Starting phenix.real_space_refine on Mon Jul 22 18:38:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk9_21225/07_2024/6vk9_21225.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk9_21225/07_2024/6vk9_21225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk9_21225/07_2024/6vk9_21225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk9_21225/07_2024/6vk9_21225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk9_21225/07_2024/6vk9_21225.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk9_21225/07_2024/6vk9_21225.cif" } resolution = 3.8 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 12432 2.51 5 N 3232 2.21 5 O 4128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O ARG 41": "NH1" <-> "NH2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 28": "NH1" <-> "NH2" Residue "Q ARG 41": "NH1" <-> "NH2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 41": "NH1" <-> "NH2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 41": "NH1" <-> "NH2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G ARG 41": "NH1" <-> "NH2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W ARG 41": "NH1" <-> "NH2" Residue "W GLU 48": "OE1" <-> "OE2" Residue "W PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 28": "NH1" <-> "NH2" Residue "Y ARG 41": "NH1" <-> "NH2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 28": "NH1" <-> "NH2" Residue "0 ARG 41": "NH1" <-> "NH2" Residue "0 GLU 48": "OE1" <-> "OE2" Residue "0 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 28": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "2 GLU 48": "OE1" <-> "OE2" Residue "2 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 28": "NH1" <-> "NH2" Residue "4 ARG 41": "NH1" <-> "NH2" Residue "4 GLU 48": "OE1" <-> "OE2" Residue "4 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19808 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "O" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "Q" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "S" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "U" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "G" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "I" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "K" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "M" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "C" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "W" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "Y" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "0" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "2" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "4" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "D" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "B" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "P" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "R" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "T" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "V" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "H" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "J" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "N" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "F" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "X" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "Z" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "1" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "3" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "5" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Time building chain proxies: 10.89, per 1000 atoms: 0.55 Number of scatterers: 19808 At special positions: 0 Unit cell: (81.378, 81.378, 255.642, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 4128 8.00 N 3232 7.00 C 12432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.19 Conformation dependent library (CDL) restraints added in 3.8 seconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 16 sheets defined 25.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 14 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL O 10 " --> pdb=" O LEU O 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA O 11 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY O 14 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA O 31 " --> pdb=" O TYR O 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER O 38 " --> pdb=" O SER O 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA O 52 " --> pdb=" O GLU O 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL Q 10 " --> pdb=" O LEU Q 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Q 11 " --> pdb=" O LEU Q 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY Q 14 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 55 removed outlier: 4.783A pdb=" N ALA Q 31 " --> pdb=" O TYR Q 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Q 38 " --> pdb=" O SER Q 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR Q 45 " --> pdb=" O ARG Q 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA Q 52 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL S 10 " --> pdb=" O LEU S 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA S 11 " --> pdb=" O LEU S 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 55 removed outlier: 4.781A pdb=" N ALA S 31 " --> pdb=" O TYR S 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR S 45 " --> pdb=" O ARG S 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA S 52 " --> pdb=" O GLU S 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL U 10 " --> pdb=" O LEU U 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA U 11 " --> pdb=" O LEU U 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY U 14 " --> pdb=" O VAL U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA U 31 " --> pdb=" O TYR U 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER U 38 " --> pdb=" O SER U 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR U 45 " --> pdb=" O ARG U 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA U 52 " --> pdb=" O GLU U 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL G 10 " --> pdb=" O LEU G 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER G 38 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR G 45 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL I 10 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA I 11 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 14 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA I 31 " --> pdb=" O TYR I 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL K 10 " --> pdb=" O LEU K 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 11 " --> pdb=" O LEU K 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY K 14 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA K 31 " --> pdb=" O TYR K 27 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 38 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR K 45 " --> pdb=" O ARG K 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL M 10 " --> pdb=" O LEU M 6 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA M 11 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY M 14 " --> pdb=" O VAL M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA M 31 " --> pdb=" O TYR M 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR M 45 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 55 removed outlier: 4.781A pdb=" N ALA C 31 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR C 45 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 14 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 55 removed outlier: 4.781A pdb=" N ALA E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL W 10 " --> pdb=" O LEU W 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA W 11 " --> pdb=" O LEU W 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY W 14 " --> pdb=" O VAL W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA W 31 " --> pdb=" O TYR W 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER W 38 " --> pdb=" O SER W 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR W 45 " --> pdb=" O ARG W 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA W 52 " --> pdb=" O GLU W 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Y 11 " --> pdb=" O LEU Y 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY Y 14 " --> pdb=" O VAL Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA Y 31 " --> pdb=" O TYR Y 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Y 38 " --> pdb=" O SER Y 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR Y 45 " --> pdb=" O ARG Y 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) Processing helix chain '0' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL 0 10 " --> pdb=" O LEU 0 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 0 11 " --> pdb=" O LEU 0 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY 0 14 " --> pdb=" O VAL 0 10 " (cutoff:3.500A) Processing helix chain '0' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA 0 31 " --> pdb=" O TYR 0 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 0 38 " --> pdb=" O SER 0 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA 0 52 " --> pdb=" O GLU 0 48 " (cutoff:3.500A) Processing helix chain '2' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL 2 10 " --> pdb=" O LEU 2 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 2 11 " --> pdb=" O LEU 2 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY 2 14 " --> pdb=" O VAL 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA 2 31 " --> pdb=" O TYR 2 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 2 38 " --> pdb=" O SER 2 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA 2 52 " --> pdb=" O GLU 2 48 " (cutoff:3.500A) Processing helix chain '4' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL 4 10 " --> pdb=" O LEU 4 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 4 11 " --> pdb=" O LEU 4 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY 4 14 " --> pdb=" O VAL 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA 4 31 " --> pdb=" O TYR 4 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 4 38 " --> pdb=" O SER 4 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR 4 45 " --> pdb=" O ARG 4 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA 4 52 " --> pdb=" O GLU 4 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 22 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 28 Processing sheet with id=AA3, first strand: chain 'P' and resid 22 through 28 Processing sheet with id=AA4, first strand: chain 'R' and resid 22 through 28 Processing sheet with id=AA5, first strand: chain 'T' and resid 22 through 28 Processing sheet with id=AA6, first strand: chain 'V' and resid 22 through 28 Processing sheet with id=AA7, first strand: chain 'H' and resid 22 through 28 Processing sheet with id=AA8, first strand: chain 'J' and resid 22 through 28 Processing sheet with id=AA9, first strand: chain 'L' and resid 22 through 28 Processing sheet with id=AB1, first strand: chain 'N' and resid 22 through 28 Processing sheet with id=AB2, first strand: chain 'F' and resid 22 through 28 Processing sheet with id=AB3, first strand: chain 'X' and resid 22 through 28 Processing sheet with id=AB4, first strand: chain 'Z' and resid 22 through 28 Processing sheet with id=AB5, first strand: chain '1' and resid 22 through 28 Processing sheet with id=AB6, first strand: chain '3' and resid 22 through 28 Processing sheet with id=AB7, first strand: chain '5' and resid 22 through 28 624 hydrogen bonds defined for protein. 1824 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: 4.66 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4197 1.33 - 1.45: 4847 1.45 - 1.57: 11100 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 20176 Sorted by residual: bond pdb=" CA PRO C 58 " pdb=" C PRO C 58 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.24e+01 bond pdb=" CA PRO 2 58 " pdb=" C PRO 2 58 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.18e+01 bond pdb=" CA PRO S 58 " pdb=" C PRO S 58 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.18e+01 bond pdb=" CA PRO K 58 " pdb=" C PRO K 58 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.16e+01 bond pdb=" CA PRO G 58 " pdb=" C PRO G 58 " ideal model delta sigma weight residual 1.514 1.540 -0.025 5.50e-03 3.31e+04 2.15e+01 ... (remaining 20171 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.95: 384 105.95 - 113.02: 9933 113.02 - 120.10: 8292 120.10 - 127.17: 8671 127.17 - 134.24: 224 Bond angle restraints: 27504 Sorted by residual: angle pdb=" N THR P 15 " pdb=" CA THR P 15 " pdb=" C THR P 15 " ideal model delta sigma weight residual 111.30 119.27 -7.97 1.36e+00 5.41e-01 3.44e+01 angle pdb=" N THR X 15 " pdb=" CA THR X 15 " pdb=" C THR X 15 " ideal model delta sigma weight residual 111.30 119.27 -7.97 1.36e+00 5.41e-01 3.44e+01 angle pdb=" N THR 5 15 " pdb=" CA THR 5 15 " pdb=" C THR 5 15 " ideal model delta sigma weight residual 111.30 119.27 -7.97 1.36e+00 5.41e-01 3.43e+01 angle pdb=" N THR Z 15 " pdb=" CA THR Z 15 " pdb=" C THR Z 15 " ideal model delta sigma weight residual 111.30 119.26 -7.96 1.36e+00 5.41e-01 3.43e+01 angle pdb=" N THR J 15 " pdb=" CA THR J 15 " pdb=" C THR J 15 " ideal model delta sigma weight residual 111.30 119.25 -7.95 1.36e+00 5.41e-01 3.42e+01 ... (remaining 27499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 10768 16.93 - 33.85: 768 33.85 - 50.77: 208 50.77 - 67.70: 64 67.70 - 84.62: 16 Dihedral angle restraints: 11824 sinusoidal: 4224 harmonic: 7600 Sorted by residual: dihedral pdb=" CA THR N 62 " pdb=" C THR N 62 " pdb=" N SER N 63 " pdb=" CA SER N 63 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR T 62 " pdb=" C THR T 62 " pdb=" N SER T 63 " pdb=" CA SER T 63 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR X 62 " pdb=" C THR X 62 " pdb=" N SER X 63 " pdb=" CA SER X 63 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 11821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2427 0.085 - 0.169: 573 0.169 - 0.254: 216 0.254 - 0.339: 16 0.339 - 0.424: 16 Chirality restraints: 3248 Sorted by residual: chirality pdb=" CA THR X 15 " pdb=" N THR X 15 " pdb=" C THR X 15 " pdb=" CB THR X 15 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CA THR R 15 " pdb=" N THR R 15 " pdb=" C THR R 15 " pdb=" CB THR R 15 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA THR J 15 " pdb=" N THR J 15 " pdb=" C THR J 15 " pdb=" CB THR J 15 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 3245 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 43 " 0.071 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR 1 43 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 43 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 43 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 43 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 43 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR 1 43 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR 1 43 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 43 " -0.071 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR N 43 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR N 43 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR N 43 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR N 43 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR N 43 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR N 43 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR N 43 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 43 " -0.071 2.00e-02 2.50e+03 4.41e-02 3.88e+01 pdb=" CG TYR 3 43 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 43 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 43 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 43 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 43 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR 3 43 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR 3 43 " -0.077 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 106 2.60 - 3.17: 19613 3.17 - 3.75: 29996 3.75 - 4.32: 43928 4.32 - 4.90: 69370 Nonbonded interactions: 163013 Sorted by model distance: nonbonded pdb=" NZ LYS S 30 " pdb=" OD1 ASP M 53 " model vdw 2.023 2.520 nonbonded pdb=" NZ LYS K 30 " pdb=" OD1 ASP E 53 " model vdw 2.043 2.520 nonbonded pdb=" OD1 ASP W 53 " pdb=" NZ LYS 2 30 " model vdw 2.085 2.520 nonbonded pdb=" NZ LYS I 30 " pdb=" OD1 ASP C 53 " model vdw 2.088 2.520 nonbonded pdb=" NZ LYS Q 30 " pdb=" OD1 ASP K 53 " model vdw 2.090 2.520 ... (remaining 163008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 51.060 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.140 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.049 20176 Z= 0.684 Angle : 1.574 7.975 27504 Z= 1.023 Chirality : 0.090 0.424 3248 Planarity : 0.012 0.068 3520 Dihedral : 13.960 84.624 6928 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Cbeta Deviations : 0.65 % 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: -3.98 (0.14), residues: 2576 helix: -3.46 (0.12), residues: 752 sheet: 0.08 (0.19), residues: 320 loop : -2.95 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.012 TRP V 66 PHE 0.065 0.009 PHE O 51 TYR 0.077 0.018 TYR N 43 ARG 0.001 0.000 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 945 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.8925 (t0) cc_final: 0.8416 (m-40) REVERT: A 51 PHE cc_start: 0.8622 (t80) cc_final: 0.8088 (t80) REVERT: Q 23 GLN cc_start: 0.7779 (mp10) cc_final: 0.7515 (mp10) REVERT: G 23 GLN cc_start: 0.8371 (mp10) cc_final: 0.8020 (mp10) REVERT: G 28 ARG cc_start: 0.8662 (ttp-170) cc_final: 0.8427 (ttm110) REVERT: G 42 ASN cc_start: 0.8652 (t0) cc_final: 0.8421 (t0) REVERT: I 42 ASN cc_start: 0.8415 (t0) cc_final: 0.8084 (m-40) REVERT: C 42 ASN cc_start: 0.8779 (t0) cc_final: 0.8419 (t0) REVERT: C 51 PHE cc_start: 0.8841 (t80) cc_final: 0.8095 (t80) REVERT: C 58 PRO cc_start: 0.9242 (Cg_exo) cc_final: 0.8994 (Cg_endo) REVERT: E 23 GLN cc_start: 0.8494 (mp10) cc_final: 0.8246 (pm20) REVERT: E 41 ARG cc_start: 0.8888 (tmt-80) cc_final: 0.8552 (tmt170) REVERT: E 42 ASN cc_start: 0.8713 (t0) cc_final: 0.8258 (t0) REVERT: E 51 PHE cc_start: 0.8913 (t80) cc_final: 0.8209 (t80) REVERT: E 58 PRO cc_start: 0.9337 (Cg_exo) cc_final: 0.9130 (Cg_endo) REVERT: Y 41 ARG cc_start: 0.8478 (tmt-80) cc_final: 0.7655 (ttp-170) REVERT: Y 55 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8704 (mp10) REVERT: Y 60 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7098 (tm-30) REVERT: 0 41 ARG cc_start: 0.8664 (tmt-80) cc_final: 0.7521 (ttp-170) REVERT: 4 37 SER cc_start: 0.9288 (p) cc_final: 0.8891 (p) REVERT: 4 41 ARG cc_start: 0.8849 (tmt-80) cc_final: 0.7776 (ttp-170) REVERT: D 21 ASN cc_start: 0.8864 (t0) cc_final: 0.8651 (t0) REVERT: D 56 PHE cc_start: 0.9071 (m-80) cc_final: 0.8711 (m-10) REVERT: D 76 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7782 (mmmm) REVERT: B 17 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8596 (mmmt) REVERT: B 21 ASN cc_start: 0.8766 (t0) cc_final: 0.8462 (t0) REVERT: B 49 ASN cc_start: 0.9098 (t0) cc_final: 0.8766 (t0) REVERT: B 76 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7647 (mmmt) REVERT: B 82 ASP cc_start: 0.6963 (p0) cc_final: 0.6555 (p0) REVERT: P 17 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8294 (mmmm) REVERT: R 82 ASP cc_start: 0.8632 (p0) cc_final: 0.8085 (p0) REVERT: T 82 ASP cc_start: 0.9032 (p0) cc_final: 0.8329 (p0) REVERT: T 93 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8232 (mtpp) REVERT: V 80 ASP cc_start: 0.8301 (m-30) cc_final: 0.8096 (m-30) REVERT: V 82 ASP cc_start: 0.8669 (p0) cc_final: 0.8215 (p0) REVERT: V 93 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8244 (mtpp) REVERT: H 21 ASN cc_start: 0.8384 (t0) cc_final: 0.8008 (t0) REVERT: H 79 SER cc_start: 0.8643 (p) cc_final: 0.8439 (p) REVERT: H 104 GLN cc_start: 0.7798 (pm20) cc_final: 0.6914 (pp30) REVERT: J 13 ASP cc_start: 0.8075 (t70) cc_final: 0.7828 (t70) REVERT: L 16 PHE cc_start: 0.8334 (t80) cc_final: 0.7822 (t80) REVERT: N 67 TYR cc_start: 0.9102 (p90) cc_final: 0.8819 (p90) REVERT: N 93 LYS cc_start: 0.8138 (mmmm) cc_final: 0.7936 (mtpp) REVERT: F 73 TRP cc_start: 0.8110 (p90) cc_final: 0.7736 (p90) REVERT: X 61 ASN cc_start: 0.8354 (p0) cc_final: 0.7714 (t0) REVERT: X 80 ASP cc_start: 0.8848 (m-30) cc_final: 0.8571 (m-30) REVERT: X 93 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8600 (mmmm) REVERT: Z 66 TRP cc_start: 0.8475 (m100) cc_final: 0.7973 (m100) REVERT: Z 93 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8631 (mmmm) REVERT: Z 101 TRP cc_start: 0.7091 (p90) cc_final: 0.6859 (p-90) REVERT: 1 67 TYR cc_start: 0.8531 (p90) cc_final: 0.8020 (p90) REVERT: 1 82 ASP cc_start: 0.8649 (p0) cc_final: 0.8077 (p0) REVERT: 1 101 TRP cc_start: 0.6986 (p90) cc_final: 0.6744 (p90) REVERT: 3 17 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7714 (mmmm) REVERT: 3 21 ASN cc_start: 0.8948 (t0) cc_final: 0.8576 (t0) REVERT: 3 82 ASP cc_start: 0.8077 (p0) cc_final: 0.7056 (p0) REVERT: 5 21 ASN cc_start: 0.8964 (t0) cc_final: 0.8593 (t0) REVERT: 5 42 ASP cc_start: 0.7735 (m-30) cc_final: 0.7498 (m-30) REVERT: 5 49 ASN cc_start: 0.8869 (t0) cc_final: 0.8669 (t0) REVERT: 5 68 ILE cc_start: 0.8319 (mt) cc_final: 0.8071 (tp) REVERT: 5 82 ASP cc_start: 0.8270 (p0) cc_final: 0.7214 (p0) REVERT: 5 93 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8683 (mmmm) outliers start: 0 outliers final: 0 residues processed: 945 average time/residue: 0.3309 time to fit residues: 476.0943 Evaluate side-chains 640 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 640 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 149 optimal weight: 0.0470 chunk 232 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 33 ASN S 33 ASN U 33 ASN E 33 ASN ** Y 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 ASN 4 33 ASN D 30 ASN D 40 ASN B 70 ASN P 21 ASN P 30 ASN P 60 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN V 30 ASN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 ASN N 21 ASN N 64 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 ASN Z 21 ASN 3 30 ASN 5 104 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20176 Z= 0.232 Angle : 0.650 8.792 27504 Z= 0.360 Chirality : 0.043 0.200 3248 Planarity : 0.005 0.037 3520 Dihedral : 8.900 84.614 2784 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.75 % Allowed : 17.08 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.32 (0.16), residues: 2576 helix: -0.97 (0.20), residues: 736 sheet: 0.09 (0.22), residues: 304 loop : -2.29 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Z 73 PHE 0.025 0.002 PHE J 56 TYR 0.019 0.002 TYR 3 43 ARG 0.007 0.001 ARG Y 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 696 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8516 (tttt) REVERT: O 19 ILE cc_start: 0.8098 (mt) cc_final: 0.7834 (mm) REVERT: Q 28 ARG cc_start: 0.7829 (ttp-110) cc_final: 0.7618 (ttp-170) REVERT: G 25 SER cc_start: 0.8919 (m) cc_final: 0.8516 (p) REVERT: G 51 PHE cc_start: 0.8771 (t80) cc_final: 0.8357 (t80) REVERT: I 34 SER cc_start: 0.9197 (m) cc_final: 0.8797 (t) REVERT: I 51 PHE cc_start: 0.8835 (t80) cc_final: 0.8458 (t80) REVERT: K 55 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8376 (mp10) REVERT: M 55 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8011 (mm-40) REVERT: C 48 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 51 PHE cc_start: 0.8785 (t80) cc_final: 0.8266 (t80) REVERT: E 25 SER cc_start: 0.9070 (m) cc_final: 0.8701 (t) REVERT: E 51 PHE cc_start: 0.8716 (t80) cc_final: 0.8279 (t80) REVERT: W 48 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7973 (tm-30) REVERT: Y 41 ARG cc_start: 0.8508 (tmt-80) cc_final: 0.7421 (ttp-170) REVERT: Y 55 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8507 (mp10) REVERT: Y 60 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7968 (mt-10) REVERT: 0 25 SER cc_start: 0.9249 (m) cc_final: 0.8921 (p) REVERT: 0 41 ARG cc_start: 0.8602 (tmt-80) cc_final: 0.7462 (ttp-170) REVERT: 4 19 ILE cc_start: 0.8607 (mm) cc_final: 0.8397 (mm) REVERT: 4 41 ARG cc_start: 0.8844 (tmt-80) cc_final: 0.7635 (ttp-170) REVERT: 4 48 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8180 (tm-30) REVERT: D 21 ASN cc_start: 0.8888 (t0) cc_final: 0.8643 (t0) REVERT: D 56 PHE cc_start: 0.9019 (m-80) cc_final: 0.8751 (m-10) REVERT: D 76 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8073 (mmmm) REVERT: B 17 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8554 (mmmt) REVERT: B 21 ASN cc_start: 0.8804 (t0) cc_final: 0.8538 (t0) REVERT: B 76 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7842 (mmmt) REVERT: B 82 ASP cc_start: 0.6990 (p0) cc_final: 0.6692 (p0) REVERT: P 17 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8372 (mmmm) REVERT: P 101 TRP cc_start: 0.6679 (p-90) cc_final: 0.6361 (p-90) REVERT: R 101 TRP cc_start: 0.6980 (p-90) cc_final: 0.6548 (p-90) REVERT: T 93 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8229 (mtpp) REVERT: V 17 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7768 (mmmm) REVERT: H 93 LYS cc_start: 0.8540 (mmmm) cc_final: 0.8311 (mmmm) REVERT: J 13 ASP cc_start: 0.8176 (t70) cc_final: 0.7868 (t70) REVERT: L 13 ASP cc_start: 0.8830 (p0) cc_final: 0.8614 (p0) REVERT: L 73 TRP cc_start: 0.8040 (p90) cc_final: 0.7455 (p90) REVERT: N 42 ASP cc_start: 0.8153 (t0) cc_final: 0.7887 (t70) REVERT: N 93 LYS cc_start: 0.8096 (mmmm) cc_final: 0.7805 (mtpp) REVERT: F 73 TRP cc_start: 0.8420 (p90) cc_final: 0.7940 (p90) REVERT: X 17 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8172 (mmmm) REVERT: X 27 PHE cc_start: 0.8520 (m-80) cc_final: 0.8293 (m-10) REVERT: X 61 ASN cc_start: 0.8405 (p0) cc_final: 0.7448 (t0) REVERT: X 69 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8225 (tm-30) REVERT: X 93 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8542 (mmmm) REVERT: Z 42 ASP cc_start: 0.8137 (t0) cc_final: 0.7737 (t70) REVERT: Z 93 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8566 (mmmm) REVERT: Z 104 GLN cc_start: 0.6929 (pp30) cc_final: 0.6635 (pp30) REVERT: 1 12 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8861 (mmmm) REVERT: 1 17 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8339 (mmmm) REVERT: 1 42 ASP cc_start: 0.8033 (t0) cc_final: 0.7513 (t70) REVERT: 1 93 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8570 (mtpt) REVERT: 1 101 TRP cc_start: 0.6912 (p90) cc_final: 0.6657 (p90) REVERT: 3 17 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8089 (mmmm) REVERT: 3 42 ASP cc_start: 0.8000 (t0) cc_final: 0.7519 (t70) REVERT: 3 82 ASP cc_start: 0.7940 (p0) cc_final: 0.7674 (p0) REVERT: 3 93 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8581 (mtpt) REVERT: 5 21 ASN cc_start: 0.8839 (t0) cc_final: 0.8126 (t0) REVERT: 5 68 ILE cc_start: 0.8064 (mt) cc_final: 0.7841 (tp) REVERT: 5 82 ASP cc_start: 0.8275 (p0) cc_final: 0.7761 (p0) outliers start: 81 outliers final: 55 residues processed: 729 average time/residue: 0.3078 time to fit residues: 338.5364 Evaluate side-chains 652 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 597 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 2 residue 13 ILE Chi-restraints excluded: chain 2 residue 19 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 30 ASN Chi-restraints excluded: chain P residue 46 ASN Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 46 ASN Chi-restraints excluded: chain R residue 61 ASN Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain V residue 30 ASN Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain X residue 13 ASP Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 70 ASN Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 59 THR Chi-restraints excluded: chain 5 residue 70 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 193 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 232 optimal weight: 0.9980 chunk 251 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN 2 33 ASN D 40 ASN P 30 ASN P 60 ASN R 21 ASN R 30 ASN T 30 ASN V 30 ASN H 21 ASN J 21 ASN L 61 ASN N 21 ASN N 64 ASN F 21 ASN Z 21 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20176 Z= 0.193 Angle : 0.596 8.675 27504 Z= 0.325 Chirality : 0.042 0.209 3248 Planarity : 0.004 0.039 3520 Dihedral : 8.368 86.036 2784 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 4.54 % Allowed : 19.03 % Favored : 76.44 % 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: -1.73 (0.17), residues: 2576 helix: -0.11 (0.21), residues: 736 sheet: 0.04 (0.24), residues: 304 loop : -2.02 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Z 73 PHE 0.019 0.002 PHE X 14 TYR 0.024 0.002 TYR X 43 ARG 0.013 0.001 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 639 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8465 (tttt) REVERT: A 51 PHE cc_start: 0.8814 (t80) cc_final: 0.8450 (t80) REVERT: S 19 ILE cc_start: 0.8181 (mm) cc_final: 0.7977 (mm) REVERT: G 23 GLN cc_start: 0.8391 (mp10) cc_final: 0.8112 (mp10) REVERT: G 25 SER cc_start: 0.8969 (m) cc_final: 0.8527 (p) REVERT: G 51 PHE cc_start: 0.8660 (t80) cc_final: 0.8222 (t80) REVERT: I 51 PHE cc_start: 0.8738 (t80) cc_final: 0.8476 (t80) REVERT: K 7 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8884 (mp) REVERT: K 55 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8356 (mp10) REVERT: C 51 PHE cc_start: 0.8671 (t80) cc_final: 0.8105 (t80) REVERT: E 51 PHE cc_start: 0.8453 (t80) cc_final: 0.8126 (t80) REVERT: W 48 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8062 (tm-30) REVERT: Y 41 ARG cc_start: 0.8488 (tmt-80) cc_final: 0.7461 (ttp-170) REVERT: 0 1 PHE cc_start: 0.6448 (t80) cc_final: 0.6244 (t80) REVERT: 0 25 SER cc_start: 0.9240 (m) cc_final: 0.8873 (p) REVERT: 0 41 ARG cc_start: 0.8533 (tmt-80) cc_final: 0.7408 (ttp-170) REVERT: 4 41 ARG cc_start: 0.8803 (tmt-80) cc_final: 0.7643 (ttp-170) REVERT: 4 47 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9064 (mp) REVERT: D 21 ASN cc_start: 0.8871 (t0) cc_final: 0.8620 (t0) REVERT: D 56 PHE cc_start: 0.9010 (m-80) cc_final: 0.8785 (m-80) REVERT: D 76 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8093 (mmmm) REVERT: B 17 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8496 (mmmt) REVERT: B 76 LYS cc_start: 0.8392 (mmtt) cc_final: 0.7838 (mmmt) REVERT: P 17 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8324 (mmmm) REVERT: R 101 TRP cc_start: 0.6986 (p-90) cc_final: 0.6599 (p-90) REVERT: T 93 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8160 (mtpp) REVERT: V 17 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7973 (mmmt) REVERT: V 93 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8484 (mtpp) REVERT: H 21 ASN cc_start: 0.7941 (t0) cc_final: 0.7479 (t0) REVERT: H 42 ASP cc_start: 0.8335 (t0) cc_final: 0.7829 (t70) REVERT: H 104 GLN cc_start: 0.7649 (pm20) cc_final: 0.7002 (pp30) REVERT: J 13 ASP cc_start: 0.8119 (t70) cc_final: 0.7779 (t70) REVERT: L 13 ASP cc_start: 0.8852 (p0) cc_final: 0.8500 (p0) REVERT: L 69 GLU cc_start: 0.7715 (tt0) cc_final: 0.7384 (tt0) REVERT: N 17 LYS cc_start: 0.8665 (mmmm) cc_final: 0.8177 (mptt) REVERT: N 67 TYR cc_start: 0.8692 (p90) cc_final: 0.8429 (p90) REVERT: N 73 TRP cc_start: 0.7693 (p90) cc_final: 0.7469 (p90) REVERT: F 73 TRP cc_start: 0.8448 (p90) cc_final: 0.7984 (p90) REVERT: X 17 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8435 (mmmm) REVERT: X 27 PHE cc_start: 0.8535 (m-80) cc_final: 0.8308 (m-10) REVERT: X 61 ASN cc_start: 0.8461 (p0) cc_final: 0.7570 (t0) REVERT: X 93 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8538 (mmmm) REVERT: Z 42 ASP cc_start: 0.8179 (t0) cc_final: 0.7839 (t0) REVERT: Z 104 GLN cc_start: 0.7133 (pp30) cc_final: 0.6823 (pp30) REVERT: 1 12 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8877 (mmmm) REVERT: 1 17 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8318 (mmmm) REVERT: 1 42 ASP cc_start: 0.8196 (t0) cc_final: 0.7713 (t0) REVERT: 1 74 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8692 (ttmt) REVERT: 1 93 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8602 (mtpt) REVERT: 1 101 TRP cc_start: 0.6862 (p90) cc_final: 0.6598 (p90) REVERT: 3 17 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8006 (mmmm) REVERT: 3 42 ASP cc_start: 0.8122 (t0) cc_final: 0.7829 (t70) REVERT: 3 93 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8657 (mtpt) REVERT: 5 21 ASN cc_start: 0.8848 (t0) cc_final: 0.8286 (t0) REVERT: 5 68 ILE cc_start: 0.7968 (mt) cc_final: 0.7704 (tp) REVERT: 5 82 ASP cc_start: 0.8365 (p0) cc_final: 0.8144 (p0) outliers start: 98 outliers final: 72 residues processed: 679 average time/residue: 0.3050 time to fit residues: 313.5359 Evaluate side-chains 650 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 576 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 48 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 2 residue 13 ILE Chi-restraints excluded: chain 2 residue 19 ILE Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain 4 residue 47 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 46 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 46 ASN Chi-restraints excluded: chain R residue 61 ASN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 61 ASN Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain X residue 13 ASP Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 70 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 42 ASN 2 33 ASN 2 42 ASN P 60 ASN ** T 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20176 Z= 0.325 Angle : 0.632 9.939 27504 Z= 0.339 Chirality : 0.044 0.224 3248 Planarity : 0.004 0.056 3520 Dihedral : 8.160 88.829 2784 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 5.88 % Allowed : 19.63 % Favored : 74.49 % 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: -1.59 (0.17), residues: 2576 helix: 0.07 (0.21), residues: 736 sheet: 0.11 (0.26), residues: 304 loop : -1.98 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Z 73 PHE 0.027 0.002 PHE X 14 TYR 0.020 0.002 TYR X 43 ARG 0.007 0.001 ARG S 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 598 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8868 (t80) cc_final: 0.8189 (t80) REVERT: O 19 ILE cc_start: 0.8159 (mt) cc_final: 0.7887 (mm) REVERT: S 19 ILE cc_start: 0.8395 (mm) cc_final: 0.8169 (mm) REVERT: S 53 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8243 (t70) REVERT: U 53 ASP cc_start: 0.8540 (m-30) cc_final: 0.8016 (t0) REVERT: G 23 GLN cc_start: 0.8388 (mp10) cc_final: 0.8056 (mp10) REVERT: G 25 SER cc_start: 0.9040 (m) cc_final: 0.8630 (p) REVERT: G 51 PHE cc_start: 0.8702 (t80) cc_final: 0.8233 (t80) REVERT: I 24 PHE cc_start: 0.8912 (m-10) cc_final: 0.8671 (m-80) REVERT: C 51 PHE cc_start: 0.8684 (t80) cc_final: 0.8141 (t80) REVERT: E 25 SER cc_start: 0.9052 (m) cc_final: 0.8738 (t) REVERT: E 42 ASN cc_start: 0.8607 (t0) cc_final: 0.8325 (m-40) REVERT: E 51 PHE cc_start: 0.8588 (t80) cc_final: 0.8270 (t80) REVERT: W 48 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8092 (tm-30) REVERT: Y 41 ARG cc_start: 0.8690 (tmt-80) cc_final: 0.7550 (ttp-170) REVERT: Y 60 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: 0 25 SER cc_start: 0.9200 (m) cc_final: 0.8955 (p) REVERT: 0 41 ARG cc_start: 0.8745 (tmt-80) cc_final: 0.7567 (ttp-170) REVERT: 4 41 ARG cc_start: 0.8987 (tmt-80) cc_final: 0.7715 (ttp-170) REVERT: 4 42 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8347 (m-40) REVERT: D 21 ASN cc_start: 0.8941 (t0) cc_final: 0.8546 (t0) REVERT: D 76 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8161 (mmmm) REVERT: B 76 LYS cc_start: 0.8503 (mmtt) cc_final: 0.7903 (mmmt) REVERT: P 17 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8443 (mmmm) REVERT: R 21 ASN cc_start: 0.8169 (t0) cc_final: 0.7727 (t0) REVERT: R 30 ASN cc_start: 0.8589 (m-40) cc_final: 0.8294 (p0) REVERT: R 101 TRP cc_start: 0.7136 (p-90) cc_final: 0.6751 (p-90) REVERT: T 93 LYS cc_start: 0.8636 (mmmm) cc_final: 0.8136 (mtpp) REVERT: V 17 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8368 (mmmt) REVERT: V 93 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8442 (mtpp) REVERT: H 21 ASN cc_start: 0.8024 (t0) cc_final: 0.7503 (t0) REVERT: J 13 ASP cc_start: 0.8106 (t70) cc_final: 0.7858 (t70) REVERT: L 13 ASP cc_start: 0.8978 (p0) cc_final: 0.8558 (p0) REVERT: L 69 GLU cc_start: 0.7886 (tt0) cc_final: 0.7558 (tt0) REVERT: N 17 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8477 (mptt) REVERT: F 17 LYS cc_start: 0.8980 (mmtp) cc_final: 0.8747 (mmtp) REVERT: F 73 TRP cc_start: 0.8474 (p90) cc_final: 0.7992 (p90) REVERT: X 17 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8619 (mmmm) REVERT: X 61 ASN cc_start: 0.8629 (p0) cc_final: 0.7672 (t0) REVERT: X 93 LYS cc_start: 0.8816 (mmmm) cc_final: 0.8482 (mmmm) REVERT: Z 42 ASP cc_start: 0.8282 (t0) cc_final: 0.7891 (t0) REVERT: Z 104 GLN cc_start: 0.7193 (pp30) cc_final: 0.6903 (pp30) REVERT: 1 17 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8517 (mmmm) REVERT: 1 42 ASP cc_start: 0.8281 (t0) cc_final: 0.7754 (t70) REVERT: 1 74 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8793 (ttmt) REVERT: 1 101 TRP cc_start: 0.7114 (p90) cc_final: 0.6891 (p90) REVERT: 3 17 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8179 (mmmm) REVERT: 3 42 ASP cc_start: 0.8336 (t0) cc_final: 0.7917 (t70) REVERT: 5 17 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7986 (mmmm) REVERT: 5 21 ASN cc_start: 0.8837 (t0) cc_final: 0.8195 (t0) REVERT: 5 68 ILE cc_start: 0.8039 (mt) cc_final: 0.7768 (tp) REVERT: 5 82 ASP cc_start: 0.8498 (p0) cc_final: 0.8290 (p0) outliers start: 127 outliers final: 100 residues processed: 651 average time/residue: 0.3150 time to fit residues: 313.4523 Evaluate side-chains 670 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 567 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 48 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 60 GLU Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 34 SER Chi-restraints excluded: chain 0 residue 42 ASN Chi-restraints excluded: chain 2 residue 12 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 42 ASN Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 42 ASN Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 46 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 46 ASN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 59 THR Chi-restraints excluded: chain 5 residue 70 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 33 ASN P 60 ASN ** T 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20176 Z= 0.426 Angle : 0.686 11.331 27504 Z= 0.367 Chirality : 0.046 0.239 3248 Planarity : 0.004 0.044 3520 Dihedral : 8.065 89.727 2784 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 6.81 % Allowed : 20.37 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.73 (0.17), residues: 2576 helix: -0.14 (0.21), residues: 752 sheet: -0.48 (0.25), residues: 400 loop : -1.97 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Z 73 PHE 0.032 0.002 PHE X 27 TYR 0.022 0.002 TYR X 43 ARG 0.007 0.001 ARG S 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 596 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.9055 (mm) cc_final: 0.8840 (mm) REVERT: A 51 PHE cc_start: 0.8894 (t80) cc_final: 0.8570 (t80) REVERT: O 19 ILE cc_start: 0.8194 (mt) cc_final: 0.7829 (mm) REVERT: U 29 VAL cc_start: 0.9362 (OUTLIER) cc_final: 0.9153 (t) REVERT: U 39 ASP cc_start: 0.8061 (t70) cc_final: 0.7839 (t70) REVERT: G 23 GLN cc_start: 0.8403 (mp10) cc_final: 0.8130 (mp10) REVERT: G 25 SER cc_start: 0.9092 (m) cc_final: 0.8710 (t) REVERT: K 7 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8909 (mp) REVERT: K 34 SER cc_start: 0.9136 (m) cc_final: 0.8707 (t) REVERT: C 51 PHE cc_start: 0.8759 (t80) cc_final: 0.8222 (t80) REVERT: E 25 SER cc_start: 0.9053 (m) cc_final: 0.8749 (t) REVERT: E 42 ASN cc_start: 0.8833 (t0) cc_final: 0.8462 (m-40) REVERT: E 48 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7800 (tm-30) REVERT: E 51 PHE cc_start: 0.8667 (t80) cc_final: 0.8347 (t80) REVERT: W 48 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8181 (tm-30) REVERT: Y 41 ARG cc_start: 0.8919 (tmt-80) cc_final: 0.7546 (ttp-170) REVERT: 2 7 LEU cc_start: 0.9490 (tp) cc_final: 0.9276 (tp) REVERT: D 21 ASN cc_start: 0.9013 (t0) cc_final: 0.8582 (t0) REVERT: B 17 LYS cc_start: 0.9092 (mmtp) cc_final: 0.8535 (mmmt) REVERT: B 76 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8004 (mmmt) REVERT: P 17 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8563 (mmmm) REVERT: P 93 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8257 (mtmt) REVERT: R 93 LYS cc_start: 0.8297 (mttm) cc_final: 0.7951 (mttm) REVERT: T 93 LYS cc_start: 0.8662 (mmmm) cc_final: 0.8282 (mtpp) REVERT: V 17 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8596 (mmmt) REVERT: V 93 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8433 (mtpp) REVERT: H 43 TYR cc_start: 0.8785 (p90) cc_final: 0.8532 (p90) REVERT: H 93 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8109 (mmmm) REVERT: H 104 GLN cc_start: 0.7838 (pm20) cc_final: 0.7354 (pp30) REVERT: J 13 ASP cc_start: 0.8118 (t70) cc_final: 0.7879 (t70) REVERT: J 83 VAL cc_start: 0.8247 (m) cc_final: 0.8005 (m) REVERT: L 13 ASP cc_start: 0.9023 (p0) cc_final: 0.8647 (p0) REVERT: L 69 GLU cc_start: 0.8143 (tt0) cc_final: 0.7788 (tt0) REVERT: N 17 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8511 (mptt) REVERT: N 67 TYR cc_start: 0.9065 (p90) cc_final: 0.8858 (p90) REVERT: F 73 TRP cc_start: 0.8503 (p90) cc_final: 0.8041 (p90) REVERT: X 17 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8666 (mmmm) REVERT: X 61 ASN cc_start: 0.8651 (p0) cc_final: 0.7755 (t0) REVERT: Z 13 ASP cc_start: 0.8424 (p0) cc_final: 0.8107 (p0) REVERT: Z 42 ASP cc_start: 0.8393 (t0) cc_final: 0.8064 (t70) REVERT: Z 93 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8358 (mmmm) REVERT: Z 104 GLN cc_start: 0.7226 (pp30) cc_final: 0.6709 (pp30) REVERT: 1 17 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8609 (mmmm) REVERT: 1 42 ASP cc_start: 0.8439 (t0) cc_final: 0.7949 (t70) REVERT: 3 17 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8386 (mmmm) REVERT: 3 21 ASN cc_start: 0.8893 (t0) cc_final: 0.8665 (t0) REVERT: 3 42 ASP cc_start: 0.8363 (t0) cc_final: 0.7930 (t70) REVERT: 5 17 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8179 (mmmm) REVERT: 5 21 ASN cc_start: 0.8888 (t0) cc_final: 0.8216 (t0) REVERT: 5 68 ILE cc_start: 0.8179 (mt) cc_final: 0.7934 (tp) REVERT: 5 82 ASP cc_start: 0.8475 (p0) cc_final: 0.8260 (p0) outliers start: 147 outliers final: 115 residues processed: 673 average time/residue: 0.2948 time to fit residues: 303.7804 Evaluate side-chains 678 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 561 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 48 GLU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 34 SER Chi-restraints excluded: chain 2 residue 12 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 37 SER Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 46 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 61 ASN Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 46 ASN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 22 VAL Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 68 ILE Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 59 THR Chi-restraints excluded: chain 5 residue 70 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 247 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 0.0020 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 42 ASN 2 33 ASN 2 42 ASN P 60 ASN ** T 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Z 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20176 Z= 0.184 Angle : 0.598 7.923 27504 Z= 0.320 Chirality : 0.042 0.189 3248 Planarity : 0.004 0.042 3520 Dihedral : 7.699 88.584 2784 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.49 % Allowed : 22.50 % Favored : 73.01 % 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: -1.47 (0.17), residues: 2576 helix: 0.31 (0.21), residues: 752 sheet: 0.08 (0.26), residues: 304 loop : -1.97 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 73 PHE 0.018 0.002 PHE F 14 TYR 0.038 0.002 TYR F 43 ARG 0.006 0.000 ARG Q 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 630 time to evaluate : 2.212 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8991 (mm) cc_final: 0.8776 (mm) REVERT: A 40 LEU cc_start: 0.8808 (tt) cc_final: 0.8390 (tp) REVERT: A 51 PHE cc_start: 0.8613 (t80) cc_final: 0.8381 (t80) REVERT: Q 53 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8332 (t0) REVERT: S 53 ASP cc_start: 0.8546 (m-30) cc_final: 0.8313 (t70) REVERT: U 28 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7458 (ttp-110) REVERT: G 23 GLN cc_start: 0.8489 (mp10) cc_final: 0.8159 (mt0) REVERT: G 25 SER cc_start: 0.9084 (m) cc_final: 0.8637 (t) REVERT: I 51 PHE cc_start: 0.8461 (t80) cc_final: 0.8106 (t80) REVERT: M 48 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7961 (mm-30) REVERT: C 51 PHE cc_start: 0.8620 (t80) cc_final: 0.7961 (t80) REVERT: E 25 SER cc_start: 0.9009 (m) cc_final: 0.8632 (t) REVERT: E 42 ASN cc_start: 0.8739 (t0) cc_final: 0.8354 (m-40) REVERT: E 51 PHE cc_start: 0.8407 (t80) cc_final: 0.8055 (t80) REVERT: W 48 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8030 (tm-30) REVERT: D 21 ASN cc_start: 0.8860 (t0) cc_final: 0.8655 (t0) REVERT: D 42 ASP cc_start: 0.8365 (t0) cc_final: 0.7682 (t70) REVERT: D 76 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8064 (mmmm) REVERT: B 13 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.7636 (t70) REVERT: B 17 LYS cc_start: 0.9067 (mmtp) cc_final: 0.8477 (mmmt) REVERT: B 76 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8028 (mmmt) REVERT: P 17 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8534 (mmmm) REVERT: P 101 TRP cc_start: 0.6640 (p-90) cc_final: 0.6338 (p-90) REVERT: R 21 ASN cc_start: 0.8156 (t0) cc_final: 0.7723 (t0) REVERT: R 101 TRP cc_start: 0.7110 (p-90) cc_final: 0.6815 (p-90) REVERT: T 93 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8085 (mtpp) REVERT: V 17 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8562 (mmmt) REVERT: V 93 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8352 (mtpp) REVERT: H 42 ASP cc_start: 0.8400 (t0) cc_final: 0.7948 (t70) REVERT: H 93 LYS cc_start: 0.8566 (mmmm) cc_final: 0.8026 (mmmm) REVERT: J 13 ASP cc_start: 0.8129 (t70) cc_final: 0.7910 (t70) REVERT: J 42 ASP cc_start: 0.8430 (t0) cc_final: 0.8136 (t0) REVERT: J 43 TYR cc_start: 0.8882 (p90) cc_final: 0.8652 (p90) REVERT: L 13 ASP cc_start: 0.9029 (p0) cc_final: 0.8599 (p0) REVERT: L 61 ASN cc_start: 0.9127 (t0) cc_final: 0.8492 (p0) REVERT: L 69 GLU cc_start: 0.7964 (tt0) cc_final: 0.7539 (tt0) REVERT: N 17 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8456 (mptt) REVERT: F 61 ASN cc_start: 0.8638 (t0) cc_final: 0.7881 (p0) REVERT: F 73 TRP cc_start: 0.8420 (p90) cc_final: 0.8073 (p90) REVERT: X 17 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8682 (mmmm) REVERT: X 61 ASN cc_start: 0.8616 (p0) cc_final: 0.7638 (t0) REVERT: Z 13 ASP cc_start: 0.8416 (p0) cc_final: 0.8082 (p0) REVERT: Z 74 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8602 (ttmt) REVERT: Z 104 GLN cc_start: 0.7202 (pp30) cc_final: 0.6624 (pp30) REVERT: 1 17 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8595 (mmmm) REVERT: 1 42 ASP cc_start: 0.8443 (t0) cc_final: 0.8000 (t70) REVERT: 3 17 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8366 (mmmm) REVERT: 3 42 ASP cc_start: 0.8378 (t0) cc_final: 0.7967 (t70) REVERT: 3 54 ARG cc_start: 0.8915 (mtp180) cc_final: 0.8535 (mtt180) REVERT: 3 82 ASP cc_start: 0.7693 (p0) cc_final: 0.6998 (t0) REVERT: 5 17 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8039 (mmmm) REVERT: 5 21 ASN cc_start: 0.8795 (t0) cc_final: 0.8187 (t0) REVERT: 5 68 ILE cc_start: 0.8041 (mt) cc_final: 0.7813 (tp) outliers start: 97 outliers final: 72 residues processed: 669 average time/residue: 0.3128 time to fit residues: 318.8779 Evaluate side-chains 642 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 568 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 48 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 2 residue 42 ASN Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain P residue 46 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 61 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 46 ASN Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 5 residue 46 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 208 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 246 optimal weight: 0.7980 chunk 154 optimal weight: 0.0030 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 42 ASN ** 4 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN L 61 ASN ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20176 Z= 0.196 Angle : 0.596 8.412 27504 Z= 0.319 Chirality : 0.041 0.172 3248 Planarity : 0.004 0.039 3520 Dihedral : 7.452 88.100 2784 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 4.72 % Allowed : 22.59 % Favored : 72.69 % 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: -1.32 (0.17), residues: 2576 helix: 0.51 (0.20), residues: 752 sheet: -0.40 (0.25), residues: 400 loop : -1.87 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 73 PHE 0.023 0.002 PHE B 27 TYR 0.030 0.002 TYR L 43 ARG 0.009 0.001 ARG Q 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 610 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8928 (mm) cc_final: 0.8711 (mm) REVERT: A 40 LEU cc_start: 0.8789 (tt) cc_final: 0.8575 (tp) REVERT: A 51 PHE cc_start: 0.8531 (t80) cc_final: 0.8299 (t80) REVERT: O 19 ILE cc_start: 0.7987 (mt) cc_final: 0.7710 (mm) REVERT: U 25 SER cc_start: 0.9026 (m) cc_final: 0.8803 (p) REVERT: U 28 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7582 (ttp-110) REVERT: G 23 GLN cc_start: 0.8507 (mp10) cc_final: 0.8116 (mt0) REVERT: G 25 SER cc_start: 0.9059 (m) cc_final: 0.8606 (p) REVERT: M 48 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7943 (mm-30) REVERT: C 48 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 51 PHE cc_start: 0.8530 (t80) cc_final: 0.8016 (t80) REVERT: E 25 SER cc_start: 0.9009 (m) cc_final: 0.8618 (t) REVERT: E 42 ASN cc_start: 0.8632 (t0) cc_final: 0.8348 (m-40) REVERT: E 51 PHE cc_start: 0.8348 (t80) cc_final: 0.7953 (t80) REVERT: W 48 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8076 (tm-30) REVERT: D 21 ASN cc_start: 0.8842 (t0) cc_final: 0.8437 (t0) REVERT: D 42 ASP cc_start: 0.8379 (t0) cc_final: 0.7774 (t70) REVERT: D 43 TYR cc_start: 0.8621 (p90) cc_final: 0.8362 (p90) REVERT: D 76 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8100 (mmmm) REVERT: B 13 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.7691 (t70) REVERT: B 17 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8545 (mmmt) REVERT: B 76 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8035 (mmmt) REVERT: P 17 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8570 (mmmm) REVERT: P 101 TRP cc_start: 0.6552 (p-90) cc_final: 0.6268 (p-90) REVERT: R 21 ASN cc_start: 0.8135 (t0) cc_final: 0.7693 (t0) REVERT: R 93 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7873 (mmtt) REVERT: R 101 TRP cc_start: 0.7109 (p-90) cc_final: 0.6811 (p-90) REVERT: T 69 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7246 (tm-30) REVERT: T 93 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8060 (mtpp) REVERT: V 93 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8353 (mtpp) REVERT: H 42 ASP cc_start: 0.8415 (t0) cc_final: 0.7953 (t70) REVERT: H 93 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8052 (mmmm) REVERT: H 104 GLN cc_start: 0.7830 (pm20) cc_final: 0.7317 (pp30) REVERT: J 42 ASP cc_start: 0.8401 (t0) cc_final: 0.8142 (t0) REVERT: L 13 ASP cc_start: 0.9058 (p0) cc_final: 0.8656 (p0) REVERT: L 61 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8485 (p0) REVERT: L 69 GLU cc_start: 0.7925 (tt0) cc_final: 0.7501 (tt0) REVERT: N 17 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8498 (mptt) REVERT: F 61 ASN cc_start: 0.8671 (t0) cc_final: 0.7809 (p0) REVERT: F 73 TRP cc_start: 0.8421 (p90) cc_final: 0.8113 (p90) REVERT: X 17 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8661 (mmmm) REVERT: X 61 ASN cc_start: 0.8571 (p0) cc_final: 0.7576 (t0) REVERT: X 93 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8251 (mtpp) REVERT: Z 21 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8115 (t0) REVERT: Z 93 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8073 (mtpp) REVERT: Z 104 GLN cc_start: 0.7227 (pp30) cc_final: 0.6620 (pp30) REVERT: 1 17 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8623 (mmmm) REVERT: 1 42 ASP cc_start: 0.8466 (t0) cc_final: 0.8030 (t70) REVERT: 3 17 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8386 (mmmm) REVERT: 3 42 ASP cc_start: 0.8394 (t0) cc_final: 0.7966 (t70) REVERT: 5 17 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8065 (mmmm) REVERT: 5 21 ASN cc_start: 0.8779 (t0) cc_final: 0.8195 (t0) REVERT: 5 68 ILE cc_start: 0.7959 (mt) cc_final: 0.7688 (tp) outliers start: 102 outliers final: 83 residues processed: 650 average time/residue: 0.2968 time to fit residues: 293.8223 Evaluate side-chains 660 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 574 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain S residue 28 ARG Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 46 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 61 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 46 ASN Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 61 ASN Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 61 ASN Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0470 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 0.0070 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN 0 55 GLN 2 33 ASN 2 42 ASN ** 4 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 60 ASN ** T 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20176 Z= 0.196 Angle : 0.602 9.196 27504 Z= 0.321 Chirality : 0.041 0.226 3248 Planarity : 0.004 0.042 3520 Dihedral : 7.257 87.051 2784 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 4.44 % Allowed : 23.38 % Favored : 72.18 % 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: -1.25 (0.17), residues: 2576 helix: 0.70 (0.20), residues: 752 sheet: -0.44 (0.25), residues: 400 loop : -1.87 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 73 PHE 0.039 0.002 PHE I 51 TYR 0.037 0.002 TYR F 43 ARG 0.008 0.001 ARG P 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 612 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8929 (mm) cc_final: 0.8714 (mm) REVERT: A 28 ARG cc_start: 0.8261 (ttp80) cc_final: 0.8032 (ttp-110) REVERT: A 40 LEU cc_start: 0.8748 (tt) cc_final: 0.8390 (tp) REVERT: O 19 ILE cc_start: 0.7930 (mt) cc_final: 0.7696 (mm) REVERT: Q 53 ASP cc_start: 0.8482 (t0) cc_final: 0.8278 (t70) REVERT: S 1 PHE cc_start: 0.7854 (t80) cc_final: 0.7529 (t80) REVERT: S 55 GLN cc_start: 0.8800 (mp10) cc_final: 0.8591 (mp10) REVERT: U 25 SER cc_start: 0.9003 (m) cc_final: 0.8780 (p) REVERT: U 28 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7585 (ttp-110) REVERT: U 53 ASP cc_start: 0.8669 (t0) cc_final: 0.7924 (t0) REVERT: G 25 SER cc_start: 0.9059 (m) cc_final: 0.8633 (p) REVERT: I 55 GLN cc_start: 0.8751 (mp10) cc_final: 0.8135 (mp10) REVERT: M 48 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7889 (mm-30) REVERT: E 42 ASN cc_start: 0.8677 (t0) cc_final: 0.8393 (m-40) REVERT: E 51 PHE cc_start: 0.8251 (t80) cc_final: 0.7927 (t80) REVERT: D 21 ASN cc_start: 0.8810 (t0) cc_final: 0.8407 (t0) REVERT: D 42 ASP cc_start: 0.8376 (t0) cc_final: 0.7735 (t70) REVERT: D 43 TYR cc_start: 0.8594 (p90) cc_final: 0.8268 (p90) REVERT: D 76 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8091 (mmmm) REVERT: B 13 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.7730 (t70) REVERT: B 17 LYS cc_start: 0.9104 (mmtp) cc_final: 0.8521 (mmmt) REVERT: B 76 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8013 (mmmt) REVERT: P 17 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8556 (mmmm) REVERT: P 101 TRP cc_start: 0.6486 (p-90) cc_final: 0.6209 (p-90) REVERT: R 21 ASN cc_start: 0.8106 (t0) cc_final: 0.7668 (t0) REVERT: R 93 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7795 (mttm) REVERT: R 101 TRP cc_start: 0.7102 (p-90) cc_final: 0.6818 (p-90) REVERT: T 93 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8058 (mtpp) REVERT: V 93 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8310 (mtpp) REVERT: H 26 TYR cc_start: 0.8337 (t80) cc_final: 0.7970 (t80) REVERT: H 42 ASP cc_start: 0.8429 (t0) cc_final: 0.7955 (t70) REVERT: H 93 LYS cc_start: 0.8551 (mmmm) cc_final: 0.8055 (mmmm) REVERT: H 104 GLN cc_start: 0.7830 (pm20) cc_final: 0.7300 (pp30) REVERT: J 42 ASP cc_start: 0.8399 (t0) cc_final: 0.8148 (t0) REVERT: J 43 TYR cc_start: 0.8780 (p90) cc_final: 0.8579 (p90) REVERT: L 13 ASP cc_start: 0.9040 (p0) cc_final: 0.8655 (p0) REVERT: L 21 ASN cc_start: 0.8563 (m110) cc_final: 0.8336 (m-40) REVERT: L 61 ASN cc_start: 0.9071 (t0) cc_final: 0.8392 (p0) REVERT: N 17 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8563 (mptt) REVERT: F 61 ASN cc_start: 0.8608 (t0) cc_final: 0.7996 (p0) REVERT: X 17 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8668 (mmmm) REVERT: X 61 ASN cc_start: 0.8497 (p0) cc_final: 0.7524 (t0) REVERT: X 93 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8189 (mtpp) REVERT: Z 21 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.7978 (t0) REVERT: Z 93 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8017 (mtpp) REVERT: Z 104 GLN cc_start: 0.7224 (pp30) cc_final: 0.6614 (pp30) REVERT: 1 17 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8711 (mmmm) REVERT: 1 42 ASP cc_start: 0.8478 (t0) cc_final: 0.8052 (t70) REVERT: 1 93 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8550 (mttp) REVERT: 3 17 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8394 (mmmm) REVERT: 3 42 ASP cc_start: 0.8202 (t0) cc_final: 0.7882 (t70) REVERT: 3 82 ASP cc_start: 0.7933 (p0) cc_final: 0.7179 (t0) REVERT: 5 17 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8087 (mmmm) REVERT: 5 21 ASN cc_start: 0.8721 (t0) cc_final: 0.8182 (t0) REVERT: 5 51 SER cc_start: 0.9195 (m) cc_final: 0.8717 (t) REVERT: 5 68 ILE cc_start: 0.7871 (mt) cc_final: 0.7651 (tp) outliers start: 96 outliers final: 86 residues processed: 660 average time/residue: 0.3040 time to fit residues: 304.8592 Evaluate side-chains 658 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 570 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 42 ASN Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 46 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 61 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 46 ASN Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 46 ASN Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 59 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.0980 chunk 236 optimal weight: 6.9990 chunk 215 optimal weight: 0.0030 chunk 229 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 217 optimal weight: 0.0870 chunk 150 optimal weight: 0.0980 overall best weight: 0.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 ASN ** 4 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 60 ASN ** T 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN V 61 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 ASN Z 21 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20176 Z= 0.187 Angle : 0.606 8.729 27504 Z= 0.323 Chirality : 0.041 0.152 3248 Planarity : 0.004 0.034 3520 Dihedral : 7.127 86.850 2784 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.98 % Allowed : 24.68 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.15 (0.17), residues: 2576 helix: 0.92 (0.20), residues: 752 sheet: -0.41 (0.25), residues: 400 loop : -1.88 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 73 PHE 0.039 0.002 PHE H 14 TYR 0.026 0.002 TYR L 43 ARG 0.008 0.001 ARG P 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 606 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8885 (mm) cc_final: 0.8669 (mm) REVERT: A 28 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7999 (ttp-110) REVERT: S 1 PHE cc_start: 0.7847 (t80) cc_final: 0.7614 (t80) REVERT: S 55 GLN cc_start: 0.8768 (mp10) cc_final: 0.8537 (mp10) REVERT: U 25 SER cc_start: 0.8943 (m) cc_final: 0.8727 (p) REVERT: U 28 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7450 (ttp-110) REVERT: U 53 ASP cc_start: 0.8602 (t0) cc_final: 0.7932 (t0) REVERT: G 23 GLN cc_start: 0.8495 (mp10) cc_final: 0.8178 (mt0) REVERT: G 25 SER cc_start: 0.9018 (m) cc_final: 0.8569 (p) REVERT: G 51 PHE cc_start: 0.8510 (t80) cc_final: 0.7915 (t80) REVERT: I 55 GLN cc_start: 0.8713 (mp10) cc_final: 0.8136 (mp10) REVERT: M 48 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7878 (mm-30) REVERT: E 42 ASN cc_start: 0.8643 (t0) cc_final: 0.8436 (m-40) REVERT: E 51 PHE cc_start: 0.8137 (t80) cc_final: 0.7906 (t80) REVERT: D 21 ASN cc_start: 0.8778 (t0) cc_final: 0.8358 (t0) REVERT: D 42 ASP cc_start: 0.8314 (t0) cc_final: 0.7756 (t70) REVERT: D 43 TYR cc_start: 0.8549 (p90) cc_final: 0.8230 (p90) REVERT: D 76 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8087 (mmmm) REVERT: B 13 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.7785 (t70) REVERT: B 17 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8543 (mmmt) REVERT: B 42 ASP cc_start: 0.8358 (t0) cc_final: 0.7897 (t0) REVERT: B 76 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8007 (mmmt) REVERT: P 17 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8545 (mmmm) REVERT: P 101 TRP cc_start: 0.6486 (p-90) cc_final: 0.6215 (p-90) REVERT: R 21 ASN cc_start: 0.8067 (t0) cc_final: 0.7637 (t0) REVERT: R 93 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7833 (mttm) REVERT: R 101 TRP cc_start: 0.7085 (p-90) cc_final: 0.6794 (p-90) REVERT: T 93 LYS cc_start: 0.8561 (mmmm) cc_final: 0.8026 (mtpp) REVERT: H 26 TYR cc_start: 0.8205 (t80) cc_final: 0.7955 (t80) REVERT: H 42 ASP cc_start: 0.8408 (t0) cc_final: 0.7921 (t70) REVERT: H 68 ILE cc_start: 0.8792 (tp) cc_final: 0.8580 (mm) REVERT: H 93 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8019 (mmmm) REVERT: H 104 GLN cc_start: 0.7853 (pm20) cc_final: 0.7287 (pp30) REVERT: J 42 ASP cc_start: 0.8407 (t0) cc_final: 0.8124 (t70) REVERT: L 13 ASP cc_start: 0.9003 (p0) cc_final: 0.8637 (p0) REVERT: L 61 ASN cc_start: 0.9025 (t0) cc_final: 0.8443 (p0) REVERT: N 17 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8567 (mptt) REVERT: F 61 ASN cc_start: 0.8623 (t0) cc_final: 0.8001 (p0) REVERT: X 17 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8663 (mmmm) REVERT: Z 21 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7874 (t0) REVERT: Z 93 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8092 (mtpp) REVERT: Z 104 GLN cc_start: 0.7288 (pp30) cc_final: 0.6640 (pp30) REVERT: 1 42 ASP cc_start: 0.8483 (t0) cc_final: 0.8091 (t70) REVERT: 1 93 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8504 (mttp) REVERT: 3 17 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8373 (mmmm) REVERT: 3 42 ASP cc_start: 0.8074 (t0) cc_final: 0.7775 (t70) REVERT: 3 82 ASP cc_start: 0.7918 (p0) cc_final: 0.7213 (t0) REVERT: 5 17 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8083 (mmmm) REVERT: 5 21 ASN cc_start: 0.8720 (t0) cc_final: 0.8252 (t0) REVERT: 5 51 SER cc_start: 0.9213 (m) cc_final: 0.8732 (t) REVERT: 5 68 ILE cc_start: 0.7854 (mt) cc_final: 0.7634 (tp) outliers start: 86 outliers final: 71 residues processed: 652 average time/residue: 0.2969 time to fit residues: 296.0331 Evaluate side-chains 645 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 572 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain S residue 28 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 61 ASN Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 46 ASN Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 61 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain X residue 21 ASN Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 46 ASN Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.2980 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 255 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 chunk 203 optimal weight: 0.0060 chunk 21 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN 2 33 ASN 2 42 ASN ** 4 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 60 ASN ** T 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20176 Z= 0.230 Angle : 0.615 11.236 27504 Z= 0.327 Chirality : 0.042 0.156 3248 Planarity : 0.004 0.037 3520 Dihedral : 7.013 87.446 2784 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.94 % Allowed : 25.23 % Favored : 70.83 % 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: -1.17 (0.17), residues: 2576 helix: 1.03 (0.20), residues: 752 sheet: 0.01 (0.27), residues: 304 loop : -2.02 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 5 73 PHE 0.027 0.002 PHE I 51 TYR 0.029 0.002 TYR F 43 ARG 0.008 0.001 ARG P 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 582 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8903 (mm) cc_final: 0.8693 (mm) REVERT: A 28 ARG cc_start: 0.8265 (ttp80) cc_final: 0.8051 (ttp-110) REVERT: A 48 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7989 (tm-30) REVERT: S 1 PHE cc_start: 0.7887 (t80) cc_final: 0.7632 (t80) REVERT: U 25 SER cc_start: 0.8988 (m) cc_final: 0.8763 (p) REVERT: U 28 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7508 (ttp-110) REVERT: U 53 ASP cc_start: 0.8628 (t0) cc_final: 0.8082 (t70) REVERT: G 25 SER cc_start: 0.9033 (m) cc_final: 0.8598 (p) REVERT: I 55 GLN cc_start: 0.8716 (mp10) cc_final: 0.8114 (mp10) REVERT: M 42 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8256 (m110) REVERT: E 42 ASN cc_start: 0.8697 (t0) cc_final: 0.8465 (m-40) REVERT: E 51 PHE cc_start: 0.8170 (t80) cc_final: 0.7909 (t80) REVERT: D 21 ASN cc_start: 0.8811 (t0) cc_final: 0.8393 (t0) REVERT: D 76 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8082 (mmmm) REVERT: B 13 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.7779 (t70) REVERT: B 17 LYS cc_start: 0.9127 (mmtp) cc_final: 0.8493 (mmmt) REVERT: B 76 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8019 (mmmt) REVERT: P 17 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8553 (mmmm) REVERT: P 101 TRP cc_start: 0.6522 (p-90) cc_final: 0.6248 (p-90) REVERT: R 21 ASN cc_start: 0.8119 (t0) cc_final: 0.7684 (t0) REVERT: R 43 TYR cc_start: 0.8805 (p90) cc_final: 0.8586 (p90) REVERT: R 93 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7794 (mttm) REVERT: R 101 TRP cc_start: 0.7118 (p-90) cc_final: 0.6818 (p-90) REVERT: T 93 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8019 (mtpp) REVERT: H 26 TYR cc_start: 0.8291 (t80) cc_final: 0.7979 (t80) REVERT: H 42 ASP cc_start: 0.8455 (t0) cc_final: 0.7959 (t70) REVERT: H 93 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8062 (mmmm) REVERT: H 104 GLN cc_start: 0.7876 (pm20) cc_final: 0.7315 (pp30) REVERT: J 42 ASP cc_start: 0.8438 (t0) cc_final: 0.8152 (t70) REVERT: L 13 ASP cc_start: 0.9004 (p0) cc_final: 0.8636 (p0) REVERT: L 61 ASN cc_start: 0.9079 (t0) cc_final: 0.8541 (p0) REVERT: N 12 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8363 (mmmt) REVERT: N 17 LYS cc_start: 0.9095 (mmmm) cc_final: 0.8600 (mptt) REVERT: F 61 ASN cc_start: 0.8512 (t0) cc_final: 0.8006 (p0) REVERT: X 17 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8701 (mmmm) REVERT: Z 21 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7909 (t0) REVERT: Z 93 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8103 (mtpp) REVERT: Z 104 GLN cc_start: 0.7235 (pp30) cc_final: 0.6590 (pp30) REVERT: 1 42 ASP cc_start: 0.8507 (t0) cc_final: 0.8110 (t70) REVERT: 1 93 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8513 (mttp) REVERT: 3 17 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8393 (mmmm) REVERT: 3 42 ASP cc_start: 0.7979 (t0) cc_final: 0.7696 (t70) REVERT: 3 82 ASP cc_start: 0.7882 (p0) cc_final: 0.7235 (t0) REVERT: 5 17 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8101 (mmmm) REVERT: 5 21 ASN cc_start: 0.8739 (t0) cc_final: 0.8258 (t0) REVERT: 5 51 SER cc_start: 0.9231 (m) cc_final: 0.8745 (t) REVERT: 5 68 ILE cc_start: 0.7876 (mt) cc_final: 0.7642 (tp) outliers start: 85 outliers final: 77 residues processed: 626 average time/residue: 0.2993 time to fit residues: 286.1316 Evaluate side-chains 644 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 564 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 42 ASN Chi-restraints excluded: chain 4 residue 12 ILE Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 61 ASN Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain V residue 61 ASN Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 46 ASN Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 187 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 56 optimal weight: 0.1980 chunk 203 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 33 ASN ** 4 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 60 ASN ** T 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.115479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092465 restraints weight = 35609.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.095601 restraints weight = 19290.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097640 restraints weight = 13100.527| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20176 Z= 0.192 Angle : 0.614 10.540 27504 Z= 0.325 Chirality : 0.041 0.150 3248 Planarity : 0.004 0.038 3520 Dihedral : 6.917 87.967 2784 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.38 % Allowed : 25.74 % Favored : 70.88 % 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: -1.14 (0.17), residues: 2576 helix: 1.13 (0.20), residues: 752 sheet: -0.02 (0.27), residues: 304 loop : -2.03 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 5 73 PHE 0.026 0.002 PHE I 51 TYR 0.030 0.002 TYR Z 26 ARG 0.007 0.001 ARG P 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5804.45 seconds wall clock time: 103 minutes 53.63 seconds (6233.63 seconds total)