Kk' and resid 34 through 52 Processing helix chain 'Po' and resid 2 through 14 Processing helix chain 'Po' and resid 16 through 32 Processing helix chain 'Po' and resid 34 through 52 Processing helix chain 'Us' and resid 2 through 14 Processing helix chain 'Us' and resid 16 through 31 Processing helix chain 'Us' and resid 34 through 52 Processing helix chain 'Hu' and resid 2 through 14 Processing helix chain 'Hu' and resid 16 through 32 Processing helix chain 'Hu' and resid 34 through 52 Processing helix chain 'P' and resid 2 through 14 Processing helix chain 'P' and resid 16 through 31 Processing helix chain 'P' and resid 34 through 52 Processing helix chain 'Gv' and resid 2 through 14 Processing helix chain 'Gv' and resid 16 through 32 Processing helix chain 'Gv' and resid 34 through 52 Processing helix chain 'Q' and resid 2 through 14 Processing helix chain 'Q' and resid 16 through 31 Processing helix chain 'Q' and resid 34 through 52 Processing helix chain 'Fw' and resid 2 through 14 Processing helix chain 'Fw' and resid 16 through 32 Processing helix chain 'Fw' and resid 34 through 52 Processing helix chain 'R' and resid 2 through 14 Processing helix chain 'R' and resid 16 through 32 Processing helix chain 'R' and resid 34 through 52 removed outlier: 3.512A pdb=" N ASN R 50 " --> pdb=" O ILE R 46 " (cutoff:3.500A) Processing helix chain 'Ex' and resid 2 through 14 Processing helix chain 'Ex' and resid 16 through 32 Processing helix chain 'Ex' and resid 34 through 52 Processing helix chain 'S' and resid 2 through 14 Processing helix chain 'S' and resid 16 through 31 Processing helix chain 'S' and resid 34 through 52 Processing helix chain 'Dy' and resid 2 through 14 Processing helix chain 'Dy' and resid 16 through 31 Processing helix chain 'Dy' and resid 34 through 52 Processing helix chain 'T' and resid 2 through 14 Processing helix chain 'T' and resid 16 through 31 Processing helix chain 'T' and resid 34 through 52 Processing helix chain 'Cz' and resid 2 through 14 Processing helix chain 'Cz' and resid 16 through 32 Processing helix chain 'Cz' and resid 34 through 52 Processing helix chain '0' and resid 2 through 14 Processing helix chain '0' and resid 16 through 32 Processing helix chain '0' and resid 34 through 52 Processing helix chain '2' and resid 2 through 14 Processing helix chain '2' and resid 16 through 32 Processing helix chain '2' and resid 34 through 52 2198 hydrogen bonds defined for protein. 6594 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: 21.95 Time building geometry restraints manager: 39.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26460 1.03 - 1.23: 0 1.23 - 1.42: 8940 1.42 - 1.61: 15360 1.61 - 1.81: 360 Bond restraints: 51120 Sorted by residual: bond pdb=" N ASNSl 50 " pdb=" CA ASNSl 50 " ideal model delta sigma weight residual 1.460 1.469 -0.009 1.22e-02 6.72e+03 5.67e-01 bond pdb=" C PHE A 45 " pdb=" O PHE A 45 " ideal model delta sigma weight residual 1.237 1.228 0.008 1.19e-02 7.06e+03 4.70e-01 bond pdb=" CB PHE A 45 " pdb=" CG PHE A 45 " ideal model delta sigma weight residual 1.502 1.515 -0.013 2.30e-02 1.89e+03 3.43e-01 bond pdb=" N GLU Z 3 " pdb=" CA GLU Z 3 " ideal model delta sigma weight residual 1.456 1.463 -0.007 1.23e-02 6.61e+03 3.35e-01 bond pdb=" C PHE D 45 " pdb=" O PHE D 45 " ideal model delta sigma weight residual 1.237 1.230 0.007 1.17e-02 7.31e+03 3.27e-01 ... (remaining 51115 not shown) Histogram of bond angle deviations from ideal: 100.14 - 105.29: 180 105.29 - 110.45: 58523 110.45 - 115.60: 13864 115.60 - 120.75: 11424 120.75 - 125.90: 9849 Bond angle restraints: 93840 Sorted by residual: angle pdb=" N GLU Z 3 " pdb=" CA GLU Z 3 " pdb=" CB GLU Z 3 " ideal model delta sigma weight residual 114.17 109.98 4.19 1.14e+00 7.69e-01 1.35e+01 angle pdb=" C MET Z 2 " pdb=" N GLU Z 3 " pdb=" CA GLU Z 3 " ideal model delta sigma weight residual 126.45 122.97 3.48 1.77e+00 3.19e-01 3.88e+00 angle pdb=" CA GLU Z 3 " pdb=" C GLU Z 3 " pdb=" N ALA Z 4 " ideal model delta sigma weight residual 119.38 117.22 2.16 1.24e+00 6.50e-01 3.02e+00 angle pdb=" N ALA Z 4 " pdb=" CA ALA Z 4 " pdb=" C ALA Z 4 " ideal model delta sigma weight residual 112.23 110.23 2.00 1.26e+00 6.30e-01 2.51e+00 angle pdb=" CA GLU Z 3 " pdb=" C GLU Z 3 " pdb=" O GLU Z 3 " ideal model delta sigma weight residual 119.00 120.48 -1.48 1.00e+00 1.00e+00 2.19e+00 ... (remaining 93835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21373 17.93 - 35.86: 1009 35.86 - 53.78: 255 53.78 - 71.71: 236 71.71 - 89.64: 47 Dihedral angle restraints: 22920 sinusoidal: 13140 harmonic: 9780 Sorted by residual: dihedral pdb=" CA GLU Z 3 " pdb=" C GLU Z 3 " pdb=" N ALA Z 4 " pdb=" CA ALA Z 4 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA MET Z 2 " pdb=" C MET Z 2 " pdb=" N GLU Z 3 " pdb=" CA GLU Z 3 " ideal model delta harmonic sigma weight residual 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARGEx 53 " pdb=" CD ARGEx 53 " pdb=" NE ARGEx 53 " pdb=" CZ ARGEx 53 " ideal model delta sinusoidal sigma weight residual 90.00 129.91 -39.91 2 1.50e+01 4.44e-03 8.78e+00 ... (remaining 22917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.018: 2318 0.018 - 0.036: 752 0.036 - 0.054: 461 0.054 - 0.072: 456 0.072 - 0.090: 93 Chirality restraints: 4080 Sorted by residual: chirality pdb=" CA ILE K 48 " pdb=" N ILE K 48 " pdb=" C ILE K 48 " pdb=" CB ILE K 48 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.04e-01 chirality pdb=" CA ILEYb 48 " pdb=" N ILEYb 48 " pdb=" C ILEYb 48 " pdb=" CB ILEYb 48 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.04e-01 chirality pdb=" CA ILEXp 48 " pdb=" N ILEXp 48 " pdb=" C ILEXp 48 " pdb=" CB ILEXp 48 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.02e-01 ... (remaining 4077 not shown) Planarity restraints: 7260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET Z 2 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C MET Z 2 " -0.017 2.00e-02 2.50e+03 pdb=" O MET Z 2 " 0.007 2.00e-02 2.50e+03 pdb=" N GLU Z 3 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 46 " -0.003 2.00e-02 2.50e+03 6.59e-03 4.35e-01 pdb=" C ILE A 46 " 0.011 2.00e-02 2.50e+03 pdb=" O ILE A 46 " -0.004 2.00e-02 2.50e+03 pdb=" N GLU A 47 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 8 " 0.007 2.00e-02 2.50e+03 3.76e-03 4.23e-01 pdb=" CG TYR Q 8 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 8 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 8 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 8 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 8 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR Q 8 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR Q 8 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR Q 8 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR Q 8 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR Q 8 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR Q 8 " 0.001 2.00e-02 2.50e+03 ... (remaining 7257 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1518 2.16 - 2.77: 105030 2.77 - 3.38: 145848 3.38 - 3.99: 182431 3.99 - 4.60: 301810 Nonbonded interactions: 736637 Sorted by model distance: nonbonded pdb=" O ALAXp 27 " pdb=" HG SERXp 31 " model vdw 1.555 1.850 nonbonded pdb=" O ALA M 27 " pdb=" HG SER M 31 " model vdw 1.576 1.850 nonbonded pdb=" O ALA V 27 " pdb=" HG SER V 31 " model vdw 1.583 1.850 nonbonded pdb=" O ALA 0 27 " pdb=" HG SER 0 31 " model vdw 1.590 1.850 nonbonded pdb=" O ALA F 27 " pdb=" HG SER F 31 " model vdw 1.592 1.850 ... (remaining 736632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain 'A' selection = chain 'Ae' selection = chain 'B' selection = chain 'Ba' selection = chain 'Bb' selection = chain 'C' selection = chain 'Ca' selection = chain 'Cz' selection = chain 'D' selection = chain 'Dc' selection = chain 'Dy' selection = chain 'E' selection = chain 'Ex' selection = chain 'F' selection = chain 'Fg' selection = chain 'Fw' selection = chain 'G' selection = chain 'Gf' selection = chain 'Gv' selection = chain 'H' selection = chain 'He' selection = chain 'Hu' selection = chain 'I' selection = chain 'Id' selection = chain 'J' selection = chain 'J1' selection = chain 'K' selection = chain 'Kk' selection = chain 'L' selection = chain 'Lj' selection = chain 'M' selection = chain 'Mi' selection = chain 'N' selection = chain 'Nh' selection = chain 'O' selection = chain 'Od' selection = chain 'P' selection = chain 'Po' selection = chain 'Q' selection = chain 'Qn' selection = chain 'R' selection = chain 'Rm' selection = chain 'S' selection = chain 'Sl' selection = chain 'T' selection = chain 'Tc' selection = chain 'U' selection = chain 'Us' selection = chain 'V' selection = chain 'Vr' selection = chain 'W' selection = chain 'Wq' selection = chain 'X' selection = chain 'Xp' selection = chain 'Y' selection = chain 'Yb' selection = chain 'Z' selection = chain 'Zt' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.750 Extract box with map and model: 9.090 Check model and map are aligned: 0.680 Set scattering table: 0.440 Process input model: 151.810 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.790 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: 0.020 Load rotamer database and sin/cos tables:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.002 0.016 24660 Z= 0.151 Angle : 0.428 4.189 32940 Z= 0.243 Chirality : 0.032 0.090 4080 Planarity : 0.002 0.018 4080 Dihedral : 11.818 89.639 9540 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3120 helix: 0.65 (0.09), residues: 2700 sheet: None (None), residues: 0 loop : 2.83 (0.48), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEUs 45 TYR 0.011 0.002 TYR Z 8 ARG 0.002 0.001 ARG Z 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 756 time to evaluate : 4.337 Fit side-chains REVERT: J1 5 MET cc_start: 0.8597 (mtt) cc_final: 0.8199 (mtt) REVERT: L 1 MET cc_start: 0.6071 (mpp) cc_final: 0.5702 (mmm) REVERT: Id 1 MET cc_start: 0.5898 (mpp) cc_final: 0.5637 (ptt) REVERT: Sl 3 GLU cc_start: 0.6785 (tp30) cc_final: 0.6564 (tp30) REVERT: Xp 1 MET cc_start: 0.6027 (mpp) cc_final: 0.5813 (ptt) REVERT: Yb 3 GLU cc_start: 0.6773 (tp30) cc_final: 0.6533 (tp30) REVERT: Ae 1 MET cc_start: 0.4394 (mmm) cc_final: 0.4104 (mmm) REVERT: Ae 5 MET cc_start: 0.8658 (mtt) cc_final: 0.8142 (mtt) REVERT: Gf 5 MET cc_start: 0.8679 (mtt) cc_final: 0.8262 (mtt) REVERT: Dc 5 MET cc_start: 0.8644 (mtt) cc_final: 0.8259 (mtt) REVERT: Us 5 MET cc_start: 0.8677 (mtt) cc_final: 0.8255 (mtt) REVERT: Hu 1 MET cc_start: 0.6225 (mpp) cc_final: 0.5412 (ptt) REVERT: P 36 VAL cc_start: 0.8434 (p) cc_final: 0.8227 (t) REVERT: Gv 1 MET cc_start: 0.5783 (mpp) cc_final: 0.5438 (ptt) REVERT: Gv 5 MET cc_start: 0.8631 (mtt) cc_final: 0.8312 (mtt) REVERT: 0 1 MET cc_start: 0.6265 (mpp) cc_final: 0.5917 (mmm) outliers start: 0 outliers final: 1 residues processed: 756 average time/residue: 2.8086 time to fit residues: 2478.2845 Evaluate side-chains 662 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 661 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 126 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Bb 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 24660 Z= 0.181 Angle : 0.504 4.559 32940 Z= 0.279 Chirality : 0.033 0.088 4080 Planarity : 0.002 0.008 4080 Dihedral : 10.059 89.923 3362 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 4.58 % Allowed : 9.73 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.15), residues: 3120 helix: 1.62 (0.09), residues: 2820 sheet: None (None), residues: 0 loop : 3.56 (0.61), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHEZt 45 TYR 0.011 0.002 TYR T 8 ARG 0.001 0.000 ARG Z 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 593 time to evaluate : 3.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7721 (mtmm) cc_final: 0.7315 (mtmp) REVERT: A 11 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: F 7 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7440 (mtmp) REVERT: F 11 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: J1 7 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7044 (mtmp) REVERT: J1 11 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: Od 11 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: Tc 7 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7258 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: Ba 7 LYS cc_start: 0.7469 (mtmt) cc_final: 0.7093 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: B 11 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: G 7 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7209 (mttp) REVERT: G 11 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: L 7 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7310 (mttp) REVERT: L 11 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: V 7 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7178 (mttp) REVERT: V 11 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: Z 11 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: Id 1 MET cc_start: 0.5878 (mpp) cc_final: 0.5513 (ptt) REVERT: Id 7 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7147 (mtpt) REVERT: Id 11 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: Nh 7 LYS cc_start: 0.7777 (mtmm) cc_final: 0.7221 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: Sl 7 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7278 (mtmp) REVERT: Sl 11 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: Xp 1 MET cc_start: 0.6071 (mpp) cc_final: 0.5760 (mmm) REVERT: Yb 11 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: C 11 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: H 7 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7220 (mtmp) REVERT: H 11 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: M 7 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7184 (mtmm) REVERT: M 11 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: W 7 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7153 (mtmm) REVERT: W 11 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: Ca 11 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: He 11 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: Mi 11 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: Rm 2 MET cc_start: 0.7151 (mtp) cc_final: 0.6812 (ttm) REVERT: Wq 7 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7017 (mtmp) REVERT: Wq 11 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: Ae 7 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7323 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: D 7 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7127 (mtmp) REVERT: D 11 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: I 7 LYS cc_start: 0.7613 (mtmm) cc_final: 0.7161 (mtmp) REVERT: I 11 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: N 11 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: X 7 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7309 (mtmm) REVERT: X 11 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: Bb 11 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: Gf 7 LYS cc_start: 0.7680 (mtmm) cc_final: 0.7141 (mtmp) REVERT: Gf 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: Lj 7 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7067 (mtmp) REVERT: Lj 11 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: Qn 7 LYS cc_start: 0.7780 (mtmp) cc_final: 0.7049 (mtpt) REVERT: Qn 11 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: Vr 7 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7370 (mtmp) REVERT: Vr 11 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: Zt 7 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7364 (mtmp) REVERT: Zt 11 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: O 7 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.6948 (mttp) REVERT: O 11 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: Y 7 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7201 (mtmp) REVERT: Y 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: Dc 7 LYS cc_start: 0.7637 (mtmm) cc_final: 0.7276 (mtmm) REVERT: Dc 11 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: Fg 11 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: Kk 11 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: Po 11 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: Us 11 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: Hu 1 MET cc_start: 0.6176 (mpp) cc_final: 0.5591 (ptt) REVERT: Hu 11 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: P 7 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7335 (mtmp) REVERT: P 11 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: Gv 1 MET cc_start: 0.5868 (mpp) cc_final: 0.5536 (ptt) REVERT: Gv 11 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: Q 7 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7229 (mttp) REVERT: Q 11 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: Fw 11 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: R 1 MET cc_start: 0.6259 (mpm) cc_final: 0.5764 (mmm) REVERT: R 7 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7477 (mtmp) REVERT: R 11 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: S 11 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: Dy 7 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7109 (mtmp) REVERT: Dy 11 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: Cz 7 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7134 (mtmp) REVERT: Cz 11 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: 0 1 MET cc_start: 0.6133 (mpp) cc_final: 0.5874 (mmm) REVERT: 2 7 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7288 (mtmp) REVERT: 2 11 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6935 (mp0) outliers start: 121 outliers final: 22 residues processed: 629 average time/residue: 2.7973 time to fit residues: 2057.6996 Evaluate side-chains 618 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 535 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain J1 residue 11 GLU Chi-restraints excluded: chain Od residue 11 GLU Chi-restraints excluded: chain Tc residue 11 GLU Chi-restraints excluded: chain Ba residue 11 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 34 ASP Chi-restraints excluded: chain Id residue 3 GLU Chi-restraints excluded: chain Id residue 7 LYS Chi-restraints excluded: chain Id residue 11 GLU Chi-restraints excluded: chain Id residue 34 ASP Chi-restraints excluded: chain Nh residue 11 GLU Chi-restraints excluded: chain Sl residue 7 LYS Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain W residue 11 GLU Chi-restraints excluded: chain Ca residue 11 GLU Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain Mi residue 11 GLU Chi-restraints excluded: chain Wq residue 7 LYS Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Ae residue 3 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain Bb residue 11 GLU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU Chi-restraints excluded: chain Lj residue 34 ASP Chi-restraints excluded: chain Qn residue 11 GLU Chi-restraints excluded: chain Vr residue 11 GLU Chi-restraints excluded: chain Zt residue 1 MET Chi-restraints excluded: chain Zt residue 7 LYS Chi-restraints excluded: chain Zt residue 11 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Dc residue 11 GLU Chi-restraints excluded: chain Fg residue 11 GLU Chi-restraints excluded: chain Kk residue 11 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP Chi-restraints excluded: chain Us residue 1 MET Chi-restraints excluded: chain Us residue 11 GLU Chi-restraints excluded: chain Hu residue 11 GLU Chi-restraints excluded: chain Hu residue 34 ASP Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain Gv residue 3 GLU Chi-restraints excluded: chain Gv residue 11 GLU Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain Dy residue 7 LYS Chi-restraints excluded: chain Dy residue 11 GLU Chi-restraints excluded: chain Dy residue 34 ASP Chi-restraints excluded: chain Cz residue 7 LYS Chi-restraints excluded: chain Cz residue 11 GLU Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 2 residue 11 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 0.2980 chunk 185 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 294 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 24660 Z= 0.194 Angle : 0.490 4.087 32940 Z= 0.261 Chirality : 0.033 0.089 4080 Planarity : 0.002 0.008 4080 Dihedral : 8.653 89.832 3360 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 4.89 % Allowed : 10.76 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.16), residues: 3120 helix: 1.83 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.25 (0.67), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE M 45 TYR 0.010 0.002 TYR Q 8 ARG 0.001 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 623 time to evaluate : 3.866 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7671 (mtmm) cc_final: 0.7286 (mtmp) REVERT: A 11 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: F 7 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7371 (mtmp) REVERT: F 11 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: J1 7 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7181 (mtmm) REVERT: J1 11 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: Od 11 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: Tc 7 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7320 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: Ba 7 LYS cc_start: 0.7519 (mtmt) cc_final: 0.7195 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: B 11 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: G 11 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: L 7 LYS cc_start: 0.7776 (mtmm) cc_final: 0.7216 (mttp) REVERT: L 11 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: V 7 LYS cc_start: 0.7651 (mtmm) cc_final: 0.7241 (mtmp) REVERT: V 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: Z 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: Id 7 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7157 (mttp) REVERT: Id 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: Nh 7 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7389 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: Sl 7 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7470 (mttp) REVERT: Sl 11 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: Yb 11 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: C 11 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: H 7 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7224 (mtmp) REVERT: H 11 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: M 7 LYS cc_start: 0.7714 (mtmm) cc_final: 0.7284 (mtmm) REVERT: M 11 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: W 7 LYS cc_start: 0.7599 (mtmm) cc_final: 0.7213 (mtmm) REVERT: W 11 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: Ca 7 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7369 (mtmp) REVERT: Ca 11 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: He 7 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7296 (mtmp) REVERT: He 11 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: Mi 11 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: Wq 7 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7203 (mtmp) REVERT: Wq 11 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: Ae 7 LYS cc_start: 0.7607 (mtmm) cc_final: 0.7341 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: D 7 LYS cc_start: 0.7695 (mtmm) cc_final: 0.7089 (mtpt) REVERT: D 11 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: I 7 LYS cc_start: 0.7661 (mtmm) cc_final: 0.7281 (mtmp) REVERT: I 11 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: N 7 LYS cc_start: 0.7595 (mtmm) cc_final: 0.7178 (mtmp) REVERT: N 11 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: X 7 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7230 (mtmp) REVERT: X 11 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: Bb 11 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: Gf 7 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7159 (mtmp) REVERT: Gf 11 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: Lj 7 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7173 (mttp) REVERT: Lj 11 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: Qn 11 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: Vr 7 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7246 (mtmp) REVERT: Vr 11 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: Zt 7 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7378 (mtmp) REVERT: Zt 11 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: O 7 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7289 (mttp) REVERT: O 11 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: Y 7 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7202 (mttp) REVERT: Y 11 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: Dc 7 LYS cc_start: 0.7602 (mtmm) cc_final: 0.7198 (mtmp) REVERT: Dc 11 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: Fg 7 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7355 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: Kk 7 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7223 (mtmp) REVERT: Kk 11 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: Po 7 LYS cc_start: 0.7671 (mtmm) cc_final: 0.7222 (mtmm) REVERT: Po 11 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: Us 11 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: Hu 1 MET cc_start: 0.6288 (mpp) cc_final: 0.5476 (mmm) REVERT: Hu 7 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7247 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: P 7 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7281 (mtmp) REVERT: P 11 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: Gv 1 MET cc_start: 0.5650 (mpp) cc_final: 0.5395 (mmm) REVERT: Gv 11 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: Q 7 LYS cc_start: 0.7689 (mtmm) cc_final: 0.7269 (mttp) REVERT: Q 11 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: Fw 7 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7342 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: Ex 7 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7484 (mttp) REVERT: S 7 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7287 (mttp) REVERT: S 11 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: Dy 1 MET cc_start: 0.5919 (mmm) cc_final: 0.5542 (mtt) REVERT: Dy 7 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7203 (mtmp) REVERT: Dy 11 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: Cz 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: 2 7 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7245 (mttp) REVERT: 2 11 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6940 (mp0) outliers start: 129 outliers final: 33 residues processed: 673 average time/residue: 2.6632 time to fit residues: 2107.0255 Evaluate side-chains 637 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 543 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain J1 residue 11 GLU Chi-restraints excluded: chain Od residue 11 GLU Chi-restraints excluded: chain Tc residue 11 GLU Chi-restraints excluded: chain Ba residue 11 GLU Chi-restraints excluded: chain Ba residue 34 ASP Chi-restraints excluded: chain Ba residue 35 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 34 ASP Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Id residue 7 LYS Chi-restraints excluded: chain Id residue 11 GLU Chi-restraints excluded: chain Nh residue 11 GLU Chi-restraints excluded: chain Sl residue 7 LYS Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain W residue 11 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain Ca residue 7 LYS Chi-restraints excluded: chain Ca residue 11 GLU Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP Chi-restraints excluded: chain Mi residue 11 GLU Chi-restraints excluded: chain Wq residue 7 LYS Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Ae residue 3 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain Ae residue 35 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain Bb residue 11 GLU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU Chi-restraints excluded: chain Lj residue 34 ASP Chi-restraints excluded: chain Lj residue 35 VAL Chi-restraints excluded: chain Qn residue 11 GLU Chi-restraints excluded: chain Vr residue 11 GLU Chi-restraints excluded: chain Vr residue 35 VAL Chi-restraints excluded: chain Zt residue 1 MET Chi-restraints excluded: chain Zt residue 7 LYS Chi-restraints excluded: chain Zt residue 11 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Dc residue 11 GLU Chi-restraints excluded: chain Fg residue 11 GLU Chi-restraints excluded: chain Kk residue 11 GLU Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP Chi-restraints excluded: chain Us residue 11 GLU Chi-restraints excluded: chain Hu residue 11 GLU Chi-restraints excluded: chain Hu residue 34 ASP Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain Gv residue 11 GLU Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain Dy residue 7 LYS Chi-restraints excluded: chain Dy residue 11 GLU Chi-restraints excluded: chain Cz residue 11 GLU Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 2 residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 259 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24660 Z= 0.315 Angle : 0.572 5.854 32940 Z= 0.301 Chirality : 0.035 0.085 4080 Planarity : 0.002 0.013 4080 Dihedral : 7.395 89.324 3360 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 5.80 % Allowed : 15.76 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.15), residues: 3120 helix: 1.26 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.47 (0.66), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE 2 45 TYR 0.012 0.003 TYR V 8 ARG 0.001 0.000 ARG V 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 586 time to evaluate : 3.894 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7309 (mtmp) REVERT: A 11 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: F 7 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7383 (mtmp) REVERT: F 11 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: J1 7 LYS cc_start: 0.7745 (mtpt) cc_final: 0.7170 (mttp) REVERT: J1 11 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: Od 11 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: Tc 7 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7383 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: Ba 7 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7273 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: B 11 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: G 11 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: L 7 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7334 (mtmp) REVERT: L 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: V 7 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7282 (mtmp) REVERT: V 11 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: Z 11 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: Id 11 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: Nh 7 LYS cc_start: 0.7788 (mtmm) cc_final: 0.7298 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: Sl 7 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7318 (mttp) REVERT: Sl 11 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: Yb 11 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: C 7 LYS cc_start: 0.7726 (mtmm) cc_final: 0.7259 (mtmp) REVERT: C 11 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: H 7 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7239 (mtmp) REVERT: H 11 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: M 7 LYS cc_start: 0.7851 (mtmm) cc_final: 0.7418 (mtmm) REVERT: M 11 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: W 7 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7368 (mtmm) REVERT: W 11 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: Ca 11 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: He 7 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7408 (mtmp) REVERT: He 11 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: Mi 11 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: Wq 11 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: Ae 7 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7448 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: D 7 LYS cc_start: 0.7715 (mtmm) cc_final: 0.7154 (mtpt) REVERT: D 11 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: I 7 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7218 (mtpt) REVERT: I 11 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: N 7 LYS cc_start: 0.7653 (mtmm) cc_final: 0.7254 (mtmp) REVERT: N 11 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: Bb 7 LYS cc_start: 0.7514 (mttp) cc_final: 0.7308 (mttp) REVERT: Bb 11 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: Gf 7 LYS cc_start: 0.7766 (mtmm) cc_final: 0.7305 (mtmp) REVERT: Gf 11 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: Lj 11 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: Qn 7 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7108 (mtpt) REVERT: Qn 11 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: Vr 7 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7301 (mtpt) REVERT: Vr 11 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: Zt 11 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: O 7 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7304 (mttp) REVERT: O 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: Y 11 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: Dc 7 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7314 (mtmp) REVERT: Dc 11 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: Fg 7 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7420 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: Kk 2 MET cc_start: 0.7172 (mtp) cc_final: 0.6971 (mtp) REVERT: Po 7 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7261 (mtmp) REVERT: Po 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: Us 11 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: Hu 1 MET cc_start: 0.6338 (mpp) cc_final: 0.5558 (mmm) REVERT: Hu 7 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7269 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: P 7 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7292 (mtmp) REVERT: P 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: Gv 1 MET cc_start: 0.5845 (mpp) cc_final: 0.5448 (mtt) REVERT: Gv 11 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: Q 11 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: Fw 7 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7340 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: Ex 7 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7552 (mttp) REVERT: S 7 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7154 (mttp) REVERT: S 11 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: Dy 1 MET cc_start: 0.5969 (mmm) cc_final: 0.5611 (mtp) REVERT: Dy 11 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: Cz 7 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7198 (mttp) REVERT: Cz 11 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: 2 11 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6939 (mp0) outliers start: 153 outliers final: 60 residues processed: 659 average time/residue: 2.8417 time to fit residues: 2182.7129 Evaluate side-chains 683 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 570 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain J1 residue 11 GLU Chi-restraints excluded: chain Od residue 11 GLU Chi-restraints excluded: chain Tc residue 11 GLU Chi-restraints excluded: chain Ba residue 3 GLU Chi-restraints excluded: chain Ba residue 11 GLU Chi-restraints excluded: chain Ba residue 34 ASP Chi-restraints excluded: chain Ba residue 35 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 34 ASP Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Id residue 3 GLU Chi-restraints excluded: chain Id residue 11 GLU Chi-restraints excluded: chain Id residue 34 ASP Chi-restraints excluded: chain Nh residue 11 GLU Chi-restraints excluded: chain Sl residue 7 LYS Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Xp residue 41 LEU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain W residue 11 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain Ca residue 11 GLU Chi-restraints excluded: chain Ca residue 35 VAL Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP Chi-restraints excluded: chain Mi residue 11 GLU Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Wq residue 34 ASP Chi-restraints excluded: chain Ae residue 3 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain Ae residue 35 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain Bb residue 11 GLU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 11 GLU Chi-restraints excluded: chain Lj residue 34 ASP Chi-restraints excluded: chain Lj residue 35 VAL Chi-restraints excluded: chain Qn residue 7 LYS Chi-restraints excluded: chain Qn residue 11 GLU Chi-restraints excluded: chain Qn residue 34 ASP Chi-restraints excluded: chain Vr residue 11 GLU Chi-restraints excluded: chain Vr residue 34 ASP Chi-restraints excluded: chain Vr residue 35 VAL Chi-restraints excluded: chain Zt residue 1 MET Chi-restraints excluded: chain Zt residue 11 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Dc residue 11 GLU Chi-restraints excluded: chain Dc residue 35 VAL Chi-restraints excluded: chain Fg residue 11 GLU Chi-restraints excluded: chain Kk residue 3 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP Chi-restraints excluded: chain Us residue 11 GLU Chi-restraints excluded: chain Hu residue 11 GLU Chi-restraints excluded: chain Hu residue 34 ASP Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Gv residue 3 GLU Chi-restraints excluded: chain Gv residue 11 GLU Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain Dy residue 11 GLU Chi-restraints excluded: chain Dy residue 34 ASP Chi-restraints excluded: chain Cz residue 7 LYS Chi-restraints excluded: chain Cz residue 11 GLU Chi-restraints excluded: chain Cz residue 34 ASP Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 2 residue 11 GLU Chi-restraints excluded: chain 2 residue 34 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 24660 Z= 0.314 Angle : 0.557 6.042 32940 Z= 0.295 Chirality : 0.035 0.081 4080 Planarity : 0.002 0.010 4080 Dihedral : 6.504 89.739 3360 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 6.78 % Allowed : 17.27 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.15), residues: 3120 helix: 1.12 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.60 (0.63), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE 2 45 TYR 0.010 0.002 TYRZt 8 ARG 0.001 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 587 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7329 (mtmp) REVERT: A 11 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: F 7 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7395 (mtmp) REVERT: F 11 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: J1 3 GLU cc_start: 0.7026 (tp30) cc_final: 0.6719 (tp30) REVERT: J1 7 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7247 (mttp) REVERT: J1 11 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: Od 11 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: Tc 7 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7367 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: Ba 7 LYS cc_start: 0.7697 (mtmt) cc_final: 0.7372 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 7 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7246 (mttp) REVERT: B 11 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: G 11 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: L 7 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7364 (mtmp) REVERT: L 11 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: V 7 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7253 (mtmp) REVERT: V 11 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: Z 11 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: Id 1 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5272 (mmm) REVERT: Id 7 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7187 (mttp) REVERT: Id 11 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: Nh 7 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7275 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: Sl 11 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: Xp 11 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: Yb 11 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: C 7 LYS cc_start: 0.7783 (mtmm) cc_final: 0.7314 (mtmp) REVERT: C 11 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: H 11 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: M 7 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7496 (mtmm) REVERT: M 11 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: W 7 LYS cc_start: 0.7750 (mtmm) cc_final: 0.7390 (mtmm) REVERT: W 11 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: Ca 11 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: He 2 MET cc_start: 0.7212 (mtp) cc_final: 0.6725 (ttm) REVERT: He 11 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: Mi 11 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: Wq 11 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: Ae 7 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7504 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: D 7 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7241 (mtpt) REVERT: D 11 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: I 7 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7255 (mtpt) REVERT: I 11 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: N 7 LYS cc_start: 0.7634 (mtmm) cc_final: 0.7214 (mtmp) REVERT: N 11 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: X 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: Bb 7 LYS cc_start: 0.7533 (mttp) cc_final: 0.7322 (mttp) REVERT: Bb 11 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: Gf 7 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7357 (mttp) REVERT: Gf 11 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: Lj 11 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: Qn 1 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5910 (ptp) REVERT: Qn 7 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7167 (mttp) REVERT: Qn 11 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: Vr 7 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7732 (mtmp) REVERT: Zt 11 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: O 7 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7137 (mttp) REVERT: O 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: Y 7 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7243 (mttp) REVERT: Y 11 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: Dc 7 LYS cc_start: 0.7744 (mtmm) cc_final: 0.7343 (mttp) REVERT: Dc 11 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: Fg 7 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7440 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: Kk 7 LYS cc_start: 0.7924 (mtmp) cc_final: 0.7474 (mtpt) REVERT: Kk 11 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: Po 7 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7251 (mtpt) REVERT: Po 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: Us 1 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.5503 (mmm) REVERT: Us 11 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: Hu 1 MET cc_start: 0.6285 (mpp) cc_final: 0.5775 (mmm) REVERT: Hu 7 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7330 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: P 7 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7320 (mtmp) REVERT: P 11 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: Gv 1 MET cc_start: 0.5807 (mpp) cc_final: 0.5448 (mtt) REVERT: Gv 7 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7255 (mttp) REVERT: Gv 11 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: Q 1 MET cc_start: 0.5748 (OUTLIER) cc_final: 0.5353 (mmm) REVERT: Q 11 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: Fw 7 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7354 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: R 7 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7400 (mtmm) REVERT: R 11 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: S 7 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7205 (mttp) REVERT: S 11 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: Dy 7 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7229 (mttp) REVERT: Dy 11 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: Cz 7 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7257 (mttp) REVERT: Cz 11 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: 2 7 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7332 (mttp) REVERT: 2 11 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6971 (mp0) outliers start: 179 outliers final: 79 residues processed: 663 average time/residue: 2.9088 time to fit residues: 2251.6928 Evaluate side-chains 721 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 576 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain J1 residue 11 GLU Chi-restraints excluded: chain Od residue 11 GLU Chi-restraints excluded: chain Tc residue 11 GLU Chi-restraints excluded: chain Tc residue 41 LEU Chi-restraints excluded: chain Ba residue 3 GLU Chi-restraints excluded: chain Ba residue 11 GLU Chi-restraints excluded: chain Ba residue 34 ASP Chi-restraints excluded: chain Ba residue 35 VAL Chi-restraints excluded: chain Ba residue 41 LEU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 34 ASP Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Id residue 1 MET Chi-restraints excluded: chain Id residue 3 GLU Chi-restraints excluded: chain Id residue 7 LYS Chi-restraints excluded: chain Id residue 11 GLU Chi-restraints excluded: chain Id residue 34 ASP Chi-restraints excluded: chain Nh residue 11 GLU Chi-restraints excluded: chain Nh residue 41 LEU Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Xp residue 11 GLU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain M residue 3 GLU Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain W residue 11 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain Ca residue 11 GLU Chi-restraints excluded: chain Ca residue 35 VAL Chi-restraints excluded: chain Ca residue 41 LEU Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP Chi-restraints excluded: chain Mi residue 11 GLU Chi-restraints excluded: chain Rm residue 3 GLU Chi-restraints excluded: chain Rm residue 41 LEU Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Wq residue 34 ASP Chi-restraints excluded: chain Ae residue 3 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain Ae residue 35 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain Bb residue 11 GLU Chi-restraints excluded: chain Bb residue 41 LEU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 11 GLU Chi-restraints excluded: chain Lj residue 34 ASP Chi-restraints excluded: chain Lj residue 35 VAL Chi-restraints excluded: chain Qn residue 1 MET Chi-restraints excluded: chain Qn residue 7 LYS Chi-restraints excluded: chain Qn residue 11 GLU Chi-restraints excluded: chain Qn residue 34 ASP Chi-restraints excluded: chain Vr residue 34 ASP Chi-restraints excluded: chain Vr residue 35 VAL Chi-restraints excluded: chain Zt residue 1 MET Chi-restraints excluded: chain Zt residue 7 LYS Chi-restraints excluded: chain Zt residue 11 GLU Chi-restraints excluded: chain Zt residue 41 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Dc residue 11 GLU Chi-restraints excluded: chain Dc residue 35 VAL Chi-restraints excluded: chain Fg residue 11 GLU Chi-restraints excluded: chain Fg residue 41 LEU Chi-restraints excluded: chain Kk residue 3 GLU Chi-restraints excluded: chain Kk residue 11 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP Chi-restraints excluded: chain Us residue 1 MET Chi-restraints excluded: chain Us residue 11 GLU Chi-restraints excluded: chain Hu residue 11 GLU Chi-restraints excluded: chain Hu residue 34 ASP Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Gv residue 3 GLU Chi-restraints excluded: chain Gv residue 7 LYS Chi-restraints excluded: chain Gv residue 11 GLU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain Fw residue 41 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain Dy residue 7 LYS Chi-restraints excluded: chain Dy residue 11 GLU Chi-restraints excluded: chain Dy residue 34 ASP Chi-restraints excluded: chain Cz residue 3 GLU Chi-restraints excluded: chain Cz residue 7 LYS Chi-restraints excluded: chain Cz residue 11 GLU Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 2 residue 11 GLU Chi-restraints excluded: chain 2 residue 34 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 24660 Z= 0.240 Angle : 0.495 5.270 32940 Z= 0.266 Chirality : 0.033 0.084 4080 Planarity : 0.002 0.007 4080 Dihedral : 5.682 89.133 3360 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 6.40 % Allowed : 18.14 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.15), residues: 3120 helix: 1.39 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.46 (0.62), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE Z 45 TYR 0.009 0.002 TYRHu 8 ARG 0.001 0.000 ARGYb 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 611 time to evaluate : 4.118 Fit side-chains REVERT: A 7 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7315 (mtmp) REVERT: A 11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: F 7 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7399 (mtmp) REVERT: F 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: K 11 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: J1 3 GLU cc_start: 0.7044 (tp30) cc_final: 0.6838 (tp30) REVERT: J1 7 LYS cc_start: 0.7765 (mtpt) cc_final: 0.7334 (mtmm) REVERT: J1 11 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: Od 11 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: Tc 7 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7385 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: Ba 7 LYS cc_start: 0.7677 (mtmt) cc_final: 0.7371 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: B 7 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7252 (mttp) REVERT: B 11 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: G 11 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: L 7 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7375 (mtmp) REVERT: L 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: V 7 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7302 (mtmp) REVERT: V 11 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: Z 7 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7386 (mtmp) REVERT: Z 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: Id 1 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5483 (mmm) REVERT: Id 7 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7166 (mttp) REVERT: Id 11 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: Nh 7 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7278 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: Sl 7 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7353 (mttp) REVERT: Sl 11 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: Yb 11 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: C 7 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7340 (mtmp) REVERT: C 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: H 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: M 7 LYS cc_start: 0.7799 (mtmm) cc_final: 0.7481 (mtmm) REVERT: M 11 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: W 7 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7431 (mtmm) REVERT: W 11 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: Ca 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: He 2 MET cc_start: 0.7158 (mtp) cc_final: 0.6746 (ttm) REVERT: He 7 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7400 (mtmp) REVERT: He 11 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: Mi 11 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: Wq 7 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7276 (mttp) REVERT: Wq 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: Ae 7 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7502 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: D 7 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7183 (mttp) REVERT: D 11 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: I 7 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7294 (mtmp) REVERT: I 11 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: N 7 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7329 (mtmp) REVERT: N 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: Bb 7 LYS cc_start: 0.7526 (mttp) cc_final: 0.7326 (mttp) REVERT: Bb 11 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: Gf 7 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7370 (mttp) REVERT: Gf 11 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: Lj 7 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7250 (mttp) REVERT: Lj 11 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: Qn 7 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7172 (mttp) REVERT: Qn 11 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: Vr 7 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7480 (mtpt) REVERT: Vr 11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: Zt 11 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: E 11 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: O 7 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7207 (mttp) REVERT: O 11 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: Y 7 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7235 (mttp) REVERT: Y 11 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: Dc 7 LYS cc_start: 0.7695 (mtmm) cc_final: 0.7373 (mttp) REVERT: Dc 11 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: Fg 7 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7446 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: Po 7 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7297 (mtpt) REVERT: Po 11 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: Us 11 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: Hu 1 MET cc_start: 0.6228 (mpp) cc_final: 0.5685 (mmm) REVERT: Hu 7 LYS cc_start: 0.7799 (mtmm) cc_final: 0.7439 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: P 7 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7322 (mtmp) REVERT: P 11 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: Gv 1 MET cc_start: 0.5874 (mpp) cc_final: 0.5446 (mtt) REVERT: Gv 11 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: Q 1 MET cc_start: 0.5539 (OUTLIER) cc_final: 0.5273 (mmm) REVERT: Q 11 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: Fw 7 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7321 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: R 7 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7588 (mtpt) REVERT: Ex 11 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: S 7 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7273 (mttp) REVERT: S 11 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: Dy 7 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7232 (mttp) REVERT: Dy 11 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: Cz 7 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7237 (mttp) REVERT: Cz 11 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: 0 11 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: 2 7 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7171 (mttp) REVERT: 2 11 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6940 (mp0) outliers start: 169 outliers final: 78 residues processed: 689 average time/residue: 2.7766 time to fit residues: 2235.2024 Evaluate side-chains 760 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 614 time to evaluate : 4.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain J1 residue 11 GLU Chi-restraints excluded: chain Od residue 11 GLU Chi-restraints excluded: chain Tc residue 11 GLU Chi-restraints excluded: chain Tc residue 41 LEU Chi-restraints excluded: chain Ba residue 3 GLU Chi-restraints excluded: chain Ba residue 11 GLU Chi-restraints excluded: chain Ba residue 34 ASP Chi-restraints excluded: chain Ba residue 35 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 34 ASP Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Id residue 1 MET Chi-restraints excluded: chain Id residue 3 GLU Chi-restraints excluded: chain Id residue 7 LYS Chi-restraints excluded: chain Id residue 11 GLU Chi-restraints excluded: chain Nh residue 11 GLU Chi-restraints excluded: chain Nh residue 41 LEU Chi-restraints excluded: chain Sl residue 7 LYS Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Xp residue 41 LEU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain M residue 3 GLU Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain W residue 11 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain Ca residue 11 GLU Chi-restraints excluded: chain Ca residue 35 VAL Chi-restraints excluded: chain Ca residue 41 LEU Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP Chi-restraints excluded: chain Mi residue 11 GLU Chi-restraints excluded: chain Mi residue 41 LEU Chi-restraints excluded: chain Rm residue 41 LEU Chi-restraints excluded: chain Wq residue 7 LYS Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Wq residue 34 ASP Chi-restraints excluded: chain Ae residue 3 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain Ae residue 35 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 41 LEU Chi-restraints excluded: chain Bb residue 11 GLU Chi-restraints excluded: chain Bb residue 41 LEU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU Chi-restraints excluded: chain Lj residue 34 ASP Chi-restraints excluded: chain Lj residue 35 VAL Chi-restraints excluded: chain Qn residue 7 LYS Chi-restraints excluded: chain Qn residue 11 GLU Chi-restraints excluded: chain Qn residue 34 ASP Chi-restraints excluded: chain Vr residue 11 GLU Chi-restraints excluded: chain Vr residue 34 ASP Chi-restraints excluded: chain Vr residue 35 VAL Chi-restraints excluded: chain Vr residue 41 LEU Chi-restraints excluded: chain Zt residue 1 MET Chi-restraints excluded: chain Zt residue 7 LYS Chi-restraints excluded: chain Zt residue 11 GLU Chi-restraints excluded: chain Zt residue 41 LEU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Dc residue 11 GLU Chi-restraints excluded: chain Dc residue 35 VAL Chi-restraints excluded: chain Fg residue 11 GLU Chi-restraints excluded: chain Kk residue 3 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Kk residue 41 LEU Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP Chi-restraints excluded: chain Po residue 41 LEU Chi-restraints excluded: chain Us residue 3 GLU Chi-restraints excluded: chain Us residue 11 GLU Chi-restraints excluded: chain Hu residue 11 GLU Chi-restraints excluded: chain Hu residue 34 ASP Chi-restraints excluded: chain Hu residue 41 LEU Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Gv residue 11 GLU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain Ex residue 11 GLU Chi-restraints excluded: chain Ex residue 41 LEU Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain Dy residue 3 GLU Chi-restraints excluded: chain Dy residue 7 LYS Chi-restraints excluded: chain Dy residue 11 GLU Chi-restraints excluded: chain Cz residue 3 GLU Chi-restraints excluded: chain Cz residue 7 LYS Chi-restraints excluded: chain Cz residue 11 GLU Chi-restraints excluded: chain 0 residue 11 GLU Chi-restraints excluded: chain 0 residue 41 LEU Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 2 residue 11 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 289 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 24660 Z= 0.275 Angle : 0.527 5.720 32940 Z= 0.279 Chirality : 0.034 0.082 4080 Planarity : 0.002 0.009 4080 Dihedral : 5.089 86.694 3360 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 7.12 % Allowed : 17.99 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.15), residues: 3120 helix: 1.32 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.37 (0.62), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE N 45 TYR 0.009 0.002 TYR V 8 ARG 0.001 0.000 ARGMi 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 602 time to evaluate : 4.559 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7238 (mtmp) REVERT: A 11 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: F 7 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7427 (mtmp) REVERT: F 11 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: K 11 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: J1 7 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7375 (mttp) REVERT: J1 11 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: Od 11 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: Tc 7 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7399 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: Ba 7 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7391 (mtpt) REVERT: Ba 11 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: B 7 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7243 (mttp) REVERT: B 11 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: G 11 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: L 7 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7354 (mtmp) REVERT: L 11 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: V 7 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7278 (mtmp) REVERT: V 11 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: Z 7 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7449 (mtmp) REVERT: Z 11 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: Id 1 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5549 (mmm) REVERT: Id 7 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7169 (mttp) REVERT: Id 11 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: Nh 7 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7225 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: Sl 7 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7299 (mttp) REVERT: Sl 11 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: Yb 11 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: C 7 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7438 (mtmp) REVERT: C 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: H 11 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: M 7 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7503 (mtmm) REVERT: M 11 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: W 7 LYS cc_start: 0.7735 (mtmm) cc_final: 0.7419 (mtmm) REVERT: W 11 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: Ca 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: He 2 MET cc_start: 0.7185 (mtp) cc_final: 0.6782 (ttm) REVERT: He 7 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7451 (mttp) REVERT: He 11 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: Mi 11 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: Wq 7 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7152 (mtpt) REVERT: Wq 11 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: Ae 7 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7541 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: D 7 LYS cc_start: 0.7725 (mtmm) cc_final: 0.7204 (mttp) REVERT: D 11 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: I 7 LYS cc_start: 0.7652 (mtmm) cc_final: 0.7250 (mtmp) REVERT: I 11 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: N 7 LYS cc_start: 0.7632 (mtmm) cc_final: 0.7362 (mtmp) REVERT: N 11 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: X 7 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7369 (mtpt) REVERT: X 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: Bb 7 LYS cc_start: 0.7528 (mttp) cc_final: 0.7323 (mttp) REVERT: Bb 11 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: Gf 7 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7411 (mttp) REVERT: Gf 11 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: Lj 7 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7259 (mttm) REVERT: Lj 11 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: Qn 1 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.5926 (ptp) REVERT: Qn 7 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7219 (mttp) REVERT: Qn 11 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: Zt 11 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: E 11 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: O 7 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7217 (mttp) REVERT: O 11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: Y 7 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7253 (mttp) REVERT: Y 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: Dc 7 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7379 (mttp) REVERT: Dc 11 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: Fg 7 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7388 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: Kk 11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: Po 7 LYS cc_start: 0.7766 (mtmm) cc_final: 0.7299 (mtpt) REVERT: Po 11 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: Us 11 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: Hu 1 MET cc_start: 0.6201 (mpp) cc_final: 0.5672 (mmm) REVERT: Hu 7 LYS cc_start: 0.7750 (mtmm) cc_final: 0.7364 (mtpt) REVERT: Hu 11 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: P 7 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7332 (mtmp) REVERT: P 11 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: Gv 1 MET cc_start: 0.5858 (mpp) cc_final: 0.5410 (mtt) REVERT: Gv 7 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7274 (mttp) REVERT: Gv 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: Q 1 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5167 (mmm) REVERT: Q 11 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: Fw 7 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7363 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: R 1 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.5641 (mmm) REVERT: R 7 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7364 (mtpt) REVERT: R 11 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: Ex 11 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: S 7 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7313 (mttp) REVERT: S 11 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: Dy 7 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7246 (mttp) REVERT: Dy 11 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: T 11 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: Cz 7 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7253 (mttp) REVERT: Cz 11 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: 0 11 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: 2 7 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7272 (mttp) REVERT: 2 11 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6951 (mp0) outliers start: 188 outliers final: 98 residues processed: 687 average time/residue: 2.8308 time to fit residues: 2275.9149 Evaluate side-chains 772 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 599 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain J1 residue 11 GLU Chi-restraints excluded: chain Od residue 11 GLU Chi-restraints excluded: chain Tc residue 11 GLU Chi-restraints excluded: chain Tc residue 41 LEU Chi-restraints excluded: chain Ba residue 3 GLU Chi-restraints excluded: chain Ba residue 11 GLU Chi-restraints excluded: chain Ba residue 34 ASP Chi-restraints excluded: chain Ba residue 35 VAL Chi-restraints excluded: chain Ba residue 41 LEU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 34 ASP Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Id residue 1 MET Chi-restraints excluded: chain Id residue 3 GLU Chi-restraints excluded: chain Id residue 7 LYS Chi-restraints excluded: chain Id residue 11 GLU Chi-restraints excluded: chain Nh residue 11 GLU Chi-restraints excluded: chain Nh residue 41 LEU Chi-restraints excluded: chain Sl residue 7 LYS Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Sl residue 41 LEU Chi-restraints excluded: chain Xp residue 41 LEU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain M residue 3 GLU Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain W residue 11 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain Ca residue 7 LYS Chi-restraints excluded: chain Ca residue 11 GLU Chi-restraints excluded: chain Ca residue 35 VAL Chi-restraints excluded: chain Ca residue 41 LEU Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP Chi-restraints excluded: chain He residue 41 LEU Chi-restraints excluded: chain Mi residue 11 GLU Chi-restraints excluded: chain Mi residue 41 LEU Chi-restraints excluded: chain Rm residue 41 LEU Chi-restraints excluded: chain Wq residue 7 LYS Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Wq residue 34 ASP Chi-restraints excluded: chain Ae residue 3 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain Ae residue 35 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 41 LEU Chi-restraints excluded: chain Bb residue 11 GLU Chi-restraints excluded: chain Bb residue 41 LEU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU Chi-restraints excluded: chain Lj residue 34 ASP Chi-restraints excluded: chain Lj residue 35 VAL Chi-restraints excluded: chain Qn residue 1 MET Chi-restraints excluded: chain Qn residue 7 LYS Chi-restraints excluded: chain Qn residue 11 GLU Chi-restraints excluded: chain Qn residue 34 ASP Chi-restraints excluded: chain Vr residue 34 ASP Chi-restraints excluded: chain Vr residue 35 VAL Chi-restraints excluded: chain Vr residue 41 LEU Chi-restraints excluded: chain Zt residue 1 MET Chi-restraints excluded: chain Zt residue 7 LYS Chi-restraints excluded: chain Zt residue 11 GLU Chi-restraints excluded: chain Zt residue 41 LEU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Dc residue 11 GLU Chi-restraints excluded: chain Dc residue 35 VAL Chi-restraints excluded: chain Dc residue 41 LEU Chi-restraints excluded: chain Fg residue 11 GLU Chi-restraints excluded: chain Fg residue 41 LEU Chi-restraints excluded: chain Kk residue 3 GLU Chi-restraints excluded: chain Kk residue 7 LYS Chi-restraints excluded: chain Kk residue 11 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Kk residue 41 LEU Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP Chi-restraints excluded: chain Po residue 41 LEU Chi-restraints excluded: chain Us residue 3 GLU Chi-restraints excluded: chain Us residue 11 GLU Chi-restraints excluded: chain Hu residue 11 GLU Chi-restraints excluded: chain Hu residue 34 ASP Chi-restraints excluded: chain Hu residue 41 LEU Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Gv residue 3 GLU Chi-restraints excluded: chain Gv residue 7 LYS Chi-restraints excluded: chain Gv residue 11 GLU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain Fw residue 41 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain Ex residue 11 GLU Chi-restraints excluded: chain Ex residue 41 LEU Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain Dy residue 3 GLU Chi-restraints excluded: chain Dy residue 7 LYS Chi-restraints excluded: chain Dy residue 11 GLU Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain Cz residue 3 GLU Chi-restraints excluded: chain Cz residue 7 LYS Chi-restraints excluded: chain Cz residue 11 GLU Chi-restraints excluded: chain 0 residue 11 GLU Chi-restraints excluded: chain 0 residue 41 LEU Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 2 residue 11 GLU Chi-restraints excluded: chain 2 residue 34 ASP Chi-restraints excluded: chain 2 residue 41 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24660 Z= 0.200 Angle : 0.459 5.730 32940 Z= 0.249 Chirality : 0.033 0.085 4080 Planarity : 0.001 0.018 4080 Dihedral : 4.560 87.445 3360 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 5.30 % Allowed : 20.27 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.15), residues: 3120 helix: 1.64 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.14 (0.62), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE N 45 TYR 0.009 0.002 TYRVr 8 ARG 0.001 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 617 time to evaluate : 3.942 Fit side-chains REVERT: A 7 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7227 (mtmp) REVERT: A 11 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: F 7 LYS cc_start: 0.7790 (mtmm) cc_final: 0.7328 (mtmp) REVERT: F 11 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: K 11 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: J1 7 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7325 (mtmm) REVERT: J1 11 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: Od 11 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: Tc 7 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7427 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: B 7 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7320 (mttp) REVERT: B 11 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: G 11 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: L 7 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7356 (mtmp) REVERT: L 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: V 7 LYS cc_start: 0.7689 (mtmm) cc_final: 0.7237 (mtmp) REVERT: V 11 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: Z 7 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7438 (mtmp) REVERT: Z 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: Id 7 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7144 (mttp) REVERT: Id 11 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: Nh 7 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7356 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: Sl 7 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7257 (mttp) REVERT: Sl 11 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: Yb 11 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: C 7 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7393 (mtmp) REVERT: C 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: H 11 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: M 7 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7398 (mttp) REVERT: M 11 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: W 7 LYS cc_start: 0.7687 (mtmm) cc_final: 0.7420 (mtmm) REVERT: W 11 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: Ca 11 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: He 2 MET cc_start: 0.7159 (mtp) cc_final: 0.6791 (ttm) REVERT: He 7 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7477 (mttp) REVERT: He 11 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: Mi 11 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: Wq 7 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7249 (mttp) REVERT: Wq 11 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: Ae 7 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7518 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: D 7 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7218 (mttp) REVERT: D 11 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: I 7 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7194 (mttp) REVERT: I 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: N 7 LYS cc_start: 0.7597 (mtmm) cc_final: 0.7384 (mtmp) REVERT: N 11 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: X 7 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7368 (mtpt) REVERT: X 11 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: Bb 11 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: Gf 7 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7428 (mttp) REVERT: Gf 11 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: Lj 7 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7289 (mttp) REVERT: Lj 11 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: Qn 1 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5919 (ptp) REVERT: Qn 7 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7188 (mttp) REVERT: Qn 11 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: Vr 7 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7449 (mtmp) REVERT: Vr 11 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: Zt 11 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: E 11 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: O 7 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7305 (mttp) REVERT: O 11 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: Y 7 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7213 (mttp) REVERT: Y 11 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: Dc 7 LYS cc_start: 0.7634 (mtmm) cc_final: 0.7377 (mttp) REVERT: Dc 11 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: Fg 7 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7363 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: Kk 11 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: Po 7 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7454 (mttp) REVERT: Po 11 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: Us 11 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: Hu 1 MET cc_start: 0.6184 (mpp) cc_final: 0.5551 (mmm) REVERT: Hu 7 LYS cc_start: 0.7764 (mtmm) cc_final: 0.7429 (mtpt) REVERT: Hu 11 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: P 7 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7278 (mtmp) REVERT: P 11 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: Gv 1 MET cc_start: 0.5866 (mpp) cc_final: 0.5382 (mtt) REVERT: Gv 7 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7307 (mttp) REVERT: Gv 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: Q 1 MET cc_start: 0.5663 (OUTLIER) cc_final: 0.5129 (mmm) REVERT: Q 11 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: Fw 7 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7338 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: R 1 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.5894 (mmm) REVERT: R 7 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7312 (mtpt) REVERT: R 11 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: Ex 11 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: S 7 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7251 (mttm) REVERT: S 11 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: Dy 7 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7195 (mttp) REVERT: Dy 11 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: T 11 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: Cz 7 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7265 (mttp) REVERT: Cz 11 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: 0 11 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: 2 7 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7364 (mttp) REVERT: 2 11 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6974 (mp0) outliers start: 140 outliers final: 55 residues processed: 680 average time/residue: 2.9213 time to fit residues: 2347.9569 Evaluate side-chains 744 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 615 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain J1 residue 11 GLU Chi-restraints excluded: chain Od residue 11 GLU Chi-restraints excluded: chain Tc residue 11 GLU Chi-restraints excluded: chain Ba residue 41 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 34 ASP Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Id residue 7 LYS Chi-restraints excluded: chain Id residue 11 GLU Chi-restraints excluded: chain Nh residue 11 GLU Chi-restraints excluded: chain Sl residue 7 LYS Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Sl residue 41 LEU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain W residue 11 GLU Chi-restraints excluded: chain Ca residue 7 LYS Chi-restraints excluded: chain Ca residue 11 GLU Chi-restraints excluded: chain Ca residue 35 VAL Chi-restraints excluded: chain Ca residue 41 LEU Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP Chi-restraints excluded: chain Mi residue 11 GLU Chi-restraints excluded: chain Mi residue 41 LEU Chi-restraints excluded: chain Wq residue 7 LYS Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Ae residue 3 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 41 LEU Chi-restraints excluded: chain Bb residue 11 GLU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU Chi-restraints excluded: chain Lj residue 35 VAL Chi-restraints excluded: chain Qn residue 1 MET Chi-restraints excluded: chain Qn residue 7 LYS Chi-restraints excluded: chain Qn residue 11 GLU Chi-restraints excluded: chain Vr residue 11 GLU Chi-restraints excluded: chain Vr residue 34 ASP Chi-restraints excluded: chain Vr residue 41 LEU Chi-restraints excluded: chain Zt residue 1 MET Chi-restraints excluded: chain Zt residue 7 LYS Chi-restraints excluded: chain Zt residue 11 GLU Chi-restraints excluded: chain Zt residue 41 LEU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Dc residue 11 GLU Chi-restraints excluded: chain Fg residue 11 GLU Chi-restraints excluded: chain Fg residue 41 LEU Chi-restraints excluded: chain Kk residue 7 LYS Chi-restraints excluded: chain Kk residue 11 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Kk residue 41 LEU Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP Chi-restraints excluded: chain Po residue 41 LEU Chi-restraints excluded: chain Us residue 11 GLU Chi-restraints excluded: chain Hu residue 11 GLU Chi-restraints excluded: chain Hu residue 34 ASP Chi-restraints excluded: chain Hu residue 41 LEU Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Gv residue 7 LYS Chi-restraints excluded: chain Gv residue 11 GLU Chi-restraints excluded: chain Gv residue 41 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain Fw residue 41 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain Ex residue 11 GLU Chi-restraints excluded: chain Ex residue 41 LEU Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain Dy residue 7 LYS Chi-restraints excluded: chain Dy residue 11 GLU Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain Cz residue 7 LYS Chi-restraints excluded: chain Cz residue 11 GLU Chi-restraints excluded: chain 0 residue 11 GLU Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 2 residue 11 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 24660 Z= 0.241 Angle : 0.493 5.156 32940 Z= 0.263 Chirality : 0.034 0.083 4080 Planarity : 0.002 0.009 4080 Dihedral : 4.352 86.190 3360 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.33 % Allowed : 19.55 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.15), residues: 3120 helix: 1.55 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.11 (0.62), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE N 45 TYR 0.009 0.002 TYRBa 8 ARG 0.001 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 599 time to evaluate : 4.329 Fit side-chains REVERT: A 7 LYS cc_start: 0.7721 (mtmm) cc_final: 0.7246 (mtmp) REVERT: A 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: F 7 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7333 (mtmp) REVERT: F 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: K 11 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: U 11 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: J1 7 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7395 (mtmm) REVERT: J1 11 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: Od 11 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: Tc 7 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7449 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: Ba 7 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7435 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: B 7 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7268 (mttp) REVERT: B 11 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: G 11 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: L 7 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7374 (mtmp) REVERT: L 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: V 7 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7256 (mtmp) REVERT: V 11 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: Z 7 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7382 (mtmp) REVERT: Z 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: Id 7 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7162 (mttp) REVERT: Id 11 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: Nh 7 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7336 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: Sl 7 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7329 (mttp) REVERT: Sl 11 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: Yb 11 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: C 7 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7426 (mtmp) REVERT: C 11 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: H 7 LYS cc_start: 0.7761 (mtmm) cc_final: 0.7459 (mttp) REVERT: H 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: M 7 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7420 (mttp) REVERT: M 11 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: W 7 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7411 (mtmm) REVERT: W 11 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: Ca 11 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: He 1 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.5820 (ptp) REVERT: He 2 MET cc_start: 0.7174 (mtp) cc_final: 0.6812 (ttm) REVERT: He 7 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7483 (mttp) REVERT: He 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: Mi 11 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: Rm 11 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: Wq 7 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7264 (mttp) REVERT: Wq 11 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: Ae 7 LYS cc_start: 0.7794 (mtmm) cc_final: 0.7539 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: D 7 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7222 (mttp) REVERT: D 11 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: I 7 LYS cc_start: 0.7622 (mtmm) cc_final: 0.7205 (mttp) REVERT: I 11 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: N 11 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: X 7 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7415 (mtpt) REVERT: X 11 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: Bb 11 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: Gf 7 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7431 (mttp) REVERT: Gf 11 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: Lj 7 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7329 (mttp) REVERT: Lj 11 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: Qn 1 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5932 (ptp) REVERT: Qn 7 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7225 (mttp) REVERT: Qn 11 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: Vr 7 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7459 (mtmp) REVERT: Vr 11 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: Zt 1 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.5634 (ptp) REVERT: Zt 11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: E 11 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: J 11 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: O 7 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7245 (mttp) REVERT: O 11 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: Y 7 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7235 (mttp) REVERT: Y 11 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: Dc 7 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7444 (mttp) REVERT: Dc 11 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: Fg 7 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7393 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: Kk 11 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: Po 7 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7467 (mttp) REVERT: Po 11 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: Us 11 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: Hu 1 MET cc_start: 0.6187 (mpp) cc_final: 0.5565 (mmm) REVERT: Hu 7 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7403 (mtpt) REVERT: Hu 11 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: P 7 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7300 (mtmp) REVERT: P 11 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: Gv 1 MET cc_start: 0.5831 (mpp) cc_final: 0.5398 (mtt) REVERT: Gv 7 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7283 (mttp) REVERT: Gv 11 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: Q 1 MET cc_start: 0.5631 (OUTLIER) cc_final: 0.5280 (mmm) REVERT: Q 11 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: Fw 7 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7363 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: R 1 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.5307 (ptt) REVERT: R 7 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7359 (mtpt) REVERT: R 11 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: Ex 11 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: S 7 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7246 (mttp) REVERT: S 11 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: Dy 7 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7213 (mttp) REVERT: Dy 11 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: T 11 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: Cz 7 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7275 (mttp) REVERT: Cz 11 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: 0 11 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: 2 7 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7149 (mttp) REVERT: 2 11 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6996 (mp0) outliers start: 167 outliers final: 80 residues processed: 680 average time/residue: 2.7490 time to fit residues: 2186.1554 Evaluate side-chains 760 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 600 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain J1 residue 11 GLU Chi-restraints excluded: chain Od residue 11 GLU Chi-restraints excluded: chain Od residue 41 LEU Chi-restraints excluded: chain Tc residue 11 GLU Chi-restraints excluded: chain Tc residue 41 LEU Chi-restraints excluded: chain Ba residue 11 GLU Chi-restraints excluded: chain Ba residue 41 LEU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 34 ASP Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Id residue 7 LYS Chi-restraints excluded: chain Id residue 11 GLU Chi-restraints excluded: chain Nh residue 11 GLU Chi-restraints excluded: chain Nh residue 41 LEU Chi-restraints excluded: chain Sl residue 7 LYS Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Sl residue 41 LEU Chi-restraints excluded: chain Xp residue 41 LEU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain W residue 11 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain Ca residue 7 LYS Chi-restraints excluded: chain Ca residue 11 GLU Chi-restraints excluded: chain Ca residue 35 VAL Chi-restraints excluded: chain Ca residue 41 LEU Chi-restraints excluded: chain He residue 1 MET Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP Chi-restraints excluded: chain He residue 41 LEU Chi-restraints excluded: chain Mi residue 11 GLU Chi-restraints excluded: chain Mi residue 41 LEU Chi-restraints excluded: chain Rm residue 11 GLU Chi-restraints excluded: chain Wq residue 7 LYS Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Wq residue 41 LEU Chi-restraints excluded: chain Ae residue 3 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 41 LEU Chi-restraints excluded: chain Bb residue 11 GLU Chi-restraints excluded: chain Bb residue 41 LEU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 3 GLU Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU Chi-restraints excluded: chain Lj residue 35 VAL Chi-restraints excluded: chain Qn residue 1 MET Chi-restraints excluded: chain Qn residue 7 LYS Chi-restraints excluded: chain Qn residue 11 GLU Chi-restraints excluded: chain Vr residue 11 GLU Chi-restraints excluded: chain Vr residue 34 ASP Chi-restraints excluded: chain Vr residue 41 LEU Chi-restraints excluded: chain Zt residue 1 MET Chi-restraints excluded: chain Zt residue 7 LYS Chi-restraints excluded: chain Zt residue 11 GLU Chi-restraints excluded: chain Zt residue 41 LEU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain J residue 11 GLU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Dc residue 11 GLU Chi-restraints excluded: chain Fg residue 11 GLU Chi-restraints excluded: chain Fg residue 41 LEU Chi-restraints excluded: chain Kk residue 7 LYS Chi-restraints excluded: chain Kk residue 11 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Kk residue 41 LEU Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP Chi-restraints excluded: chain Po residue 41 LEU Chi-restraints excluded: chain Us residue 11 GLU Chi-restraints excluded: chain Hu residue 11 GLU Chi-restraints excluded: chain Hu residue 34 ASP Chi-restraints excluded: chain Hu residue 41 LEU Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Gv residue 3 GLU Chi-restraints excluded: chain Gv residue 7 LYS Chi-restraints excluded: chain Gv residue 11 GLU Chi-restraints excluded: chain Gv residue 41 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain Fw residue 41 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain Ex residue 11 GLU Chi-restraints excluded: chain Ex residue 41 LEU Chi-restraints excluded: chain S residue 3 GLU Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain Dy residue 7 LYS Chi-restraints excluded: chain Dy residue 11 GLU Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain Cz residue 3 GLU Chi-restraints excluded: chain Cz residue 7 LYS Chi-restraints excluded: chain Cz residue 11 GLU Chi-restraints excluded: chain Cz residue 41 LEU Chi-restraints excluded: chain 0 residue 11 GLU Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 2 residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24660 Z= 0.203 Angle : 0.466 8.445 32940 Z= 0.251 Chirality : 0.033 0.084 4080 Planarity : 0.001 0.026 4080 Dihedral : 4.123 81.101 3360 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 5.98 % Allowed : 20.08 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.15), residues: 3120 helix: 1.71 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.06 (0.61), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE N 45 TYR 0.008 0.002 TYR R 8 ARG 0.001 0.000 ARG E 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 610 time to evaluate : 3.208 Fit side-chains REVERT: A 7 LYS cc_start: 0.7710 (mtmm) cc_final: 0.7237 (mtmp) REVERT: A 11 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: F 7 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7317 (mtmp) REVERT: F 11 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: K 11 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: U 11 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: J1 7 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7368 (mtmm) REVERT: J1 11 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: Od 11 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: Tc 7 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7428 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: Ba 7 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7474 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: B 7 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7325 (mttp) REVERT: B 11 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: G 11 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: L 7 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7352 (mtmp) REVERT: L 11 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: V 7 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7242 (mtmp) REVERT: V 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: Z 7 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7469 (mtmp) REVERT: Z 11 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: Id 7 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7155 (mttp) REVERT: Id 11 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: Nh 7 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7339 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: Sl 7 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7304 (mttp) REVERT: Sl 11 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: Yb 11 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: C 7 LYS cc_start: 0.7689 (mtmm) cc_final: 0.7432 (mtmp) REVERT: C 11 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: H 7 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7463 (mttp) REVERT: H 11 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: M 7 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7381 (mttp) REVERT: M 11 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: W 7 LYS cc_start: 0.7684 (mtmm) cc_final: 0.7415 (mtmm) REVERT: W 11 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: Ca 11 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: He 1 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.5813 (ptp) REVERT: He 2 MET cc_start: 0.7172 (mtp) cc_final: 0.6837 (ttm) REVERT: He 7 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7505 (mttp) REVERT: He 11 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: Mi 11 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: Rm 11 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: Wq 7 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7237 (mttp) REVERT: Wq 11 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: Ae 7 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7533 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: D 7 LYS cc_start: 0.7713 (mtmm) cc_final: 0.7219 (mttp) REVERT: D 11 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: I 7 LYS cc_start: 0.7673 (mtmm) cc_final: 0.7227 (mttp) REVERT: I 11 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: N 11 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: X 7 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7395 (mtpt) REVERT: X 11 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: Bb 11 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: Gf 7 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7403 (mttp) REVERT: Gf 11 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: Lj 7 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7285 (mttp) REVERT: Lj 11 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: Qn 1 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.5973 (ptp) REVERT: Qn 7 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7204 (mttp) REVERT: Qn 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: Vr 7 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7445 (mtmp) REVERT: Vr 11 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: Zt 11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: E 11 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: J 11 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: O 7 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7256 (mttp) REVERT: O 11 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: Y 7 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7209 (mttp) REVERT: Y 11 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: Dc 7 LYS cc_start: 0.7670 (mtmm) cc_final: 0.7413 (mttp) REVERT: Dc 11 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: Fg 7 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7410 (mttp) REVERT: Fg 11 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: Kk 7 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7464 (mtmm) REVERT: Kk 11 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: Po 7 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7454 (mttp) REVERT: Po 11 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: Us 11 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: Hu 1 MET cc_start: 0.6177 (mpp) cc_final: 0.5588 (mmm) REVERT: Hu 7 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7433 (mtpt) REVERT: Hu 11 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: P 7 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7280 (mtmp) REVERT: P 11 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: Gv 1 MET cc_start: 0.5851 (mpp) cc_final: 0.5383 (mtt) REVERT: Gv 7 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7309 (mttp) REVERT: Gv 11 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: Q 11 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: Fw 7 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7334 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: R 1 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.6054 (mmm) REVERT: R 7 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7303 (mtpt) REVERT: R 11 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: Ex 11 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: S 7 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7218 (mttp) REVERT: S 11 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: Dy 7 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7182 (mttp) REVERT: Dy 11 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: T 11 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: Cz 7 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7252 (mttp) REVERT: Cz 11 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: 0 11 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: 2 7 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7389 (mttp) REVERT: 2 11 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6994 (mp0) outliers start: 158 outliers final: 74 residues processed: 684 average time/residue: 2.7392 time to fit residues: 2195.7327 Evaluate side-chains 760 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 607 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain J1 residue 11 GLU Chi-restraints excluded: chain Od residue 11 GLU Chi-restraints excluded: chain Od residue 41 LEU Chi-restraints excluded: chain Tc residue 11 GLU Chi-restraints excluded: chain Tc residue 41 LEU Chi-restraints excluded: chain Ba residue 11 GLU Chi-restraints excluded: chain Ba residue 41 LEU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 34 ASP Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Id residue 7 LYS Chi-restraints excluded: chain Id residue 11 GLU Chi-restraints excluded: chain Nh residue 11 GLU Chi-restraints excluded: chain Nh residue 41 LEU Chi-restraints excluded: chain Sl residue 7 LYS Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Sl residue 41 LEU Chi-restraints excluded: chain Xp residue 41 LEU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain M residue 3 GLU Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain W residue 11 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain Ca residue 7 LYS Chi-restraints excluded: chain Ca residue 11 GLU Chi-restraints excluded: chain Ca residue 35 VAL Chi-restraints excluded: chain Ca residue 41 LEU Chi-restraints excluded: chain He residue 1 MET Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP Chi-restraints excluded: chain He residue 41 LEU Chi-restraints excluded: chain Mi residue 11 GLU Chi-restraints excluded: chain Mi residue 41 LEU Chi-restraints excluded: chain Rm residue 11 GLU Chi-restraints excluded: chain Wq residue 7 LYS Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Wq residue 41 LEU Chi-restraints excluded: chain Ae residue 3 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 41 LEU Chi-restraints excluded: chain Bb residue 11 GLU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU Chi-restraints excluded: chain Lj residue 34 ASP Chi-restraints excluded: chain Lj residue 35 VAL Chi-restraints excluded: chain Qn residue 1 MET Chi-restraints excluded: chain Qn residue 7 LYS Chi-restraints excluded: chain Qn residue 11 GLU Chi-restraints excluded: chain Vr residue 11 GLU Chi-restraints excluded: chain Vr residue 34 ASP Chi-restraints excluded: chain Vr residue 41 LEU Chi-restraints excluded: chain Zt residue 7 LYS Chi-restraints excluded: chain Zt residue 11 GLU Chi-restraints excluded: chain Zt residue 41 LEU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain J residue 11 GLU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Dc residue 11 GLU Chi-restraints excluded: chain Dc residue 41 LEU Chi-restraints excluded: chain Fg residue 11 GLU Chi-restraints excluded: chain Fg residue 41 LEU Chi-restraints excluded: chain Kk residue 7 LYS Chi-restraints excluded: chain Kk residue 11 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Kk residue 41 LEU Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP Chi-restraints excluded: chain Po residue 41 LEU Chi-restraints excluded: chain Us residue 11 GLU Chi-restraints excluded: chain Hu residue 11 GLU Chi-restraints excluded: chain Hu residue 34 ASP Chi-restraints excluded: chain Hu residue 41 LEU Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Gv residue 7 LYS Chi-restraints excluded: chain Gv residue 11 GLU Chi-restraints excluded: chain Gv residue 41 LEU Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain Fw residue 41 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain Ex residue 11 GLU Chi-restraints excluded: chain Ex residue 41 LEU Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain Dy residue 3 GLU Chi-restraints excluded: chain Dy residue 7 LYS Chi-restraints excluded: chain Dy residue 11 GLU Chi-restraints excluded: chain Dy residue 41 LEU Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain Cz residue 3 GLU Chi-restraints excluded: chain Cz residue 7 LYS Chi-restraints excluded: chain Cz residue 11 GLU Chi-restraints excluded: chain Cz residue 41 LEU Chi-restraints excluded: chain 0 residue 11 GLU Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 2 residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.171896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132598 restraints weight = 68996.967| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.61 r_work: 0.3248 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 24660 Z= 0.241 Angle : 0.490 5.082 32940 Z= 0.262 Chirality : 0.034 0.085 4080 Planarity : 0.002 0.008 4080 Dihedral : 4.020 75.229 3360 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.48 % Allowed : 19.47 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.15), residues: 3120 helix: 1.58 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.07 (0.62), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE N 45 TYR 0.008 0.002 TYRHu 8 ARG 0.000 0.000 ARG E 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27190.61 seconds wall clock time: 471 minutes 9.63 seconds (28269.63 seconds total)