Starting phenix.real_space_refine on Tue Sep 24 06:11:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/09_2024/8f53_28859.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/09_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_28859/09_2024/8f53_28859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/09_2024/8f53_28859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/09_2024/8f53_28859.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f53_28859/09_2024/8f53_28859.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 18.46, per 1000 atoms: 0.36 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.60 Conformation dependent library (CDL) restraints added in 3.0 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: 2.65 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: 15.07 Time building geometry restraints manager: 11.83 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: 0.00 - 0.84: 82188 0.84 - 1.68: 11198 1.68 - 2.51: 406 2.51 - 3.35: 37 3.35 - 4.19: 11 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 2.450 nonbonded pdb=" O ALA M 27 " pdb=" HG SER M 31 " model vdw 1.576 2.450 nonbonded pdb=" O ALA V 27 " pdb=" HG SER V 31 " model vdw 1.583 2.450 nonbonded pdb=" O ALA 0 27 " pdb=" HG SER 0 31 " model vdw 1.590 2.450 nonbonded pdb=" O ALA F 27 " pdb=" HG SER F 31 " model vdw 1.592 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 1.190 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: 0.640 Extract box with map and model: 1.520 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 77.170 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.240 ------------------------------------------------------------------------------- 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 : 3.062 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: 2.3504 time to fit residues: 2070.7286 Evaluate side-chains 662 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 661 time to evaluate : 3.080 ------------------------------------------------------------------------------- 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: 0.9990 chunk 227 optimal weight: 2.9990 chunk 126 optimal weight: 0.0010 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- 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: 0.7459 moved from start: 0.2367 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= 0.219 Angle : 0.534 4.421 32940 Z= 0.293 Chirality : 0.034 0.088 4080 Planarity : 0.002 0.009 4080 Dihedral : 10.135 89.253 3362 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 5.42 % Allowed : 9.02 % Favored : 85.57 % 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: 2.43 (0.15), residues: 3120 helix: 1.50 (0.09), residues: 2820 sheet: None (None), residues: 0 loop : 3.50 (0.61), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHEZt 45 TYR 0.011 0.002 TYR T 8 ARG 0.001 0.000 ARG U 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 715 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 572 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7695 (mtmm) cc_final: 0.7309 (mtmp) REVERT: A 11 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: F 7 LYS cc_start: 0.7830 (mtmm) cc_final: 0.7407 (mtmp) REVERT: F 11 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: K 7 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7458 (mttp) REVERT: J1 7 LYS cc_start: 0.7683 (mtpt) cc_final: 0.7009 (mtmp) REVERT: J1 11 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: Od 11 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: Tc 7 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7274 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: Ba 7 LYS cc_start: 0.7505 (mtmt) cc_final: 0.7066 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: B 11 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: G 7 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7215 (mttp) REVERT: G 11 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: L 7 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7370 (mttp) REVERT: L 11 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: V 7 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7216 (mttp) REVERT: V 11 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: Z 11 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: Id 7 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7096 (mtpt) REVERT: Id 11 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: Nh 7 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7210 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: Sl 7 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7304 (mtmp) REVERT: Sl 11 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: Xp 1 MET cc_start: 0.6064 (mpp) cc_final: 0.5748 (mmm) REVERT: Yb 7 LYS cc_start: 0.7587 (mtpt) cc_final: 0.7315 (mttp) REVERT: Yb 11 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: C 11 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: H 7 LYS cc_start: 0.7776 (mtmm) cc_final: 0.7217 (mtmm) REVERT: H 11 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: M 7 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7211 (mtmm) REVERT: M 11 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: W 7 LYS cc_start: 0.7723 (mtmm) cc_final: 0.7137 (mtmm) REVERT: W 11 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: Ca 11 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: He 7 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7043 (mtmm) REVERT: He 11 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: Mi 11 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: Rm 2 MET cc_start: 0.7202 (mtp) cc_final: 0.6841 (ttm) REVERT: Wq 7 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7054 (mtmp) REVERT: Wq 11 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: Ae 7 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7291 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: D 7 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7166 (mtmp) REVERT: D 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: I 7 LYS cc_start: 0.7628 (mtmm) cc_final: 0.7162 (mtmp) REVERT: I 11 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: N 11 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: X 7 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7210 (mtmm) REVERT: X 11 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: Bb 11 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: Gf 7 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7158 (mtmp) REVERT: Gf 11 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: Lj 7 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7106 (mtmp) REVERT: Lj 11 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: Qn 7 LYS cc_start: 0.7807 (mtmp) cc_final: 0.7091 (mtpt) REVERT: Qn 11 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: Vr 7 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7174 (mtmp) REVERT: Vr 11 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: Zt 7 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7303 (mtmp) REVERT: Zt 11 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: O 7 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.6967 (mttp) REVERT: O 11 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: Y 7 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7211 (mtmp) REVERT: Y 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: Dc 7 LYS cc_start: 0.7682 (mtmm) cc_final: 0.7291 (mtmm) REVERT: Dc 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: Fg 11 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: Kk 11 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: Po 11 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: Us 11 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: Hu 1 MET cc_start: 0.6215 (mpp) cc_final: 0.5701 (mmm) REVERT: Hu 11 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: P 7 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7346 (mtmp) REVERT: P 11 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: Gv 1 MET cc_start: 0.5862 (mpp) cc_final: 0.5561 (ptt) REVERT: Gv 11 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: Q 7 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7230 (mttp) REVERT: Q 11 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: Fw 7 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7182 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: R 1 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5770 (mmm) REVERT: R 7 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7272 (mtmp) REVERT: R 11 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: Ex 7 LYS cc_start: 0.7778 (mtmm) cc_final: 0.7422 (mttp) REVERT: S 11 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: Dy 7 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7102 (mtmp) REVERT: Dy 11 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: Cz 7 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7165 (mtmp) REVERT: Cz 11 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: 0 1 MET cc_start: 0.6090 (mpp) cc_final: 0.5783 (mmm) REVERT: 2 7 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7291 (mtmp) REVERT: 2 11 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6920 (mp0) outliers start: 143 outliers final: 39 residues processed: 622 average time/residue: 2.2617 time to fit residues: 1648.1321 Evaluate side-chains 623 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 522 time to evaluate : 3.036 ------------------------------------------------------------------------------- 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 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 C residue 34 ASP 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 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 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 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 N residue 35 VAL 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 35 VAL 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 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 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 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 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 1 MET Chi-restraints excluded: chain Fw residue 11 GLU Chi-restraints excluded: chain R residue 1 MET 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 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 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 Chi-restraints excluded: chain 2 residue 34 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 0.1980 chunk 185 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 272 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 270 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.7417 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 24660 Z= 0.159 Angle : 0.448 3.781 32940 Z= 0.244 Chirality : 0.033 0.085 4080 Planarity : 0.001 0.008 4080 Dihedral : 8.750 89.905 3360 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 3.75 % Allowed : 12.65 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.15), residues: 3120 helix: 2.15 (0.09), residues: 2820 sheet: None (None), residues: 0 loop : 3.35 (0.57), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEOd 45 TYR 0.009 0.002 TYR Q 8 ARG 0.001 0.000 ARGEx 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 744 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 645 time to evaluate : 3.023 Fit side-chains REVERT: A 1 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5949 (ptp) REVERT: A 7 LYS cc_start: 0.7623 (mtmm) cc_final: 0.7243 (mtmp) REVERT: A 11 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: F 7 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7341 (mtmp) REVERT: F 11 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: J1 7 LYS cc_start: 0.7613 (mtpt) cc_final: 0.7164 (mtmm) REVERT: J1 11 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: Od 11 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: Tc 7 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7319 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: Ba 7 LYS cc_start: 0.7507 (mtmt) cc_final: 0.7247 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: B 11 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: G 11 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: L 7 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7244 (mttp) REVERT: L 11 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: V 7 LYS cc_start: 0.7673 (mtmm) cc_final: 0.7235 (mtmp) REVERT: V 11 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: Z 11 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: Id 7 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7141 (mttp) REVERT: Id 11 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: Nh 7 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7332 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: Sl 7 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7440 (mttp) REVERT: Sl 11 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: Yb 7 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7332 (mttp) REVERT: Yb 11 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: C 11 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: H 7 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7182 (mtmp) REVERT: H 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: M 7 LYS cc_start: 0.7675 (mtmm) cc_final: 0.7267 (mtmm) REVERT: M 11 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: W 7 LYS cc_start: 0.7586 (mtmm) cc_final: 0.7239 (mtmm) REVERT: W 11 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: Ca 7 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7335 (mtmp) REVERT: Ca 11 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: He 11 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: Wq 7 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7154 (mtmp) REVERT: Wq 11 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: Ae 7 LYS cc_start: 0.7570 (mtmm) cc_final: 0.7346 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: D 7 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7037 (mtmm) REVERT: D 11 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: I 7 LYS cc_start: 0.7643 (mtmm) cc_final: 0.7203 (mtmp) REVERT: I 11 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: N 7 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7142 (mtmp) REVERT: N 11 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: X 7 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7153 (mtmp) REVERT: X 11 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: Gf 7 LYS cc_start: 0.7572 (mtmm) cc_final: 0.7127 (mtmp) REVERT: Gf 11 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: Lj 7 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7149 (mttp) REVERT: Lj 11 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: Qn 11 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: Vr 2 MET cc_start: 0.7137 (mtp) cc_final: 0.6889 (mtp) REVERT: Vr 7 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7144 (mtmp) REVERT: Vr 11 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: Zt 7 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7330 (mtmp) REVERT: Zt 11 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: O 7 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7244 (mttp) REVERT: O 11 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: Y 7 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7171 (mttp) REVERT: Y 11 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: Dc 7 LYS cc_start: 0.7577 (mtmm) cc_final: 0.7187 (mtmp) REVERT: Dc 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: Fg 7 LYS cc_start: 0.7783 (mtmm) cc_final: 0.7334 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: Kk 7 LYS cc_start: 0.7652 (mtmm) cc_final: 0.7186 (mtmp) REVERT: Kk 11 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: Po 7 LYS cc_start: 0.7671 (mtmm) cc_final: 0.7180 (mtmm) REVERT: Po 11 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: Us 11 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: Hu 1 MET cc_start: 0.6280 (mpp) cc_final: 0.5512 (mmm) REVERT: Hu 7 LYS cc_start: 0.7643 (mtmm) cc_final: 0.7150 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: P 7 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7251 (mtmp) REVERT: P 11 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: Gv 1 MET cc_start: 0.5633 (mpp) cc_final: 0.5356 (mtt) REVERT: Gv 11 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: Q 11 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: Fw 7 LYS cc_start: 0.7761 (mtmm) cc_final: 0.7280 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: R 1 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5622 (mmm) REVERT: R 7 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7237 (mtmm) REVERT: R 11 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: Ex 7 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7492 (mttp) REVERT: S 7 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7240 (mttp) REVERT: S 11 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: Dy 1 MET cc_start: 0.5927 (mmm) cc_final: 0.5655 (mtt) REVERT: Dy 7 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7140 (mtmp) REVERT: Dy 11 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: Cz 11 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: 2 7 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7190 (mttp) REVERT: 2 11 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6902 (mp0) outliers start: 99 outliers final: 12 residues processed: 663 average time/residue: 2.3389 time to fit residues: 1838.5171 Evaluate side-chains 633 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 559 time to evaluate : 3.004 ------------------------------------------------------------------------------- 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 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 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 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 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 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 Wq residue 7 LYS Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Gf residue 30 ILE Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU 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 Zt residue 1 MET Chi-restraints excluded: chain Zt residue 7 LYS Chi-restraints excluded: chain Zt residue 11 GLU 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 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 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 1 MET 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 Dy residue 7 LYS Chi-restraints excluded: chain Dy residue 11 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 0.2980 chunk 289 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.7442 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 24660 Z= 0.175 Angle : 0.443 3.855 32940 Z= 0.243 Chirality : 0.033 0.086 4080 Planarity : 0.001 0.007 4080 Dihedral : 6.928 88.960 3360 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 4.24 % Allowed : 16.06 % Favored : 79.70 % 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: 3.38 (0.15), residues: 3120 helix: 2.05 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.38 (0.63), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE N 45 TYR 0.009 0.002 TYR Q 8 ARG 0.001 0.000 ARGEx 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 699 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 587 time to evaluate : 3.070 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7582 (mtmm) cc_final: 0.7222 (mtmp) REVERT: A 11 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: F 7 LYS cc_start: 0.7721 (mtmm) cc_final: 0.7353 (mtmp) REVERT: F 11 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: J1 7 LYS cc_start: 0.7614 (mtpt) cc_final: 0.7077 (mtmp) REVERT: J1 11 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: Od 11 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: Tc 7 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7248 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: Ba 2 MET cc_start: 0.7133 (mtp) cc_final: 0.6904 (mtp) REVERT: Ba 7 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7301 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: B 11 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: G 7 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7508 (mtmm) REVERT: G 11 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: L 7 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7260 (mtmp) REVERT: L 11 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: V 7 LYS cc_start: 0.7602 (mtmm) cc_final: 0.7144 (mtmp) REVERT: V 11 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: Z 11 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: Id 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: Nh 7 LYS cc_start: 0.7725 (mtmm) cc_final: 0.7337 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: Sl 7 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7398 (mttp) REVERT: Sl 11 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: Yb 7 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7358 (mttp) REVERT: Yb 11 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: C 7 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7170 (mtmp) REVERT: C 11 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: H 7 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7199 (mtmp) REVERT: H 11 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: M 7 LYS cc_start: 0.7652 (mtmm) cc_final: 0.7297 (mtmm) REVERT: M 11 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: W 7 LYS cc_start: 0.7604 (mtmm) cc_final: 0.7310 (mtmm) REVERT: W 11 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: Ca 11 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: He 11 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: Wq 11 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: Ae 11 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: D 7 LYS cc_start: 0.7625 (mtmm) cc_final: 0.7163 (mttp) REVERT: D 11 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: I 7 LYS cc_start: 0.7613 (mtmm) cc_final: 0.7226 (mtmp) REVERT: I 11 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: N 7 LYS cc_start: 0.7492 (mtmm) cc_final: 0.7148 (mtmp) REVERT: N 11 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: X 7 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7258 (mtmp) REVERT: X 11 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: Gf 7 LYS cc_start: 0.7586 (mtmm) cc_final: 0.7167 (mtmp) REVERT: Gf 11 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: Lj 7 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7141 (mttp) REVERT: Lj 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: Qn 7 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7100 (mttp) REVERT: Qn 11 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: Vr 7 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7235 (mtmp) REVERT: Vr 11 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: Zt 11 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: O 7 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7180 (mttp) REVERT: O 11 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: Y 7 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7224 (mttp) REVERT: Y 11 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: Dc 7 LYS cc_start: 0.7588 (mtmm) cc_final: 0.7159 (mtmp) REVERT: Dc 11 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: Fg 7 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7335 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: Kk 2 MET cc_start: 0.7068 (mtp) cc_final: 0.6841 (mtp) REVERT: Kk 7 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7219 (mtmp) REVERT: Kk 11 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: Po 7 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7235 (mtmp) REVERT: Po 11 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: Us 11 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: Hu 1 MET cc_start: 0.6141 (mpp) cc_final: 0.5404 (mmm) REVERT: Hu 7 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7343 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: P 7 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7304 (mtmp) REVERT: P 11 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: Gv 1 MET cc_start: 0.5711 (mpp) cc_final: 0.5429 (mtt) REVERT: Gv 11 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: Q 11 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: Fw 7 LYS cc_start: 0.7710 (mtmm) cc_final: 0.7258 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: R 7 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7333 (mtmm) REVERT: R 11 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: S 7 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7253 (mttp) REVERT: S 11 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: Dy 11 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: Cz 7 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7222 (mttp) REVERT: Cz 11 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: 2 7 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7203 (mttp) REVERT: 2 11 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6938 (mp0) outliers start: 112 outliers final: 16 residues processed: 620 average time/residue: 2.2684 time to fit residues: 1648.2199 Evaluate side-chains 630 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 557 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain F residue 11 GLU 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 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 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 1 MET Chi-restraints excluded: chain C residue 11 GLU 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 W residue 11 GLU Chi-restraints excluded: chain Ca residue 11 GLU 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 Wq residue 11 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain D residue 11 GLU 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 Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU 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 Zt residue 11 GLU Chi-restraints excluded: chain E residue 34 ASP 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 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 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 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 35 VAL Chi-restraints excluded: chain Dy residue 11 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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: 0.7483 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 24660 Z= 0.234 Angle : 0.492 5.030 32940 Z= 0.263 Chirality : 0.034 0.083 4080 Planarity : 0.002 0.008 4080 Dihedral : 5.482 87.848 3360 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 5.42 % Allowed : 17.01 % Favored : 77.58 % 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: 2.95 (0.15), residues: 3120 helix: 1.75 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.55 (0.62), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE N 45 TYR 0.011 0.002 TYR V 8 ARG 0.001 0.000 ARG V 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 743 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 600 time to evaluate : 3.058 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7249 (mtmp) REVERT: A 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: F 7 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7335 (mtmp) REVERT: F 11 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: J1 1 MET cc_start: 0.4639 (mmm) cc_final: 0.4416 (mmt) REVERT: J1 7 LYS cc_start: 0.7706 (mtpt) cc_final: 0.7210 (mttp) REVERT: J1 11 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: Od 11 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: Tc 7 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7323 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: Ba 2 MET cc_start: 0.7230 (mtp) cc_final: 0.6990 (mtp) REVERT: Ba 7 LYS cc_start: 0.7684 (mtmt) cc_final: 0.7372 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: B 11 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: G 7 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7500 (mtmm) REVERT: G 11 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: L 7 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7256 (mtmp) REVERT: L 11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: V 7 LYS cc_start: 0.7655 (mtmm) cc_final: 0.7199 (mtmp) REVERT: V 11 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: Z 11 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: Id 7 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7197 (mttp) REVERT: Id 11 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: Nh 7 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7340 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: Sl 7 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7339 (mttp) REVERT: Sl 11 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: Yb 11 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: C 7 LYS cc_start: 0.7671 (mtmm) cc_final: 0.7220 (mtmp) REVERT: C 11 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: H 1 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.5892 (ptp) REVERT: H 7 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7232 (mtmp) REVERT: H 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: M 7 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7435 (mtmm) REVERT: M 11 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: W 7 LYS cc_start: 0.7659 (mtmm) cc_final: 0.7352 (mtmm) REVERT: W 11 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: Ca 11 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: He 11 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: Wq 7 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7164 (mttp) REVERT: Wq 11 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: Ae 11 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: D 7 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7194 (mttp) REVERT: D 11 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: I 7 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7185 (mtpt) REVERT: I 11 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: N 7 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7291 (mtmp) REVERT: N 11 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: X 7 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7386 (mtmp) REVERT: X 11 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: Gf 7 LYS cc_start: 0.7694 (mtmm) cc_final: 0.7278 (mtmp) REVERT: Gf 11 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: Lj 11 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: Qn 7 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7154 (mttp) REVERT: Qn 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: Vr 7 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7475 (mtmp) REVERT: Vr 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: Zt 1 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5575 (ptp) REVERT: Zt 11 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: O 7 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7303 (mttp) REVERT: O 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: Y 11 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: Dc 7 LYS cc_start: 0.7675 (mtmm) cc_final: 0.7271 (mtmp) REVERT: Dc 11 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: Fg 7 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7412 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: Kk 7 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7428 (mtmp) REVERT: Kk 11 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: Po 7 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7439 (mtmm) REVERT: Po 11 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: Us 11 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: Hu 1 MET cc_start: 0.6167 (mpp) cc_final: 0.5617 (mmm) REVERT: Hu 7 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7318 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: P 7 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7317 (mtmp) REVERT: P 11 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: Gv 1 MET cc_start: 0.5673 (mpp) cc_final: 0.5460 (mtt) REVERT: Gv 11 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: Q 11 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: Fw 7 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7238 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: R 1 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.5630 (ptt) REVERT: S 7 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7261 (mttp) REVERT: S 11 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: Dy 7 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7198 (mttp) REVERT: Dy 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: Cz 7 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7276 (mttp) REVERT: Cz 11 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: 0 1 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.5620 (mmm) REVERT: 2 7 LYS cc_start: 0.7635 (mtmp) cc_final: 0.7257 (mttp) REVERT: 2 11 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6983 (mp0) outliers start: 143 outliers final: 45 residues processed: 671 average time/residue: 2.3207 time to fit residues: 1819.4984 Evaluate side-chains 708 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 603 time to evaluate : 3.023 ------------------------------------------------------------------------------- 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 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 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 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 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 1 MET Chi-restraints excluded: chain H residue 11 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 He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP 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 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 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 N residue 11 GLU Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 34 ASP 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 35 VAL 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 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 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 11 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Po residue 1 MET 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 11 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 35 VAL Chi-restraints excluded: chain Dy residue 7 LYS Chi-restraints excluded: chain Dy 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 1 MET Chi-restraints excluded: chain 0 residue 41 LEU Chi-restraints excluded: chain 2 residue 11 GLU 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: 6.9990 chunk 57 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 24660 Z= 0.240 Angle : 0.485 4.959 32940 Z= 0.261 Chirality : 0.034 0.083 4080 Planarity : 0.002 0.009 4080 Dihedral : 4.589 77.258 3360 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 4.73 % Allowed : 19.02 % Favored : 76.25 % 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: 2.77 (0.15), residues: 3120 helix: 1.64 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.41 (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 ARG U 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 727 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 602 time to evaluate : 3.068 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7680 (mtmm) cc_final: 0.7198 (mtmp) REVERT: A 11 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: F 7 LYS cc_start: 0.7783 (mtmm) cc_final: 0.7342 (mtmp) REVERT: F 11 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: J1 7 LYS cc_start: 0.7720 (mtpt) cc_final: 0.7239 (mttp) REVERT: J1 11 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: Od 11 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: Tc 7 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7331 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: Ba 2 MET cc_start: 0.7257 (mtp) cc_final: 0.7013 (mtp) REVERT: Ba 7 LYS cc_start: 0.7661 (mtmt) cc_final: 0.7381 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: B 11 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: G 7 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7599 (mtmm) REVERT: G 11 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: L 7 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7309 (mtmp) REVERT: L 11 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: V 7 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7218 (mtmp) REVERT: V 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: Z 7 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7447 (mtmp) REVERT: Z 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: Id 7 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7122 (mttp) REVERT: Id 11 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: Nh 7 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7374 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: Sl 7 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7276 (mttp) REVERT: Sl 11 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: Yb 11 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: C 7 LYS cc_start: 0.7607 (mtmm) cc_final: 0.7135 (mtmp) REVERT: C 11 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: H 3 GLU cc_start: 0.6989 (tp30) cc_final: 0.6771 (tp30) REVERT: H 7 LYS cc_start: 0.7769 (mtmm) cc_final: 0.7186 (mtpt) REVERT: H 11 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: M 7 LYS cc_start: 0.7762 (mtmm) cc_final: 0.7293 (mttp) REVERT: M 11 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: W 7 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7392 (mtmm) REVERT: W 11 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: Ca 11 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: He 11 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: Wq 7 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7143 (mttp) REVERT: Wq 11 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: Ae 7 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7579 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: D 7 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7185 (mttp) REVERT: D 11 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: I 7 LYS cc_start: 0.7689 (mtmm) cc_final: 0.7282 (mttp) REVERT: I 11 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: N 7 LYS cc_start: 0.7584 (mtmm) cc_final: 0.7364 (mtmp) REVERT: N 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: X 7 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7417 (mttp) REVERT: X 11 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: Gf 7 LYS cc_start: 0.7769 (mtmm) cc_final: 0.7353 (mtmp) REVERT: Gf 11 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: Lj 11 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: Qn 1 MET cc_start: 0.6252 (pmm) cc_final: 0.5850 (ptp) REVERT: Qn 7 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7208 (mttp) REVERT: Qn 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: Vr 7 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7450 (mtmm) REVERT: Vr 11 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: Zt 1 MET cc_start: 0.6083 (OUTLIER) cc_final: 0.5572 (ptp) REVERT: Zt 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: O 7 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7159 (mttp) REVERT: O 11 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: Y 11 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: Dc 7 LYS cc_start: 0.7684 (mtmm) cc_final: 0.7311 (mttp) REVERT: Dc 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: Fg 7 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7381 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: Kk 7 LYS cc_start: 0.7715 (mtmm) cc_final: 0.7505 (mtmp) REVERT: Kk 11 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: Po 7 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7423 (mtmm) REVERT: Po 11 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: Us 11 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: Hu 1 MET cc_start: 0.6122 (mpp) cc_final: 0.5520 (mmm) REVERT: Hu 7 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7274 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: P 7 LYS cc_start: 0.7860 (mtmm) cc_final: 0.7281 (mtmp) REVERT: P 11 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: Gv 1 MET cc_start: 0.5830 (mpp) cc_final: 0.5493 (mtt) REVERT: Gv 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: Q 11 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: Fw 7 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7211 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: R 1 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.5505 (ptt) REVERT: R 7 LYS cc_start: 0.7836 (mtmm) cc_final: 0.7495 (mtmp) REVERT: R 11 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: Ex 11 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: S 7 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7219 (mttp) REVERT: S 11 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: Dy 7 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7126 (mttm) REVERT: Dy 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: T 11 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: Cz 7 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7279 (mttp) REVERT: Cz 11 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: 2 11 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6925 (mp0) outliers start: 125 outliers final: 39 residues processed: 646 average time/residue: 2.3703 time to fit residues: 1784.1362 Evaluate side-chains 698 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 597 time to evaluate : 3.037 ------------------------------------------------------------------------------- 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 B residue 11 GLU Chi-restraints excluded: chain G residue 3 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 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 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 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 1 MET Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain M residue 3 GLU Chi-restraints excluded: chain M residue 11 GLU 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 He residue 1 MET Chi-restraints excluded: chain He residue 11 GLU Chi-restraints excluded: chain He residue 34 ASP 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 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 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 11 GLU Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain Bb residue 41 LEU Chi-restraints excluded: chain Gf residue 3 GLU Chi-restraints excluded: chain Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 11 GLU 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 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 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 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 1 MET Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP 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 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 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 11 GLU Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain Ex residue 11 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 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 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: 4.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 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: 0.7493 moved from start: 0.3957 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= 0.241 Angle : 0.486 5.076 32940 Z= 0.261 Chirality : 0.034 0.082 4080 Planarity : 0.002 0.008 4080 Dihedral : 4.068 70.577 3360 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 5.30 % Allowed : 19.24 % 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: 2.74 (0.15), residues: 3120 helix: 1.62 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.27 (0.62), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE N 45 TYR 0.009 0.002 TYR V 8 ARG 0.001 0.000 ARGAe 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 750 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 610 time to evaluate : 3.068 Fit side-chains REVERT: A 7 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7238 (mtmp) REVERT: A 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: F 7 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7317 (mtmp) REVERT: F 11 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: J1 7 LYS cc_start: 0.7735 (mtpt) cc_final: 0.7292 (mtmm) REVERT: J1 11 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: Od 11 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: Tc 7 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7353 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: Ba 2 MET cc_start: 0.7317 (mtp) cc_final: 0.7031 (mtp) REVERT: Ba 7 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7410 (mtmp) REVERT: Ba 11 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: B 11 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: G 7 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7545 (mtmm) REVERT: G 11 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: L 7 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7321 (mtmp) REVERT: L 11 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: V 7 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7250 (mtmp) REVERT: V 11 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: Z 7 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7448 (mtmp) REVERT: Z 11 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: Id 7 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7117 (mttp) REVERT: Id 11 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: Nh 7 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7287 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: Sl 7 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7361 (mttp) REVERT: Sl 11 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: Xp 11 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: Yb 11 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: C 7 LYS cc_start: 0.7617 (mtmm) cc_final: 0.7237 (mtmp) REVERT: C 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: H 7 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7336 (mtpt) REVERT: H 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: M 7 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7361 (mttp) REVERT: M 11 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: W 7 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7410 (mtmm) REVERT: W 11 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: Ca 11 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: He 11 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: Mi 11 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: Wq 7 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7140 (mttp) REVERT: Wq 11 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: Ae 7 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7609 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: D 7 LYS cc_start: 0.7684 (mtmm) cc_final: 0.7212 (mttp) REVERT: D 11 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: I 7 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7258 (mttp) REVERT: I 11 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: N 7 LYS cc_start: 0.7607 (mtmm) cc_final: 0.7362 (mtmp) REVERT: N 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: X 7 LYS cc_start: 0.7764 (mtmm) cc_final: 0.7448 (mttp) REVERT: X 11 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: Gf 7 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7375 (mttp) REVERT: Gf 11 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: Lj 11 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: Qn 1 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5796 (ptp) REVERT: Qn 7 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7202 (mttp) REVERT: Qn 11 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: Vr 7 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7469 (mtmm) REVERT: Vr 11 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: Zt 1 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5622 (ptp) REVERT: Zt 11 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: O 7 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7187 (mttp) REVERT: O 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: Y 11 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: Dc 7 LYS cc_start: 0.7649 (mtmm) cc_final: 0.7316 (mttp) REVERT: Dc 11 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: Fg 7 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7390 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: Kk 7 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7503 (mtmp) REVERT: Kk 11 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: Po 7 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7490 (mtmm) REVERT: Po 11 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: Us 11 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: Hu 1 MET cc_start: 0.6112 (mpp) cc_final: 0.5613 (mmm) REVERT: Hu 7 LYS cc_start: 0.7661 (mtmm) cc_final: 0.7448 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: P 7 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7305 (mtmp) REVERT: P 11 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: Gv 1 MET cc_start: 0.5781 (mpp) cc_final: 0.5468 (mtt) REVERT: Gv 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: Q 11 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: Fw 7 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7221 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: R 1 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.5315 (ptt) REVERT: R 7 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7476 (mtmp) REVERT: R 11 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: Ex 11 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: S 7 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7233 (mttp) REVERT: S 11 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: Dy 7 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7197 (mttp) REVERT: Dy 11 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: T 11 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: Cz 7 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7217 (mttp) REVERT: Cz 11 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: 2 7 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7339 (mttp) REVERT: 2 11 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6978 (mp0) outliers start: 140 outliers final: 60 residues processed: 664 average time/residue: 2.3742 time to fit residues: 1839.6124 Evaluate side-chains 732 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 606 time to evaluate : 3.082 ------------------------------------------------------------------------------- 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 11 GLU Chi-restraints excluded: chain Ba residue 34 ASP 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 L residue 11 GLU Chi-restraints excluded: chain V residue 11 GLU 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 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 Sl residue 7 LYS Chi-restraints excluded: chain Sl residue 11 GLU Chi-restraints excluded: chain Xp 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 1 MET Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain H residue 1 MET 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 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 Mi residue 11 GLU 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 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 X residue 11 GLU Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain Bb residue 41 LEU Chi-restraints excluded: chain Gf residue 3 GLU Chi-restraints excluded: chain Gf residue 11 GLU 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 3 GLU 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 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 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 1 MET Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP 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 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 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 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 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 3 GLU Chi-restraints excluded: chain Cz residue 7 LYS Chi-restraints excluded: chain Cz 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=2.00 ------------------------------------------------------------------------------- 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: 2.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7502 moved from start: 0.4043 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= 0.257 Angle : 0.500 5.356 32940 Z= 0.267 Chirality : 0.034 0.082 4080 Planarity : 0.002 0.008 4080 Dihedral : 3.687 55.098 3360 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 5.57 % Allowed : 19.24 % Favored : 75.19 % 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: 2.63 (0.15), residues: 3120 helix: 1.56 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 5.15 (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 TYRHe 8 ARG 0.001 0.000 ARGAe 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 758 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 611 time to evaluate : 3.105 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7251 (mtmp) REVERT: A 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: F 7 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7315 (mtmp) REVERT: F 11 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: J1 7 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7294 (mtmm) REVERT: J1 11 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: Od 11 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: Tc 7 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7418 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: Ba 2 MET cc_start: 0.7265 (mtp) cc_final: 0.6996 (mtp) REVERT: Ba 11 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: B 11 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: G 11 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: L 7 LYS cc_start: 0.7834 (mtmm) cc_final: 0.7388 (mtmp) REVERT: L 11 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: V 7 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7255 (mtmp) REVERT: V 11 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: Z 7 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7507 (mtmp) REVERT: Z 11 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: Id 7 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7137 (mttp) REVERT: Id 11 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: Nh 7 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7302 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: Sl 7 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7304 (mttp) REVERT: Sl 11 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: Xp 11 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: Yb 11 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: C 7 LYS cc_start: 0.7651 (mtmm) cc_final: 0.7401 (mtmp) REVERT: C 11 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: H 7 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7451 (mttp) REVERT: H 11 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: M 7 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7404 (mttp) REVERT: M 11 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: W 7 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7443 (mtmm) REVERT: W 11 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: Ca 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: He 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: Mi 11 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: Wq 7 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7220 (mttp) REVERT: Wq 11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: Ae 7 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7604 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: D 7 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7206 (mttp) REVERT: D 11 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: I 7 LYS cc_start: 0.7662 (mtmm) cc_final: 0.7242 (mttp) REVERT: I 11 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: N 7 LYS cc_start: 0.7622 (mtmm) cc_final: 0.7374 (mtmp) REVERT: N 11 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: Gf 7 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7422 (mttp) REVERT: Gf 11 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: Lj 7 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7243 (mttp) REVERT: Lj 11 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: Qn 1 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5770 (ptp) REVERT: Qn 7 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7228 (mttp) REVERT: Qn 11 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: Vr 7 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7331 (mtpt) REVERT: Vr 11 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: Zt 1 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.5622 (ptp) REVERT: Zt 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: O 7 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7301 (mttp) REVERT: O 11 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: Y 11 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: Dc 7 LYS cc_start: 0.7671 (mtmm) cc_final: 0.7385 (mttp) REVERT: Dc 11 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: Fg 7 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7410 (mtmp) REVERT: Fg 11 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: Kk 7 LYS cc_start: 0.7794 (mtmm) cc_final: 0.7571 (mtmp) REVERT: Kk 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: Po 7 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7285 (mtpt) REVERT: Po 11 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: Us 11 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: Hu 1 MET cc_start: 0.6210 (mpp) cc_final: 0.5603 (mmm) REVERT: Hu 7 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7458 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: P 7 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7320 (mtmp) REVERT: P 11 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: Gv 1 MET cc_start: 0.5913 (mpp) cc_final: 0.5515 (ptp) REVERT: Gv 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: Q 11 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: Fw 7 LYS cc_start: 0.7695 (mtmm) cc_final: 0.7203 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: R 1 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6025 (mmm) REVERT: R 7 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7362 (mtpt) REVERT: R 11 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: Ex 11 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: S 7 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7272 (mttp) REVERT: S 11 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: Dy 7 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7156 (mttp) REVERT: Dy 11 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: T 11 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: Cz 7 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7226 (mttp) REVERT: Cz 11 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: 2 7 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7360 (mttp) REVERT: 2 11 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7019 (mp0) outliers start: 147 outliers final: 71 residues processed: 673 average time/residue: 2.4111 time to fit residues: 1907.7309 Evaluate side-chains 746 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 609 time to evaluate : 3.072 ------------------------------------------------------------------------------- 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 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 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 11 GLU 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 11 GLU 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 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 11 GLU Chi-restraints excluded: chain Xp residue 41 LEU Chi-restraints excluded: chain Yb residue 11 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain H residue 1 MET 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 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 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 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 34 ASP Chi-restraints excluded: chain Bb residue 41 LEU Chi-restraints excluded: chain Gf residue 3 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 3 GLU 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 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 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 11 GLU Chi-restraints excluded: chain Kk residue 34 ASP Chi-restraints excluded: chain Po residue 1 MET Chi-restraints excluded: chain Po residue 11 GLU Chi-restraints excluded: chain Po residue 34 ASP 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 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 Fw residue 41 LEU Chi-restraints excluded: chain R residue 1 MET 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 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 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 41 LEU 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: 1.9990 chunk 252 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 276 optimal weight: 0.3980 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 268 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.7445 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 24660 Z= 0.145 Angle : 0.403 4.059 32940 Z= 0.223 Chirality : 0.033 0.086 4080 Planarity : 0.001 0.007 4080 Dihedral : 3.029 33.352 3360 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Rotamer: Outliers : 3.48 % Allowed : 21.78 % Favored : 74.73 % 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: 3.45 (0.15), residues: 3120 helix: 2.12 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 4.90 (0.61), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE U 45 TYR 0.006 0.001 TYRHe 8 ARG 0.001 0.000 ARG 2 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 700 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 608 time to evaluate : 3.082 Fit side-chains REVERT: A 7 LYS cc_start: 0.7697 (mtmm) cc_final: 0.7250 (mtmp) REVERT: A 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: F 7 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7341 (mtmp) REVERT: F 11 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: K 11 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: J1 7 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7304 (mtmm) REVERT: J1 11 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: Od 11 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: Tc 7 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7402 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: Ba 2 MET cc_start: 0.7181 (mtp) cc_final: 0.6924 (mtp) REVERT: B 11 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: G 11 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: L 7 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7383 (mtmp) REVERT: L 11 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: V 7 LYS cc_start: 0.7673 (mtmm) cc_final: 0.7260 (mtmp) REVERT: V 11 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: Z 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: Id 7 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7197 (mttp) REVERT: Id 11 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: Nh 7 LYS cc_start: 0.7653 (mtmm) cc_final: 0.7282 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: Sl 7 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7284 (mttp) REVERT: Sl 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: Xp 11 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: Yb 11 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: C 1 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.5885 (ptp) REVERT: C 7 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7396 (mtmp) REVERT: C 11 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: H 1 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5868 (ptp) REVERT: H 7 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7500 (mtmm) REVERT: H 11 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: M 7 LYS cc_start: 0.7689 (mtmm) cc_final: 0.7391 (mttp) REVERT: M 11 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: W 7 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7391 (mtmm) REVERT: W 11 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: Ca 11 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: He 7 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7545 (mttp) REVERT: He 11 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: Mi 11 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: Rm 50 ASN cc_start: 0.6628 (m-40) cc_final: 0.6426 (m-40) REVERT: Wq 7 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7167 (mttp) REVERT: Wq 11 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: Ae 7 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7606 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: D 7 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7221 (mttp) REVERT: D 11 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: I 7 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7331 (mttp) REVERT: I 11 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: N 7 LYS cc_start: 0.7513 (mtmm) cc_final: 0.7308 (mtmp) REVERT: N 11 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: X 11 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: Bb 11 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: Gf 7 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7443 (mttp) REVERT: Gf 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: Lj 7 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7234 (mttp) REVERT: Lj 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: Qn 1 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5801 (ptp) REVERT: Qn 7 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7239 (mttp) REVERT: Qn 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: Zt 1 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5544 (ptp) REVERT: Zt 7 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7468 (mttp) REVERT: Zt 11 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: E 11 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: J 50 ASN cc_start: 0.6568 (m-40) cc_final: 0.6368 (m-40) REVERT: O 7 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7307 (mttp) REVERT: O 11 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: Y 11 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: Fg 7 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7404 (mttp) REVERT: Fg 11 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: Kk 11 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: Po 1 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.5791 (ptp) REVERT: Po 7 LYS cc_start: 0.7777 (mtmm) cc_final: 0.7510 (mtmm) REVERT: Po 11 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: Us 11 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: Hu 1 MET cc_start: 0.6121 (mpp) cc_final: 0.5574 (mmm) REVERT: Hu 7 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7386 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: P 7 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7283 (mtmp) REVERT: P 11 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: Gv 1 MET cc_start: 0.5717 (mpp) cc_final: 0.5396 (mtt) REVERT: Gv 11 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: Q 11 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: Fw 7 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7312 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: R 1 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5256 (ptt) REVERT: R 11 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: Ex 50 ASN cc_start: 0.6652 (m-40) cc_final: 0.6427 (m-40) REVERT: S 7 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7210 (mttp) REVERT: S 11 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: Dy 7 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7194 (mttp) REVERT: Dy 11 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: T 11 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: Cz 7 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7292 (mttp) REVERT: Cz 11 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: 0 11 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: 2 7 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7228 (mttm) REVERT: 2 11 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6973 (mp0) outliers start: 92 outliers final: 15 residues processed: 630 average time/residue: 2.4145 time to fit residues: 1765.2392 Evaluate side-chains 687 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 602 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain K residue 11 GLU 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 11 GLU 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 11 GLU Chi-restraints excluded: chain Z residue 11 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 Sl residue 7 LYS 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 1 MET Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain M residue 11 GLU 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 He residue 1 MET 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 11 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain N residue 11 GLU 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 Gf residue 11 GLU Chi-restraints excluded: chain Lj residue 7 LYS Chi-restraints excluded: chain Lj residue 11 GLU 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 34 ASP 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 11 GLU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain Y 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 1 MET 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 11 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 6.9990 chunk 284 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 chunk 275 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.7454 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24660 Z= 0.160 Angle : 0.420 8.248 32940 Z= 0.230 Chirality : 0.033 0.086 4080 Planarity : 0.001 0.027 4080 Dihedral : 2.883 20.478 3360 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 3.56 % Allowed : 21.78 % Favored : 74.66 % 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: 3.55 (0.15), residues: 3120 helix: 2.19 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 4.83 (0.61), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE D 45 TYR 0.007 0.002 TYR V 8 ARG 0.001 0.000 ARG U 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 680 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 586 time to evaluate : 3.065 Fit side-chains REVERT: A 7 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7288 (mtmp) REVERT: A 11 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: F 7 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7345 (mtmp) REVERT: F 11 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: K 11 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: U 11 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: J1 7 LYS cc_start: 0.7628 (mtpt) cc_final: 0.7309 (mtmm) REVERT: J1 11 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: Od 11 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: Tc 7 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7394 (mtmp) REVERT: Tc 11 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: Ba 2 MET cc_start: 0.7222 (mtp) cc_final: 0.6947 (mtp) REVERT: Ba 11 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: B 11 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: G 11 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: L 7 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7349 (mtmp) REVERT: L 11 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: V 7 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7293 (mtmp) REVERT: V 11 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: Z 11 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: Id 7 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7261 (mttp) REVERT: Id 11 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: Nh 7 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7271 (mtmp) REVERT: Nh 11 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: Sl 7 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7266 (mttp) REVERT: Sl 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: Xp 11 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: Yb 11 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: C 1 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.5860 (ptp) REVERT: C 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: H 1 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.5850 (ptp) REVERT: H 7 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7538 (mtmm) REVERT: H 11 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: M 7 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7382 (mttp) REVERT: M 11 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: W 11 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: Ca 11 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: He 1 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.5754 (ptp) REVERT: He 7 LYS cc_start: 0.7818 (mtmm) cc_final: 0.7588 (mttp) REVERT: He 11 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: Mi 11 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: Rm 11 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: Rm 50 ASN cc_start: 0.6624 (m-40) cc_final: 0.6396 (m-40) REVERT: Wq 7 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7165 (mttp) REVERT: Wq 11 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: Ae 7 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7605 (mtmm) REVERT: Ae 11 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: D 7 LYS cc_start: 0.7690 (mtmm) cc_final: 0.7223 (mttp) REVERT: D 11 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: I 7 LYS cc_start: 0.7686 (mtmm) cc_final: 0.7267 (mttp) REVERT: I 11 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: N 11 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: X 11 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: Bb 11 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: Gf 7 LYS cc_start: 0.7734 (mtmm) cc_final: 0.7436 (mttp) REVERT: Gf 11 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: Lj 7 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7219 (mttp) REVERT: Lj 11 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: Qn 1 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5785 (ptp) REVERT: Qn 11 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: Vr 11 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: Zt 1 MET cc_start: 0.5933 (OUTLIER) cc_final: 0.5509 (ptp) REVERT: Zt 7 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7471 (mttp) REVERT: Zt 11 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: E 11 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: J 11 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: J 50 ASN cc_start: 0.6559 (m-40) cc_final: 0.6335 (m-40) REVERT: O 7 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7305 (mttp) REVERT: O 11 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: Y 11 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: Dc 11 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: Fg 7 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7436 (mttp) REVERT: Fg 11 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: Kk 11 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: Po 1 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5775 (ptp) REVERT: Po 7 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7518 (mtmm) REVERT: Po 11 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: Us 11 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: Hu 1 MET cc_start: 0.6076 (mpp) cc_final: 0.5562 (mmm) REVERT: Hu 7 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7393 (mtmp) REVERT: Hu 11 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: P 7 LYS cc_start: 0.7848 (mtmm) cc_final: 0.7305 (mtmp) REVERT: P 11 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: Gv 1 MET cc_start: 0.5763 (mpp) cc_final: 0.5480 (ptp) REVERT: Gv 11 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: Q 11 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: Fw 7 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7306 (mtmp) REVERT: Fw 11 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: R 1 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.5276 (ptt) REVERT: R 11 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: Ex 50 ASN cc_start: 0.6608 (m-40) cc_final: 0.6352 (m-40) REVERT: S 7 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7214 (mttp) REVERT: S 11 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: Dy 7 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7198 (mttp) REVERT: Dy 11 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: Cz 7 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7265 (mttp) REVERT: Cz 11 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: 0 11 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: 2 7 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7249 (mttm) REVERT: 2 11 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7038 (mp0) outliers start: 94 outliers final: 16 residues processed: 610 average time/residue: 2.4379 time to fit residues: 1728.3316 Evaluate side-chains 676 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 585 time to evaluate : 3.038 ------------------------------------------------------------------------------- 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 K residue 11 GLU 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 Tc residue 11 GLU Chi-restraints excluded: chain Ba residue 11 GLU Chi-restraints excluded: chain Ba residue 41 LEU 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 L residue 41 LEU Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain Z residue 11 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 Sl residue 7 LYS 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 1 MET Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain M residue 11 GLU 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 He residue 1 MET 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 11 GLU Chi-restraints excluded: chain Wq residue 7 LYS Chi-restraints excluded: chain Wq residue 11 GLU Chi-restraints excluded: chain Ae residue 11 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain N residue 11 GLU 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 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 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 41 LEU Chi-restraints excluded: chain J residue 11 GLU Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain Y residue 11 GLU 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 1 MET 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 11 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 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 Dy residue 7 LYS Chi-restraints excluded: chain Dy 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 3.9990 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: 1.9990 chunk 238 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.172765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133669 restraints weight = 68807.449| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.61 r_work: 0.3248 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 24660 Z= 0.262 Angle : 0.499 5.169 32940 Z= 0.266 Chirality : 0.034 0.092 4080 Planarity : 0.002 0.008 4080 Dihedral : 3.166 19.219 3360 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 4.13 % Allowed : 21.10 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.92 (0.15), residues: 3120 helix: 1.76 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : 4.98 (0.62), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE A 45 TYR 0.009 0.002 TYR V 8 ARG 0.001 0.000 ARGOd 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22801.89 seconds wall clock time: 384 minutes 31.67 seconds (23071.67 seconds total)