Starting phenix.real_space_refine on Tue Mar 19 05:27:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tea_10478/03_2024/6tea_10478.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tea_10478/03_2024/6tea_10478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tea_10478/03_2024/6tea_10478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tea_10478/03_2024/6tea_10478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tea_10478/03_2024/6tea_10478.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tea_10478/03_2024/6tea_10478.pdb" } resolution = 3.89 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= 0.001 sd= 0.008 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 48 5.16 5 C 14688 2.51 5 N 3912 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 51": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 28": "NH1" <-> "NH2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ARG 80": "NH1" <-> "NH2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 28": "NH1" <-> "NH2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "J PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "L PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 31": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 28": "NH1" <-> "NH2" Residue "N ARG 31": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "N PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O ARG 31": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ARG 80": "NH1" <-> "NH2" Residue "O PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P ARG 31": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 28": "NH1" <-> "NH2" Residue "Q ARG 31": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q ARG 80": "NH1" <-> "NH2" Residue "Q PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 28": "NH1" <-> "NH2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R ARG 51": "NH1" <-> "NH2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 31": "NH1" <-> "NH2" Residue "S ARG 51": "NH1" <-> "NH2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 28": "NH1" <-> "NH2" Residue "T ARG 31": "NH1" <-> "NH2" Residue "T ARG 51": "NH1" <-> "NH2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ARG 80": "NH1" <-> "NH2" Residue "T PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 31": "NH1" <-> "NH2" Residue "U ARG 51": "NH1" <-> "NH2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "V ARG 31": "NH1" <-> "NH2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "V ARG 80": "NH1" <-> "NH2" Residue "V PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ARG 51": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 80": "NH1" <-> "NH2" Residue "W PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 28": "NH1" <-> "NH2" Residue "X ARG 31": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ARG 60": "NH1" <-> "NH2" Residue "X ARG 80": "NH1" <-> "NH2" Residue "X PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23328 Number of models: 1 Model: "" Number of chains: 24 Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "A" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "E" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "J" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "K" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "L" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "M" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "N" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "O" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "P" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "Q" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "R" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "S" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "T" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "U" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "V" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "W" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "X" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Time building chain proxies: 12.44, per 1000 atoms: 0.53 Number of scatterers: 23328 At special positions: 0 Unit cell: (98.859, 98.859, 170.08, 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 48 16.00 O 4680 8.00 N 3912 7.00 C 14688 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: 9.60 Conformation dependent library (CDL) restraints added in 4.6 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 24 sheets defined 10.0% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA G 79 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG H 80 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG I 80 " --> pdb=" O ASP I 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA J 79 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA K 79 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA L 79 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG L 80 " --> pdb=" O ASP L 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG M 80 " --> pdb=" O ASP M 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA N 79 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG O 80 " --> pdb=" O ASP O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA P 79 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG P 80 " --> pdb=" O ASP P 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA Q 79 " --> pdb=" O THR Q 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG Q 80 " --> pdb=" O ASP Q 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG R 80 " --> pdb=" O ASP R 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA S 79 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG S 80 " --> pdb=" O ASP S 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA T 79 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG T 80 " --> pdb=" O ASP T 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA U 79 " --> pdb=" O THR U 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG U 80 " --> pdb=" O ASP U 76 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA V 79 " --> pdb=" O THR V 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG V 80 " --> pdb=" O ASP V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG W 80 " --> pdb=" O ASP W 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA X 79 " --> pdb=" O THR X 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG X 80 " --> pdb=" O ASP X 76 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE D 107 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA D 127 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA D 62 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE B 107 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA B 127 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA B 62 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE C 107 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA C 127 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA C 62 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE A 107 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA A 127 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA A 62 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE E 107 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA E 127 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA E 62 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'F' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE F 107 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA F 127 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA F 62 " --> pdb=" O SER F 128 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'G' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE G 107 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA G 127 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA G 62 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'H' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE H 107 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA H 127 " --> pdb=" O ILE H 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA H 62 " --> pdb=" O SER H 128 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'I' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE I 107 " --> pdb=" O ALA I 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA I 127 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA I 62 " --> pdb=" O SER I 128 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'J' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE J 107 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA J 127 " --> pdb=" O ILE J 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA J 62 " --> pdb=" O SER J 128 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'K' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE K 107 " --> pdb=" O ALA K 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA K 127 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA K 62 " --> pdb=" O SER K 128 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'L' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE L 107 " --> pdb=" O ALA L 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA L 127 " --> pdb=" O ILE L 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA L 62 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'M' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE M 107 " --> pdb=" O ALA M 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA M 127 " --> pdb=" O ILE M 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA M 62 " --> pdb=" O SER M 128 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'N' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE N 107 " --> pdb=" O ALA N 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA N 127 " --> pdb=" O ILE N 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA N 62 " --> pdb=" O SER N 128 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'O' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE O 107 " --> pdb=" O ALA O 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA O 127 " --> pdb=" O ILE O 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA O 62 " --> pdb=" O SER O 128 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'P' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE P 107 " --> pdb=" O ALA P 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA P 127 " --> pdb=" O ILE P 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA P 62 " --> pdb=" O SER P 128 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Q' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE Q 107 " --> pdb=" O ALA Q 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA Q 127 " --> pdb=" O ILE Q 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA Q 62 " --> pdb=" O SER Q 128 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'R' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE R 107 " --> pdb=" O ALA R 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA R 127 " --> pdb=" O ILE R 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA R 62 " --> pdb=" O SER R 128 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'S' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE S 107 " --> pdb=" O ALA S 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA S 127 " --> pdb=" O ILE S 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA S 62 " --> pdb=" O SER S 128 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'T' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE T 107 " --> pdb=" O ALA T 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA T 127 " --> pdb=" O ILE T 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA T 62 " --> pdb=" O SER T 128 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'U' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE U 107 " --> pdb=" O ALA U 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA U 127 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA U 62 " --> pdb=" O SER U 128 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'V' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE V 107 " --> pdb=" O ALA V 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA V 127 " --> pdb=" O ILE V 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA V 62 " --> pdb=" O SER V 128 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'W' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE W 107 " --> pdb=" O ALA W 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA W 127 " --> pdb=" O ILE W 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA W 62 " --> pdb=" O SER W 128 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'X' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE X 107 " --> pdb=" O ALA X 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA X 127 " --> pdb=" O ILE X 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA X 62 " --> pdb=" O SER X 128 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 10.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7872 1.34 - 1.45: 3954 1.45 - 1.57: 11766 1.57 - 1.68: 0 1.68 - 1.80: 96 Bond restraints: 23688 Sorted by residual: bond pdb=" C ILE F 95 " pdb=" N PRO F 96 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.09e+00 bond pdb=" C ILE R 95 " pdb=" N PRO R 96 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.09e+00 bond pdb=" C ILE B 95 " pdb=" N PRO B 96 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.07e+00 bond pdb=" C ILE N 95 " pdb=" N PRO N 96 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.07e+00 bond pdb=" C ILE V 95 " pdb=" N PRO V 96 " ideal model delta sigma weight residual 1.334 1.391 -0.058 2.34e-02 1.83e+03 6.05e+00 ... (remaining 23683 not shown) Histogram of bond angle deviations from ideal: 101.16 - 107.70: 1180 107.70 - 114.24: 12176 114.24 - 120.79: 10194 120.79 - 127.33: 8274 127.33 - 133.88: 144 Bond angle restraints: 31968 Sorted by residual: angle pdb=" C ILE H 107 " pdb=" N THR H 108 " pdb=" CA THR H 108 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ILE T 107 " pdb=" N THR T 108 " pdb=" CA THR T 108 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ILE P 107 " pdb=" N THR P 108 " pdb=" CA THR P 108 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C ILE A 107 " pdb=" N THR A 108 " pdb=" CA THR A 108 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C ILE L 107 " pdb=" N THR L 108 " pdb=" CA THR L 108 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 ... (remaining 31963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 12648 15.50 - 30.99: 888 30.99 - 46.48: 288 46.48 - 61.98: 0 61.98 - 77.47: 24 Dihedral angle restraints: 13848 sinusoidal: 5208 harmonic: 8640 Sorted by residual: dihedral pdb=" CA GLU T 119 " pdb=" C GLU T 119 " pdb=" N ALA T 120 " pdb=" CA ALA T 120 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA GLU H 119 " pdb=" C GLU H 119 " pdb=" N ALA H 120 " pdb=" CA ALA H 120 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA GLU A 119 " pdb=" C GLU A 119 " pdb=" N ALA A 120 " pdb=" CA ALA A 120 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 13845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2934 0.092 - 0.184: 546 0.184 - 0.276: 48 0.276 - 0.368: 0 0.368 - 0.460: 48 Chirality restraints: 3576 Sorted by residual: chirality pdb=" CB THR S 42 " pdb=" CA THR S 42 " pdb=" OG1 THR S 42 " pdb=" CG2 THR S 42 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CB THR G 42 " pdb=" CA THR G 42 " pdb=" OG1 THR G 42 " pdb=" CG2 THR G 42 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CB THR K 42 " pdb=" CA THR K 42 " pdb=" OG1 THR K 42 " pdb=" CG2 THR K 42 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 3573 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU M 27 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C LEU M 27 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU M 27 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG M 28 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 27 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C LEU D 27 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU D 27 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG D 28 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 27 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C LEU E 27 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU E 27 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG E 28 " -0.013 2.00e-02 2.50e+03 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6908 2.80 - 3.32: 21790 3.32 - 3.85: 41808 3.85 - 4.37: 48164 4.37 - 4.90: 83098 Nonbonded interactions: 201768 Sorted by model distance: nonbonded pdb=" OD2 ASP A 111 " pdb=" NH2 ARG X 31 " model vdw 2.273 2.520 nonbonded pdb=" NH2 ARG L 31 " pdb=" OD2 ASP P 111 " model vdw 2.273 2.520 nonbonded pdb=" NH2 ARG A 31 " pdb=" OD2 ASP H 111 " model vdw 2.274 2.520 nonbonded pdb=" NH2 ARG P 31 " pdb=" OD2 ASP T 111 " model vdw 2.274 2.520 nonbonded pdb=" NH2 ARG H 31 " pdb=" OD2 ASP L 111 " model vdw 2.274 2.520 ... (remaining 201763 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 5.060 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 62.980 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.008 0.058 23688 Z= 0.545 Angle : 1.337 15.408 31968 Z= 0.686 Chirality : 0.085 0.460 3576 Planarity : 0.006 0.047 4248 Dihedral : 12.642 77.473 8328 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.12), residues: 3024 helix: -3.41 (0.16), residues: 456 sheet: -2.70 (0.13), residues: 1056 loop : -3.57 (0.12), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP U 50 HIS 0.004 0.002 HIS L 116 PHE 0.022 0.004 PHE J 98 TYR 0.008 0.002 TYR B 122 ARG 0.008 0.002 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1414 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 ASN cc_start: 0.8345 (t0) cc_final: 0.8124 (t0) REVERT: D 24 ILE cc_start: 0.9006 (pt) cc_final: 0.8751 (tp) REVERT: D 77 GLU cc_start: 0.9500 (tm-30) cc_final: 0.9095 (tm-30) REVERT: D 82 ILE cc_start: 0.9530 (mt) cc_final: 0.8919 (tp) REVERT: D 85 ASP cc_start: 0.9217 (m-30) cc_final: 0.8825 (m-30) REVERT: D 124 LEU cc_start: 0.9292 (tt) cc_final: 0.8916 (tt) REVERT: B 4 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8052 (mp10) REVERT: B 8 ASP cc_start: 0.8894 (m-30) cc_final: 0.8502 (m-30) REVERT: B 24 ILE cc_start: 0.9182 (pt) cc_final: 0.8934 (mp) REVERT: B 70 PHE cc_start: 0.8534 (t80) cc_final: 0.8330 (t80) REVERT: B 112 TYR cc_start: 0.9384 (m-80) cc_final: 0.9156 (m-80) REVERT: C 35 ASN cc_start: 0.9193 (m-40) cc_final: 0.8957 (m-40) REVERT: C 76 ASP cc_start: 0.9154 (t0) cc_final: 0.8919 (t0) REVERT: C 82 ILE cc_start: 0.9562 (mt) cc_final: 0.9238 (mt) REVERT: C 111 ASP cc_start: 0.8490 (p0) cc_final: 0.7907 (p0) REVERT: A 60 ARG cc_start: 0.8918 (ptp-110) cc_final: 0.8520 (mtm-85) REVERT: A 91 PHE cc_start: 0.8798 (m-80) cc_final: 0.8415 (m-80) REVERT: A 92 GLN cc_start: 0.9203 (tt0) cc_final: 0.8853 (tt0) REVERT: A 106 MET cc_start: 0.8571 (ptp) cc_final: 0.8303 (ptp) REVERT: A 107 ILE cc_start: 0.9675 (tp) cc_final: 0.9190 (tp) REVERT: A 124 LEU cc_start: 0.9162 (tt) cc_final: 0.8549 (tt) REVERT: E 24 ILE cc_start: 0.9124 (pt) cc_final: 0.8858 (tp) REVERT: E 51 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.7954 (ttp-170) REVERT: E 53 LEU cc_start: 0.8520 (mm) cc_final: 0.8288 (mm) REVERT: E 77 GLU cc_start: 0.9512 (tm-30) cc_final: 0.9183 (tm-30) REVERT: E 82 ILE cc_start: 0.9499 (mt) cc_final: 0.8846 (tp) REVERT: E 85 ASP cc_start: 0.9223 (m-30) cc_final: 0.8850 (m-30) REVERT: E 124 LEU cc_start: 0.9225 (tt) cc_final: 0.8884 (tt) REVERT: F 4 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8212 (mp10) REVERT: F 8 ASP cc_start: 0.8980 (m-30) cc_final: 0.8540 (m-30) REVERT: F 60 ARG cc_start: 0.8871 (ptp-110) cc_final: 0.8551 (mpp80) REVERT: F 70 PHE cc_start: 0.8594 (t80) cc_final: 0.8202 (t80) REVERT: F 76 ASP cc_start: 0.9157 (t0) cc_final: 0.8877 (t0) REVERT: F 90 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8724 (mm-30) REVERT: G 35 ASN cc_start: 0.9207 (m-40) cc_final: 0.8929 (m-40) REVERT: G 70 PHE cc_start: 0.8726 (t80) cc_final: 0.8496 (t80) REVERT: G 76 ASP cc_start: 0.9190 (t0) cc_final: 0.8972 (t0) REVERT: G 81 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8614 (tm-30) REVERT: G 82 ILE cc_start: 0.9555 (mt) cc_final: 0.9112 (mm) REVERT: G 85 ASP cc_start: 0.8994 (m-30) cc_final: 0.8780 (m-30) REVERT: G 87 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8665 (mt-10) REVERT: G 111 ASP cc_start: 0.8379 (p0) cc_final: 0.8106 (p0) REVERT: H 11 ILE cc_start: 0.9177 (pt) cc_final: 0.8955 (pt) REVERT: H 60 ARG cc_start: 0.8843 (ptp-110) cc_final: 0.8577 (mtm-85) REVERT: H 70 PHE cc_start: 0.8983 (t80) cc_final: 0.8704 (t80) REVERT: H 82 ILE cc_start: 0.9817 (mt) cc_final: 0.9616 (mm) REVERT: H 91 PHE cc_start: 0.8823 (m-80) cc_final: 0.8568 (m-80) REVERT: H 92 GLN cc_start: 0.9130 (tt0) cc_final: 0.8855 (tt0) REVERT: H 124 LEU cc_start: 0.9022 (tt) cc_final: 0.8281 (tt) REVERT: I 22 GLU cc_start: 0.7843 (mp0) cc_final: 0.7600 (mp0) REVERT: I 24 ILE cc_start: 0.8957 (pt) cc_final: 0.8730 (tp) REVERT: I 51 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8043 (ttp-110) REVERT: I 77 GLU cc_start: 0.9521 (tm-30) cc_final: 0.9124 (tm-30) REVERT: I 82 ILE cc_start: 0.9512 (mt) cc_final: 0.8924 (tp) REVERT: I 85 ASP cc_start: 0.9199 (m-30) cc_final: 0.8896 (m-30) REVERT: I 124 LEU cc_start: 0.9209 (tt) cc_final: 0.8842 (tp) REVERT: J 4 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8227 (mp10) REVERT: J 8 ASP cc_start: 0.8921 (m-30) cc_final: 0.8544 (m-30) REVERT: J 35 ASN cc_start: 0.9011 (m-40) cc_final: 0.8801 (m-40) REVERT: J 60 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8671 (mpp80) REVERT: J 70 PHE cc_start: 0.8523 (t80) cc_final: 0.7925 (t80) REVERT: J 76 ASP cc_start: 0.9134 (t0) cc_final: 0.8887 (t0) REVERT: J 112 TYR cc_start: 0.9385 (m-80) cc_final: 0.9157 (m-80) REVERT: K 70 PHE cc_start: 0.8833 (t80) cc_final: 0.8467 (t80) REVERT: K 76 ASP cc_start: 0.9200 (t0) cc_final: 0.8986 (t0) REVERT: K 81 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8487 (pp30) REVERT: K 82 ILE cc_start: 0.9580 (mt) cc_final: 0.9222 (mt) REVERT: K 85 ASP cc_start: 0.8989 (m-30) cc_final: 0.8755 (m-30) REVERT: K 87 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8781 (mt-10) REVERT: L 60 ARG cc_start: 0.8890 (ptp-110) cc_final: 0.8604 (mtm-85) REVERT: L 70 PHE cc_start: 0.9057 (t80) cc_final: 0.8665 (t80) REVERT: L 91 PHE cc_start: 0.8713 (m-80) cc_final: 0.8279 (m-80) REVERT: L 92 GLN cc_start: 0.9213 (tt0) cc_final: 0.8979 (tt0) REVERT: L 112 TYR cc_start: 0.9084 (m-80) cc_final: 0.8860 (m-10) REVERT: L 124 LEU cc_start: 0.9048 (tt) cc_final: 0.8284 (tt) REVERT: M 5 ASN cc_start: 0.8351 (t0) cc_final: 0.8130 (t0) REVERT: M 24 ILE cc_start: 0.9003 (pt) cc_final: 0.8747 (tp) REVERT: M 77 GLU cc_start: 0.9501 (tm-30) cc_final: 0.9096 (tm-30) REVERT: M 82 ILE cc_start: 0.9530 (mt) cc_final: 0.8913 (tp) REVERT: M 85 ASP cc_start: 0.9216 (m-30) cc_final: 0.8825 (m-30) REVERT: M 124 LEU cc_start: 0.9292 (tt) cc_final: 0.8916 (tt) REVERT: N 4 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8049 (mp10) REVERT: N 8 ASP cc_start: 0.8896 (m-30) cc_final: 0.8504 (m-30) REVERT: N 24 ILE cc_start: 0.9182 (pt) cc_final: 0.8942 (mp) REVERT: N 70 PHE cc_start: 0.8541 (t80) cc_final: 0.7781 (t80) REVERT: N 112 TYR cc_start: 0.9384 (m-80) cc_final: 0.9181 (m-80) REVERT: O 35 ASN cc_start: 0.9191 (m-40) cc_final: 0.8954 (m-40) REVERT: O 76 ASP cc_start: 0.9153 (t0) cc_final: 0.8911 (t0) REVERT: O 82 ILE cc_start: 0.9561 (mt) cc_final: 0.9236 (mt) REVERT: P 60 ARG cc_start: 0.8917 (ptp-110) cc_final: 0.8523 (mtm-85) REVERT: P 91 PHE cc_start: 0.8797 (m-80) cc_final: 0.8415 (m-80) REVERT: P 92 GLN cc_start: 0.9197 (tt0) cc_final: 0.8851 (tt0) REVERT: P 106 MET cc_start: 0.8578 (ptp) cc_final: 0.8305 (ptp) REVERT: P 107 ILE cc_start: 0.9675 (tp) cc_final: 0.9191 (tp) REVERT: P 124 LEU cc_start: 0.9164 (tt) cc_final: 0.8555 (tt) REVERT: Q 24 ILE cc_start: 0.9123 (pt) cc_final: 0.8856 (tp) REVERT: Q 51 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.7953 (ttp-170) REVERT: Q 53 LEU cc_start: 0.8519 (mm) cc_final: 0.8285 (mm) REVERT: Q 77 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9181 (tm-30) REVERT: Q 82 ILE cc_start: 0.9501 (mt) cc_final: 0.8848 (tp) REVERT: Q 85 ASP cc_start: 0.9220 (m-30) cc_final: 0.8852 (m-30) REVERT: Q 124 LEU cc_start: 0.9225 (tt) cc_final: 0.8882 (tt) REVERT: R 4 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8214 (mp10) REVERT: R 8 ASP cc_start: 0.8981 (m-30) cc_final: 0.8541 (m-30) REVERT: R 60 ARG cc_start: 0.8870 (ptp-110) cc_final: 0.8549 (mpp80) REVERT: R 70 PHE cc_start: 0.8594 (t80) cc_final: 0.8197 (t80) REVERT: R 76 ASP cc_start: 0.9157 (t0) cc_final: 0.8876 (t0) REVERT: R 90 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8724 (mm-30) REVERT: S 35 ASN cc_start: 0.9209 (m-40) cc_final: 0.8933 (m-40) REVERT: S 70 PHE cc_start: 0.8728 (t80) cc_final: 0.8497 (t80) REVERT: S 76 ASP cc_start: 0.9188 (t0) cc_final: 0.8970 (t0) REVERT: S 81 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8615 (tm-30) REVERT: S 82 ILE cc_start: 0.9550 (mt) cc_final: 0.9108 (mm) REVERT: S 85 ASP cc_start: 0.8996 (m-30) cc_final: 0.8778 (m-30) REVERT: S 87 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8662 (mt-10) REVERT: S 111 ASP cc_start: 0.8378 (p0) cc_final: 0.8100 (p0) REVERT: T 11 ILE cc_start: 0.9177 (pt) cc_final: 0.8954 (pt) REVERT: T 60 ARG cc_start: 0.8847 (ptp-110) cc_final: 0.8582 (mtm-85) REVERT: T 70 PHE cc_start: 0.8982 (t80) cc_final: 0.8706 (t80) REVERT: T 91 PHE cc_start: 0.8825 (m-80) cc_final: 0.8563 (m-80) REVERT: T 92 GLN cc_start: 0.9125 (tt0) cc_final: 0.8846 (tt0) REVERT: T 124 LEU cc_start: 0.9019 (tt) cc_final: 0.8279 (tt) REVERT: U 22 GLU cc_start: 0.7839 (mp0) cc_final: 0.7598 (mp0) REVERT: U 24 ILE cc_start: 0.8953 (pt) cc_final: 0.8730 (tp) REVERT: U 51 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8038 (ttp-110) REVERT: U 77 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9122 (tm-30) REVERT: U 82 ILE cc_start: 0.9511 (mt) cc_final: 0.8924 (tp) REVERT: U 85 ASP cc_start: 0.9197 (m-30) cc_final: 0.8894 (m-30) REVERT: U 124 LEU cc_start: 0.9206 (tt) cc_final: 0.8844 (tp) REVERT: V 4 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8353 (mm-40) REVERT: V 8 ASP cc_start: 0.8922 (m-30) cc_final: 0.8531 (m-30) REVERT: V 35 ASN cc_start: 0.9013 (m-40) cc_final: 0.8801 (m-40) REVERT: V 60 ARG cc_start: 0.8891 (ptp-110) cc_final: 0.8675 (mpp80) REVERT: V 70 PHE cc_start: 0.8523 (t80) cc_final: 0.7922 (t80) REVERT: V 76 ASP cc_start: 0.9133 (t0) cc_final: 0.8885 (t0) REVERT: V 112 TYR cc_start: 0.9387 (m-80) cc_final: 0.9151 (m-80) REVERT: W 70 PHE cc_start: 0.8834 (t80) cc_final: 0.8465 (t80) REVERT: W 76 ASP cc_start: 0.9196 (t0) cc_final: 0.8983 (t0) REVERT: W 81 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8487 (pp30) REVERT: W 82 ILE cc_start: 0.9576 (mt) cc_final: 0.9219 (mt) REVERT: W 85 ASP cc_start: 0.8985 (m-30) cc_final: 0.8753 (m-30) REVERT: W 87 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8778 (mt-10) REVERT: X 60 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8603 (mtm-85) REVERT: X 70 PHE cc_start: 0.9058 (t80) cc_final: 0.8664 (t80) REVERT: X 91 PHE cc_start: 0.8713 (m-80) cc_final: 0.8273 (m-80) REVERT: X 92 GLN cc_start: 0.9210 (tt0) cc_final: 0.8976 (tt0) REVERT: X 112 TYR cc_start: 0.9080 (m-80) cc_final: 0.8854 (m-10) REVERT: X 124 LEU cc_start: 0.9048 (tt) cc_final: 0.8282 (tt) outliers start: 0 outliers final: 0 residues processed: 1414 average time/residue: 0.3868 time to fit residues: 822.7246 Evaluate side-chains 877 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 877 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 7.9990 chunk 236 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN D 92 GLN D 102 GLN D 116 HIS B 20 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN A 116 HIS E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN E 116 HIS ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN H 116 HIS I 20 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN I 116 HIS ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 HIS M 20 GLN M 92 GLN M 102 GLN M 116 HIS N 20 GLN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN P 116 HIS Q 20 GLN ** Q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 GLN Q 116 HIS ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN T 116 HIS U 20 GLN ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 102 GLN U 116 HIS ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 116 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23688 Z= 0.239 Angle : 0.810 9.166 31968 Z= 0.411 Chirality : 0.052 0.243 3576 Planarity : 0.005 0.038 4248 Dihedral : 6.451 23.696 3264 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 9.09 % Allowed : 21.25 % Favored : 69.65 % 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: -4.07 (0.13), residues: 3024 helix: -2.38 (0.20), residues: 456 sheet: -1.81 (0.15), residues: 1104 loop : -3.57 (0.13), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 50 HIS 0.007 0.002 HIS I 116 PHE 0.029 0.002 PHE E 70 TYR 0.008 0.001 TYR M 112 ARG 0.006 0.001 ARG H 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 976 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8645 (t) REVERT: D 51 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.7409 (ttp-170) REVERT: D 52 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7963 (mp0) REVERT: D 76 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.9110 (m-30) REVERT: D 78 ARG cc_start: 0.9313 (tpp80) cc_final: 0.9024 (tpt-90) REVERT: B 4 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8133 (mp10) REVERT: B 8 ASP cc_start: 0.8934 (m-30) cc_final: 0.8693 (m-30) REVERT: B 74 ASP cc_start: 0.9059 (p0) cc_final: 0.8763 (p0) REVERT: B 92 GLN cc_start: 0.9218 (tt0) cc_final: 0.8648 (tt0) REVERT: B 123 GLU cc_start: 0.8437 (mp0) cc_final: 0.7676 (mp0) REVERT: C 53 LEU cc_start: 0.9389 (mm) cc_final: 0.9094 (mt) REVERT: A 35 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8921 (p0) REVERT: A 76 ASP cc_start: 0.9005 (t0) cc_final: 0.8641 (t0) REVERT: A 85 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8256 (p0) REVERT: A 87 GLU cc_start: 0.8858 (mt-10) cc_final: 0.7210 (mt-10) REVERT: A 124 LEU cc_start: 0.8983 (tt) cc_final: 0.8630 (tt) REVERT: E 5 ASN cc_start: 0.8488 (t0) cc_final: 0.7420 (t0) REVERT: E 7 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8960 (mtmm) REVERT: E 24 ILE cc_start: 0.9078 (pt) cc_final: 0.8781 (tp) REVERT: E 52 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7600 (mp0) REVERT: F 31 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8107 (ttm-80) REVERT: F 70 PHE cc_start: 0.8495 (t80) cc_final: 0.7949 (t80) REVERT: F 76 ASP cc_start: 0.9224 (t0) cc_final: 0.8792 (t0) REVERT: F 90 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8557 (mm-30) REVERT: F 92 GLN cc_start: 0.9128 (tt0) cc_final: 0.8882 (tt0) REVERT: G 31 ARG cc_start: 0.8480 (ttt90) cc_final: 0.7957 (ttt90) REVERT: G 78 ARG cc_start: 0.9356 (tpp80) cc_final: 0.8597 (tpp80) REVERT: G 81 GLN cc_start: 0.8943 (tm-30) cc_final: 0.7265 (tm-30) REVERT: G 82 ILE cc_start: 0.9515 (mt) cc_final: 0.8864 (mm) REVERT: G 85 ASP cc_start: 0.9055 (m-30) cc_final: 0.8315 (p0) REVERT: G 87 GLU cc_start: 0.8789 (mt-10) cc_final: 0.7612 (mt-10) REVERT: G 92 GLN cc_start: 0.9044 (tt0) cc_final: 0.8824 (tt0) REVERT: H 14 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6669 (t70) REVERT: H 20 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7561 (pp30) REVERT: H 31 ARG cc_start: 0.9115 (ptm160) cc_final: 0.8764 (ptm-80) REVERT: H 124 LEU cc_start: 0.8944 (tt) cc_final: 0.8709 (tt) REVERT: H 126 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8673 (mmm) REVERT: I 24 ILE cc_start: 0.8809 (pt) cc_final: 0.8470 (tp) REVERT: I 51 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.7976 (ttp-110) REVERT: I 52 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7714 (mt-10) REVERT: I 78 ARG cc_start: 0.9337 (tpp80) cc_final: 0.9072 (mmm160) REVERT: I 94 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9218 (tp) REVERT: I 126 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8701 (mtm) REVERT: J 4 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8190 (mp10) REVERT: J 31 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.8231 (ttm-80) REVERT: J 51 ARG cc_start: 0.9067 (ttp-110) cc_final: 0.8849 (ttp-110) REVERT: J 52 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8352 (mt-10) REVERT: J 60 ARG cc_start: 0.8823 (ptp-110) cc_final: 0.8217 (mtp85) REVERT: J 70 PHE cc_start: 0.8418 (t80) cc_final: 0.6916 (t80) REVERT: J 76 ASP cc_start: 0.9205 (t0) cc_final: 0.8853 (t0) REVERT: K 20 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: K 47 GLN cc_start: 0.8373 (mp10) cc_final: 0.8096 (mp10) REVERT: K 81 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8096 (tm-30) REVERT: K 82 ILE cc_start: 0.9473 (mt) cc_final: 0.9049 (mt) REVERT: K 85 ASP cc_start: 0.9104 (m-30) cc_final: 0.8427 (p0) REVERT: K 87 GLU cc_start: 0.8962 (mt-10) cc_final: 0.7488 (mt-10) REVERT: L 31 ARG cc_start: 0.9178 (ptm160) cc_final: 0.8847 (ptm160) REVERT: L 52 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8465 (mt-10) REVERT: L 60 ARG cc_start: 0.8748 (ptp-110) cc_final: 0.8457 (mpp80) REVERT: L 92 GLN cc_start: 0.9004 (tt0) cc_final: 0.8616 (tt0) REVERT: L 126 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8488 (mmm) REVERT: M 30 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8644 (t) REVERT: M 51 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.7409 (ttp-170) REVERT: M 52 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7966 (mp0) REVERT: M 76 ASP cc_start: 0.9408 (OUTLIER) cc_final: 0.9095 (m-30) REVERT: M 78 ARG cc_start: 0.9314 (tpp80) cc_final: 0.9024 (tpt-90) REVERT: N 4 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8133 (mp10) REVERT: N 8 ASP cc_start: 0.8937 (m-30) cc_final: 0.8694 (m-30) REVERT: N 70 PHE cc_start: 0.8259 (t80) cc_final: 0.7829 (t80) REVERT: N 74 ASP cc_start: 0.9060 (p0) cc_final: 0.8766 (p0) REVERT: N 92 GLN cc_start: 0.9220 (tt0) cc_final: 0.8648 (tt0) REVERT: N 123 GLU cc_start: 0.8405 (mp0) cc_final: 0.7715 (mp0) REVERT: O 53 LEU cc_start: 0.9390 (mm) cc_final: 0.9094 (mt) REVERT: P 35 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8928 (p0) REVERT: P 76 ASP cc_start: 0.9004 (t0) cc_final: 0.8606 (t0) REVERT: P 85 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8259 (p0) REVERT: P 87 GLU cc_start: 0.8866 (mt-10) cc_final: 0.7222 (mt-10) REVERT: P 124 LEU cc_start: 0.8974 (tt) cc_final: 0.8621 (tt) REVERT: Q 5 ASN cc_start: 0.8495 (t0) cc_final: 0.7420 (t0) REVERT: Q 7 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8959 (mtmm) REVERT: Q 24 ILE cc_start: 0.9082 (pt) cc_final: 0.8783 (tp) REVERT: Q 52 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7606 (mp0) REVERT: R 31 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8103 (ttm-80) REVERT: R 70 PHE cc_start: 0.8491 (t80) cc_final: 0.7945 (t80) REVERT: R 76 ASP cc_start: 0.9224 (t0) cc_final: 0.8799 (t0) REVERT: R 90 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8549 (mm-30) REVERT: R 92 GLN cc_start: 0.9130 (tt0) cc_final: 0.8884 (tt0) REVERT: S 31 ARG cc_start: 0.8471 (ttt90) cc_final: 0.7951 (ttt90) REVERT: S 78 ARG cc_start: 0.9358 (tpp80) cc_final: 0.8599 (tpp80) REVERT: S 81 GLN cc_start: 0.8944 (tm-30) cc_final: 0.7261 (tm-30) REVERT: S 82 ILE cc_start: 0.9513 (mt) cc_final: 0.8861 (mm) REVERT: S 85 ASP cc_start: 0.9054 (m-30) cc_final: 0.8312 (p0) REVERT: S 87 GLU cc_start: 0.8797 (mt-10) cc_final: 0.7616 (mt-10) REVERT: S 92 GLN cc_start: 0.9040 (tt0) cc_final: 0.8824 (tt0) REVERT: T 14 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6696 (t70) REVERT: T 20 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7555 (pp30) REVERT: T 31 ARG cc_start: 0.9120 (ptm160) cc_final: 0.8766 (ptm-80) REVERT: T 124 LEU cc_start: 0.8941 (tt) cc_final: 0.8708 (tt) REVERT: T 126 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8692 (mmm) REVERT: U 24 ILE cc_start: 0.8801 (pt) cc_final: 0.8472 (tp) REVERT: U 51 ARG cc_start: 0.8681 (ttp-110) cc_final: 0.7979 (ttp-110) REVERT: U 52 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7714 (mt-10) REVERT: U 78 ARG cc_start: 0.9339 (tpp80) cc_final: 0.9070 (mmm160) REVERT: U 94 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9214 (tp) REVERT: V 31 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8193 (ttm-80) REVERT: V 51 ARG cc_start: 0.9067 (ttp-110) cc_final: 0.8838 (ttp-110) REVERT: V 52 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8358 (mt-10) REVERT: V 60 ARG cc_start: 0.8826 (ptp-110) cc_final: 0.8224 (mtp85) REVERT: V 70 PHE cc_start: 0.8420 (t80) cc_final: 0.6909 (t80) REVERT: V 76 ASP cc_start: 0.9201 (t0) cc_final: 0.8855 (t0) REVERT: W 20 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7127 (pm20) REVERT: W 47 GLN cc_start: 0.8379 (mp10) cc_final: 0.8098 (mp10) REVERT: W 81 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8094 (tm-30) REVERT: W 82 ILE cc_start: 0.9473 (mt) cc_final: 0.9048 (mt) REVERT: W 85 ASP cc_start: 0.9102 (m-30) cc_final: 0.8427 (p0) REVERT: W 87 GLU cc_start: 0.8963 (mt-10) cc_final: 0.7492 (mt-10) REVERT: X 31 ARG cc_start: 0.9192 (mtp-110) cc_final: 0.8971 (ttm-80) REVERT: X 52 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8476 (mt-10) REVERT: X 60 ARG cc_start: 0.8743 (ptp-110) cc_final: 0.8453 (mpp80) REVERT: X 92 GLN cc_start: 0.9008 (tt0) cc_final: 0.8616 (tt0) REVERT: X 126 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8341 (mmm) outliers start: 216 outliers final: 108 residues processed: 1028 average time/residue: 0.3397 time to fit residues: 538.7201 Evaluate side-chains 974 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 845 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 126 MET Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 14 ASP Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 126 MET Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 20 GLN Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 14 ASP Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 126 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 283 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 252 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 102 GLN E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN P 102 GLN Q 20 GLN ** Q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 102 GLN ** W 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23688 Z= 0.289 Angle : 0.816 9.538 31968 Z= 0.401 Chirality : 0.051 0.270 3576 Planarity : 0.004 0.032 4248 Dihedral : 5.864 21.883 3264 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 28.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 11.66 % Allowed : 21.80 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.14), residues: 3024 helix: -1.79 (0.22), residues: 456 sheet: -1.50 (0.14), residues: 1104 loop : -3.42 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 50 HIS 0.003 0.001 HIS S 116 PHE 0.022 0.002 PHE N 91 TYR 0.008 0.001 TYR W 112 ARG 0.005 0.001 ARG M 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 855 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 ASN cc_start: 0.8581 (t0) cc_final: 0.8232 (t0) REVERT: D 51 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.7542 (ttp-170) REVERT: D 52 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7943 (mp0) REVERT: D 76 ASP cc_start: 0.9350 (OUTLIER) cc_final: 0.9062 (m-30) REVERT: B 31 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.7866 (ttt90) REVERT: B 74 ASP cc_start: 0.9156 (p0) cc_final: 0.8838 (p0) REVERT: B 76 ASP cc_start: 0.8845 (t0) cc_final: 0.7804 (t0) REVERT: B 98 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.6504 (m-10) REVERT: B 123 GLU cc_start: 0.8486 (mp0) cc_final: 0.7894 (mp0) REVERT: C 31 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.7997 (ttm-80) REVERT: C 81 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8283 (pp30) REVERT: C 87 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8398 (mt-10) REVERT: A 70 PHE cc_start: 0.8844 (t80) cc_final: 0.7502 (t80) REVERT: A 76 ASP cc_start: 0.9085 (t0) cc_final: 0.8293 (t0) REVERT: A 85 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8307 (p0) REVERT: A 87 GLU cc_start: 0.8810 (mt-10) cc_final: 0.7449 (mt-10) REVERT: A 98 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.6842 (m-10) REVERT: A 126 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8423 (mmm) REVERT: E 5 ASN cc_start: 0.8456 (t0) cc_final: 0.7761 (t0) REVERT: E 7 LYS cc_start: 0.9291 (mtpt) cc_final: 0.9022 (mtmm) REVERT: E 24 ILE cc_start: 0.8994 (pt) cc_final: 0.8565 (tp) REVERT: E 51 ARG cc_start: 0.8871 (ttp-110) cc_final: 0.8013 (ttp-170) REVERT: E 52 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7705 (mp0) REVERT: E 92 GLN cc_start: 0.8185 (tt0) cc_final: 0.7409 (tp-100) REVERT: E 100 ILE cc_start: 0.8766 (pt) cc_final: 0.8337 (pp) REVERT: F 74 ASP cc_start: 0.9249 (p0) cc_final: 0.8957 (p0) REVERT: F 76 ASP cc_start: 0.9194 (t0) cc_final: 0.8570 (t0) REVERT: F 90 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8575 (mm-30) REVERT: F 98 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.6745 (m-10) REVERT: G 81 GLN cc_start: 0.8972 (tm-30) cc_final: 0.7386 (tm-30) REVERT: G 82 ILE cc_start: 0.9487 (mt) cc_final: 0.8896 (mm) REVERT: G 85 ASP cc_start: 0.9089 (m-30) cc_final: 0.8365 (p0) REVERT: G 87 GLU cc_start: 0.8837 (mt-10) cc_final: 0.7626 (mt-10) REVERT: G 106 MET cc_start: 0.7944 (pmm) cc_final: 0.7724 (pmm) REVERT: H 31 ARG cc_start: 0.9142 (ptm160) cc_final: 0.8632 (ptm-80) REVERT: H 76 ASP cc_start: 0.8734 (t0) cc_final: 0.7416 (t0) REVERT: H 85 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8437 (p0) REVERT: H 87 GLU cc_start: 0.8890 (mt-10) cc_final: 0.7778 (mt-10) REVERT: H 92 GLN cc_start: 0.8922 (tt0) cc_final: 0.8402 (tt0) REVERT: H 98 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7176 (m-10) REVERT: H 100 ILE cc_start: 0.9526 (pt) cc_final: 0.9194 (pt) REVERT: H 126 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8448 (mmm) REVERT: I 5 ASN cc_start: 0.8652 (t0) cc_final: 0.7453 (t0) REVERT: I 7 LYS cc_start: 0.9329 (mtpt) cc_final: 0.8954 (mtmm) REVERT: I 24 ILE cc_start: 0.8933 (pt) cc_final: 0.8627 (tp) REVERT: I 51 ARG cc_start: 0.8849 (ttp-110) cc_final: 0.7875 (ttp-170) REVERT: I 70 PHE cc_start: 0.9086 (t80) cc_final: 0.8692 (t80) REVERT: I 78 ARG cc_start: 0.9398 (tpp80) cc_final: 0.9070 (mmm160) REVERT: I 82 ILE cc_start: 0.9416 (mt) cc_final: 0.9110 (mt) REVERT: I 94 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9246 (tp) REVERT: I 124 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.8680 (tt) REVERT: J 4 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8184 (mm-40) REVERT: J 60 ARG cc_start: 0.8723 (ptp-110) cc_final: 0.8436 (mtp85) REVERT: J 76 ASP cc_start: 0.9187 (t0) cc_final: 0.8535 (t0) REVERT: J 98 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: K 7 LYS cc_start: 0.9468 (mtmt) cc_final: 0.9168 (mtmm) REVERT: K 76 ASP cc_start: 0.9308 (t0) cc_final: 0.8991 (t0) REVERT: K 81 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8388 (tm-30) REVERT: K 82 ILE cc_start: 0.9462 (mt) cc_final: 0.8998 (mt) REVERT: K 85 ASP cc_start: 0.9126 (m-30) cc_final: 0.8533 (p0) REVERT: L 35 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.9046 (p0) REVERT: L 60 ARG cc_start: 0.8696 (ptp-110) cc_final: 0.8442 (ptp90) REVERT: L 76 ASP cc_start: 0.8637 (t0) cc_final: 0.7377 (t0) REVERT: L 92 GLN cc_start: 0.9001 (tt0) cc_final: 0.8654 (tt0) REVERT: L 98 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: M 5 ASN cc_start: 0.8582 (t0) cc_final: 0.8232 (t0) REVERT: M 51 ARG cc_start: 0.8725 (ttp-110) cc_final: 0.7545 (ttp-170) REVERT: M 52 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7944 (mp0) REVERT: M 76 ASP cc_start: 0.9361 (OUTLIER) cc_final: 0.9068 (m-30) REVERT: N 31 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.7869 (ttt90) REVERT: N 70 PHE cc_start: 0.8477 (t80) cc_final: 0.6448 (t80) REVERT: N 74 ASP cc_start: 0.9157 (p0) cc_final: 0.8829 (p0) REVERT: N 76 ASP cc_start: 0.8896 (t0) cc_final: 0.8394 (t0) REVERT: N 98 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.6495 (m-10) REVERT: N 123 GLU cc_start: 0.8454 (mp0) cc_final: 0.7846 (mp0) REVERT: O 31 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.7985 (ttm-80) REVERT: O 81 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8286 (pp30) REVERT: O 87 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8394 (mt-10) REVERT: O 111 ASP cc_start: 0.8355 (p0) cc_final: 0.7681 (p0) REVERT: O 123 GLU cc_start: 0.8258 (mp0) cc_final: 0.7772 (mp0) REVERT: P 70 PHE cc_start: 0.8840 (t80) cc_final: 0.8486 (t80) REVERT: P 76 ASP cc_start: 0.9078 (t0) cc_final: 0.8804 (t0) REVERT: P 77 GLU cc_start: 0.9171 (tp30) cc_final: 0.8962 (tp30) REVERT: P 85 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8312 (p0) REVERT: P 87 GLU cc_start: 0.8813 (mt-10) cc_final: 0.7456 (mt-10) REVERT: P 98 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: P 126 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8402 (mmm) REVERT: Q 5 ASN cc_start: 0.8452 (t0) cc_final: 0.7751 (t0) REVERT: Q 7 LYS cc_start: 0.9289 (mtpt) cc_final: 0.9019 (mtmm) REVERT: Q 24 ILE cc_start: 0.8996 (pt) cc_final: 0.8567 (tp) REVERT: Q 51 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8020 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7706 (mp0) REVERT: Q 92 GLN cc_start: 0.8185 (tt0) cc_final: 0.7408 (tp-100) REVERT: Q 100 ILE cc_start: 0.8770 (pt) cc_final: 0.8341 (pp) REVERT: R 74 ASP cc_start: 0.9253 (p0) cc_final: 0.8962 (p0) REVERT: R 76 ASP cc_start: 0.9188 (t0) cc_final: 0.8564 (t0) REVERT: R 90 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8568 (mm-30) REVERT: R 98 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.6745 (m-10) REVERT: S 81 GLN cc_start: 0.8965 (tm-30) cc_final: 0.7381 (tm-30) REVERT: S 82 ILE cc_start: 0.9484 (mt) cc_final: 0.8892 (mm) REVERT: S 85 ASP cc_start: 0.9086 (m-30) cc_final: 0.8359 (p0) REVERT: S 87 GLU cc_start: 0.8838 (mt-10) cc_final: 0.7620 (mt-10) REVERT: S 106 MET cc_start: 0.7939 (pmm) cc_final: 0.7723 (pmm) REVERT: T 31 ARG cc_start: 0.9147 (ptm160) cc_final: 0.8639 (ptm-80) REVERT: T 76 ASP cc_start: 0.8753 (t0) cc_final: 0.7424 (t0) REVERT: T 85 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8450 (p0) REVERT: T 87 GLU cc_start: 0.8877 (mt-10) cc_final: 0.7717 (mt-10) REVERT: T 92 GLN cc_start: 0.8918 (tt0) cc_final: 0.8394 (tt0) REVERT: T 98 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: T 100 ILE cc_start: 0.9524 (pt) cc_final: 0.9192 (pt) REVERT: T 126 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8540 (mmm) REVERT: U 5 ASN cc_start: 0.8644 (t0) cc_final: 0.7454 (t0) REVERT: U 7 LYS cc_start: 0.9329 (mtpt) cc_final: 0.8954 (mtmm) REVERT: U 24 ILE cc_start: 0.8937 (pt) cc_final: 0.8630 (tp) REVERT: U 51 ARG cc_start: 0.8855 (ttp-110) cc_final: 0.7870 (ttp-170) REVERT: U 70 PHE cc_start: 0.9105 (t80) cc_final: 0.8711 (t80) REVERT: U 78 ARG cc_start: 0.9399 (tpp80) cc_final: 0.9069 (mmm160) REVERT: U 82 ILE cc_start: 0.9417 (mt) cc_final: 0.9110 (mt) REVERT: U 94 ILE cc_start: 0.9587 (OUTLIER) cc_final: 0.9259 (tp) REVERT: U 124 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8670 (tt) REVERT: V 60 ARG cc_start: 0.8731 (ptp-110) cc_final: 0.8440 (mtp85) REVERT: V 76 ASP cc_start: 0.9190 (t0) cc_final: 0.8538 (t0) REVERT: V 98 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.6862 (m-10) REVERT: W 7 LYS cc_start: 0.9469 (mtmt) cc_final: 0.9163 (mtmm) REVERT: W 76 ASP cc_start: 0.9302 (t0) cc_final: 0.8985 (t0) REVERT: W 81 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8390 (tm-30) REVERT: W 82 ILE cc_start: 0.9461 (mt) cc_final: 0.8999 (mt) REVERT: W 85 ASP cc_start: 0.9125 (m-30) cc_final: 0.8535 (p0) REVERT: X 35 ASN cc_start: 0.9285 (OUTLIER) cc_final: 0.9083 (p0) REVERT: X 60 ARG cc_start: 0.8698 (ptp-110) cc_final: 0.8439 (ptp90) REVERT: X 76 ASP cc_start: 0.8630 (t0) cc_final: 0.7365 (t0) REVERT: X 92 GLN cc_start: 0.9000 (tt0) cc_final: 0.8649 (tt0) REVERT: X 98 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.6879 (m-10) outliers start: 277 outliers final: 155 residues processed: 975 average time/residue: 0.3294 time to fit residues: 501.2327 Evaluate side-chains 980 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 795 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 126 MET Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 117 ASN Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 117 ASN Chi-restraints excluded: chain P residue 126 MET Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 117 ASN Chi-restraints excluded: chain T residue 126 MET Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 14 ASP Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 117 ASN Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 147 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 0.7980 chunk 148 optimal weight: 20.0000 chunk 269 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN E 92 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 92 GLN G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN Q 92 GLN ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23688 Z= 0.297 Angle : 0.800 10.398 31968 Z= 0.395 Chirality : 0.051 0.257 3576 Planarity : 0.004 0.032 4248 Dihedral : 5.765 24.996 3264 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 28.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 11.78 % Allowed : 24.79 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.14), residues: 3024 helix: -1.38 (0.23), residues: 456 sheet: -1.51 (0.13), residues: 1224 loop : -3.59 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP J 50 HIS 0.003 0.001 HIS C 116 PHE 0.032 0.002 PHE B 91 TYR 0.016 0.001 TYR L 122 ARG 0.007 0.001 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 826 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 ASN cc_start: 0.8689 (t0) cc_final: 0.8051 (t0) REVERT: D 7 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9053 (mtmm) REVERT: D 51 ARG cc_start: 0.8792 (ttp-110) cc_final: 0.7862 (ttp-170) REVERT: D 52 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7894 (mp0) REVERT: D 76 ASP cc_start: 0.9375 (t0) cc_final: 0.8966 (m-30) REVERT: D 87 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: B 8 ASP cc_start: 0.8993 (m-30) cc_final: 0.8712 (m-30) REVERT: B 74 ASP cc_start: 0.9210 (p0) cc_final: 0.8910 (p0) REVERT: B 76 ASP cc_start: 0.8732 (t0) cc_final: 0.7415 (t0) REVERT: B 98 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.6285 (m-10) REVERT: B 123 GLU cc_start: 0.8505 (mp0) cc_final: 0.7933 (mp0) REVERT: C 81 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8458 (pp30) REVERT: C 82 ILE cc_start: 0.9389 (mt) cc_final: 0.9172 (mp) REVERT: A 70 PHE cc_start: 0.8870 (t80) cc_final: 0.7562 (t80) REVERT: A 76 ASP cc_start: 0.9067 (t0) cc_final: 0.8355 (t0) REVERT: A 85 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8454 (p0) REVERT: A 98 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.6663 (m-10) REVERT: E 5 ASN cc_start: 0.8435 (t0) cc_final: 0.7050 (t0) REVERT: E 7 LYS cc_start: 0.9300 (mtpt) cc_final: 0.8893 (mtmm) REVERT: E 31 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8565 (mmm-85) REVERT: E 51 ARG cc_start: 0.8884 (ttp-110) cc_final: 0.7979 (ttp-170) REVERT: E 52 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7488 (mp0) REVERT: E 82 ILE cc_start: 0.9447 (mt) cc_final: 0.9179 (mm) REVERT: E 92 GLN cc_start: 0.8072 (tt0) cc_final: 0.7466 (tp-100) REVERT: E 100 ILE cc_start: 0.8979 (pt) cc_final: 0.8547 (pp) REVERT: F 74 ASP cc_start: 0.9302 (p0) cc_final: 0.8964 (p0) REVERT: F 76 ASP cc_start: 0.9161 (t0) cc_final: 0.8509 (t0) REVERT: F 98 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.6176 (m-10) REVERT: G 71 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8389 (mtmm) REVERT: G 81 GLN cc_start: 0.9021 (tm-30) cc_final: 0.7742 (tm-30) REVERT: G 82 ILE cc_start: 0.9467 (mt) cc_final: 0.9051 (mt) REVERT: G 85 ASP cc_start: 0.9133 (m-30) cc_final: 0.8435 (p0) REVERT: G 87 GLU cc_start: 0.8761 (mt-10) cc_final: 0.7521 (mt-10) REVERT: G 111 ASP cc_start: 0.8303 (p0) cc_final: 0.7483 (p0) REVERT: H 31 ARG cc_start: 0.9214 (ptm160) cc_final: 0.8757 (ptm-80) REVERT: H 76 ASP cc_start: 0.8778 (t0) cc_final: 0.7319 (t0) REVERT: H 85 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8455 (p0) REVERT: H 87 GLU cc_start: 0.8880 (mt-10) cc_final: 0.7798 (mt-10) REVERT: H 92 GLN cc_start: 0.8946 (tt0) cc_final: 0.8666 (tt0) REVERT: H 98 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7118 (m-10) REVERT: H 126 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8546 (mmm) REVERT: I 5 ASN cc_start: 0.8640 (t0) cc_final: 0.8299 (t0) REVERT: I 13 LEU cc_start: 0.9313 (pp) cc_final: 0.9084 (pp) REVERT: I 24 ILE cc_start: 0.8986 (pt) cc_final: 0.8600 (tp) REVERT: I 51 ARG cc_start: 0.8953 (ttp-170) cc_final: 0.8331 (ttp-170) REVERT: I 70 PHE cc_start: 0.9201 (t80) cc_final: 0.8672 (t80) REVERT: I 94 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9279 (tp) REVERT: I 98 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: J 4 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8135 (mm-40) REVERT: J 51 ARG cc_start: 0.9155 (ttp-110) cc_final: 0.8859 (ttp-110) REVERT: J 60 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8222 (mtp85) REVERT: J 70 PHE cc_start: 0.8846 (t80) cc_final: 0.5448 (t80) REVERT: J 76 ASP cc_start: 0.9146 (t0) cc_final: 0.8519 (t0) REVERT: J 98 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.6961 (m-10) REVERT: K 7 LYS cc_start: 0.9481 (mtmt) cc_final: 0.9217 (mtmm) REVERT: K 81 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8070 (tm-30) REVERT: K 82 ILE cc_start: 0.9435 (mt) cc_final: 0.8244 (mt) REVERT: K 85 ASP cc_start: 0.9137 (m-30) cc_final: 0.7969 (p0) REVERT: K 87 GLU cc_start: 0.8997 (mt-10) cc_final: 0.7928 (mp0) REVERT: K 98 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.6671 (m-10) REVERT: K 111 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7761 (p0) REVERT: K 123 GLU cc_start: 0.8402 (mp0) cc_final: 0.7788 (mp0) REVERT: L 31 ARG cc_start: 0.9193 (ptm160) cc_final: 0.8804 (ptm-80) REVERT: L 35 ASN cc_start: 0.9335 (OUTLIER) cc_final: 0.9117 (p0) REVERT: L 76 ASP cc_start: 0.8659 (t0) cc_final: 0.7226 (t0) REVERT: L 92 GLN cc_start: 0.9032 (tt0) cc_final: 0.8646 (tt0) REVERT: L 98 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: L 126 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8528 (mmm) REVERT: M 5 ASN cc_start: 0.8688 (t0) cc_final: 0.8059 (t0) REVERT: M 7 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9049 (mtmm) REVERT: M 51 ARG cc_start: 0.8788 (ttp-110) cc_final: 0.7857 (ttp-170) REVERT: M 52 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7894 (mp0) REVERT: M 76 ASP cc_start: 0.9383 (t0) cc_final: 0.8972 (m-30) REVERT: M 87 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: N 8 ASP cc_start: 0.8981 (m-30) cc_final: 0.8696 (m-30) REVERT: N 70 PHE cc_start: 0.8561 (t80) cc_final: 0.6532 (t80) REVERT: N 74 ASP cc_start: 0.9173 (p0) cc_final: 0.8867 (p0) REVERT: N 76 ASP cc_start: 0.8845 (t0) cc_final: 0.8172 (t0) REVERT: N 98 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.6285 (m-10) REVERT: N 123 GLU cc_start: 0.8508 (mp0) cc_final: 0.7943 (mp0) REVERT: O 76 ASP cc_start: 0.9328 (t0) cc_final: 0.8797 (t0) REVERT: O 81 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8461 (pp30) REVERT: O 82 ILE cc_start: 0.9384 (mt) cc_final: 0.9165 (mp) REVERT: O 111 ASP cc_start: 0.8358 (p0) cc_final: 0.7673 (p0) REVERT: O 123 GLU cc_start: 0.8238 (mp0) cc_final: 0.7739 (mp0) REVERT: P 70 PHE cc_start: 0.8867 (t80) cc_final: 0.8459 (t80) REVERT: P 85 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8456 (p0) REVERT: P 98 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.6675 (m-10) REVERT: Q 5 ASN cc_start: 0.8441 (t0) cc_final: 0.7052 (t0) REVERT: Q 7 LYS cc_start: 0.9300 (mtpt) cc_final: 0.8889 (mtmm) REVERT: Q 31 ARG cc_start: 0.8788 (mmm-85) cc_final: 0.8566 (mmm-85) REVERT: Q 51 ARG cc_start: 0.8886 (ttp-110) cc_final: 0.7980 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7482 (mp0) REVERT: Q 82 ILE cc_start: 0.9444 (mt) cc_final: 0.9179 (mm) REVERT: Q 92 GLN cc_start: 0.8076 (tt0) cc_final: 0.7470 (tp-100) REVERT: Q 100 ILE cc_start: 0.8976 (pt) cc_final: 0.8547 (pp) REVERT: R 74 ASP cc_start: 0.9304 (p0) cc_final: 0.8970 (p0) REVERT: R 76 ASP cc_start: 0.9160 (t0) cc_final: 0.8514 (t0) REVERT: R 98 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.6209 (m-10) REVERT: S 71 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8387 (mtmm) REVERT: S 81 GLN cc_start: 0.9016 (tm-30) cc_final: 0.7737 (tm-30) REVERT: S 82 ILE cc_start: 0.9466 (mt) cc_final: 0.9050 (mt) REVERT: S 85 ASP cc_start: 0.9131 (m-30) cc_final: 0.8430 (p0) REVERT: S 87 GLU cc_start: 0.8760 (mt-10) cc_final: 0.7516 (mt-10) REVERT: S 111 ASP cc_start: 0.8300 (p0) cc_final: 0.7482 (p0) REVERT: T 31 ARG cc_start: 0.9220 (ptm160) cc_final: 0.8770 (ptm-80) REVERT: T 76 ASP cc_start: 0.8846 (t0) cc_final: 0.7414 (t0) REVERT: T 85 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8605 (p0) REVERT: T 92 GLN cc_start: 0.8944 (tt0) cc_final: 0.8659 (tt0) REVERT: T 98 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7116 (m-10) REVERT: T 126 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8537 (mmm) REVERT: U 5 ASN cc_start: 0.8638 (t0) cc_final: 0.8287 (t0) REVERT: U 13 LEU cc_start: 0.9314 (pp) cc_final: 0.9085 (pp) REVERT: U 24 ILE cc_start: 0.8990 (pt) cc_final: 0.8613 (tp) REVERT: U 51 ARG cc_start: 0.8948 (ttp-170) cc_final: 0.8327 (ttp-170) REVERT: U 70 PHE cc_start: 0.9219 (t80) cc_final: 0.8642 (t80) REVERT: U 94 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9263 (tp) REVERT: U 98 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: V 51 ARG cc_start: 0.9154 (ttp-110) cc_final: 0.8852 (ttp-110) REVERT: V 60 ARG cc_start: 0.8658 (ptp-110) cc_final: 0.8213 (mtp85) REVERT: V 70 PHE cc_start: 0.8850 (t80) cc_final: 0.5504 (t80) REVERT: V 76 ASP cc_start: 0.9148 (t0) cc_final: 0.8535 (t0) REVERT: V 98 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: W 7 LYS cc_start: 0.9481 (mtmt) cc_final: 0.9217 (mtmm) REVERT: W 81 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8072 (tm-30) REVERT: W 82 ILE cc_start: 0.9436 (mt) cc_final: 0.8246 (mt) REVERT: W 85 ASP cc_start: 0.9135 (m-30) cc_final: 0.7966 (p0) REVERT: W 87 GLU cc_start: 0.8997 (mt-10) cc_final: 0.7927 (mp0) REVERT: W 98 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.7076 (m-10) REVERT: W 111 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7769 (p0) REVERT: W 123 GLU cc_start: 0.8388 (mp0) cc_final: 0.7784 (mp0) REVERT: X 35 ASN cc_start: 0.9365 (OUTLIER) cc_final: 0.9141 (p0) REVERT: X 76 ASP cc_start: 0.8650 (t0) cc_final: 0.7214 (t0) REVERT: X 92 GLN cc_start: 0.9028 (tt0) cc_final: 0.8678 (tt0) REVERT: X 98 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.6752 (m-10) REVERT: X 126 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8495 (mmm) outliers start: 280 outliers final: 164 residues processed: 972 average time/residue: 0.3286 time to fit residues: 498.8348 Evaluate side-chains 963 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 763 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 126 MET Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 117 ASN Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 87 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 117 ASN Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 117 ASN Chi-restraints excluded: chain T residue 126 MET Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 117 ASN Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 126 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 9.9990 chunk 171 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN M 20 GLN ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 GLN ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN V 4 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23688 Z= 0.337 Angle : 0.801 9.276 31968 Z= 0.401 Chirality : 0.050 0.236 3576 Planarity : 0.004 0.032 4248 Dihedral : 5.784 24.564 3264 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 31.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 12.58 % Allowed : 24.96 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.14), residues: 3024 helix: -1.17 (0.23), residues: 456 sheet: -1.35 (0.13), residues: 1224 loop : -3.53 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP V 50 HIS 0.004 0.001 HIS C 116 PHE 0.021 0.002 PHE F 91 TYR 0.010 0.001 TYR C 112 ARG 0.008 0.001 ARG S 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 777 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 ASN cc_start: 0.8654 (t0) cc_final: 0.8016 (t0) REVERT: D 7 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.9024 (mtmm) REVERT: D 31 ARG cc_start: 0.9128 (ttp80) cc_final: 0.8810 (mmm-85) REVERT: D 51 ARG cc_start: 0.8764 (ttp-170) cc_final: 0.7887 (ttp-170) REVERT: D 52 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7735 (mp0) REVERT: D 76 ASP cc_start: 0.9354 (t0) cc_final: 0.9033 (m-30) REVERT: B 8 ASP cc_start: 0.9017 (m-30) cc_final: 0.8720 (m-30) REVERT: B 74 ASP cc_start: 0.9220 (p0) cc_final: 0.8941 (p0) REVERT: B 76 ASP cc_start: 0.8737 (t0) cc_final: 0.7392 (t0) REVERT: B 98 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.5902 (m-10) REVERT: B 123 GLU cc_start: 0.8547 (mp0) cc_final: 0.8002 (mp0) REVERT: C 81 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8248 (pp30) REVERT: C 82 ILE cc_start: 0.9394 (mt) cc_final: 0.9004 (mt) REVERT: C 87 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8374 (mt-10) REVERT: C 111 ASP cc_start: 0.8497 (p0) cc_final: 0.8047 (p0) REVERT: A 70 PHE cc_start: 0.8825 (t80) cc_final: 0.7252 (t80) REVERT: A 76 ASP cc_start: 0.9042 (t0) cc_final: 0.8365 (t0) REVERT: A 85 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8480 (p0) REVERT: A 98 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: E 7 LYS cc_start: 0.9266 (mtpt) cc_final: 0.8715 (mtmt) REVERT: E 31 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.8563 (mmm-85) REVERT: E 51 ARG cc_start: 0.8873 (ttp-170) cc_final: 0.8095 (ttp-170) REVERT: E 52 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7482 (mp0) REVERT: E 87 GLU cc_start: 0.8741 (pm20) cc_final: 0.8173 (pm20) REVERT: E 132 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8839 (mm) REVERT: F 70 PHE cc_start: 0.8823 (t80) cc_final: 0.6196 (t80) REVERT: F 74 ASP cc_start: 0.9324 (p0) cc_final: 0.9018 (p0) REVERT: F 76 ASP cc_start: 0.9202 (t0) cc_final: 0.8583 (t0) REVERT: F 98 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.6472 (m-10) REVERT: G 71 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8360 (mtmm) REVERT: G 81 GLN cc_start: 0.9024 (tm-30) cc_final: 0.7885 (tm-30) REVERT: G 82 ILE cc_start: 0.9455 (mt) cc_final: 0.9059 (mt) REVERT: G 85 ASP cc_start: 0.9101 (m-30) cc_final: 0.8643 (p0) REVERT: H 31 ARG cc_start: 0.9243 (ptm160) cc_final: 0.8801 (ptm-80) REVERT: H 71 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8053 (mtmm) REVERT: H 76 ASP cc_start: 0.8762 (t0) cc_final: 0.7219 (t0) REVERT: H 85 ASP cc_start: 0.9235 (OUTLIER) cc_final: 0.8461 (p0) REVERT: H 87 GLU cc_start: 0.8914 (mt-10) cc_final: 0.7891 (mt-10) REVERT: H 92 GLN cc_start: 0.8961 (tt0) cc_final: 0.8749 (tt0) REVERT: H 98 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7127 (m-10) REVERT: I 5 ASN cc_start: 0.8596 (t0) cc_final: 0.8278 (t0) REVERT: I 24 ILE cc_start: 0.9151 (pt) cc_final: 0.8801 (tp) REVERT: I 51 ARG cc_start: 0.8930 (ttp-170) cc_final: 0.7986 (ttp-170) REVERT: J 4 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8365 (mm-40) REVERT: J 8 ASP cc_start: 0.9022 (m-30) cc_final: 0.8666 (m-30) REVERT: J 59 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7965 (p) REVERT: J 70 PHE cc_start: 0.8937 (t80) cc_final: 0.5745 (t80) REVERT: J 76 ASP cc_start: 0.9149 (t0) cc_final: 0.8555 (t0) REVERT: J 98 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: K 81 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8516 (tm-30) REVERT: K 82 ILE cc_start: 0.9434 (mt) cc_final: 0.8832 (mt) REVERT: K 85 ASP cc_start: 0.9144 (m-30) cc_final: 0.8504 (p0) REVERT: K 111 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8045 (p0) REVERT: K 123 GLU cc_start: 0.8480 (mp0) cc_final: 0.7997 (mp0) REVERT: L 35 ASN cc_start: 0.9400 (OUTLIER) cc_final: 0.9073 (p0) REVERT: L 76 ASP cc_start: 0.8697 (t0) cc_final: 0.7289 (t0) REVERT: L 92 GLN cc_start: 0.9048 (tt0) cc_final: 0.8699 (tt0) REVERT: L 98 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: L 126 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8424 (mmm) REVERT: M 5 ASN cc_start: 0.8658 (t0) cc_final: 0.8026 (t0) REVERT: M 7 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9030 (mtmm) REVERT: M 31 ARG cc_start: 0.9135 (ttp80) cc_final: 0.8822 (mmm-85) REVERT: M 51 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.7884 (ttp-170) REVERT: M 52 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7736 (mp0) REVERT: M 76 ASP cc_start: 0.9363 (t0) cc_final: 0.9035 (m-30) REVERT: N 8 ASP cc_start: 0.9019 (m-30) cc_final: 0.8720 (m-30) REVERT: N 74 ASP cc_start: 0.9210 (p0) cc_final: 0.8887 (p0) REVERT: N 76 ASP cc_start: 0.8863 (t0) cc_final: 0.7783 (t0) REVERT: N 98 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.6171 (m-10) REVERT: N 123 GLU cc_start: 0.8542 (mp0) cc_final: 0.7988 (mp0) REVERT: O 81 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8252 (pp30) REVERT: O 82 ILE cc_start: 0.9396 (mt) cc_final: 0.9004 (mt) REVERT: O 87 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8361 (mt-10) REVERT: O 111 ASP cc_start: 0.8429 (p0) cc_final: 0.7754 (p0) REVERT: O 123 GLU cc_start: 0.8328 (mp0) cc_final: 0.7790 (mp0) REVERT: P 70 PHE cc_start: 0.8787 (t80) cc_final: 0.8390 (t80) REVERT: P 85 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8482 (p0) REVERT: P 92 GLN cc_start: 0.9135 (tt0) cc_final: 0.8855 (tp-100) REVERT: P 98 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.6737 (m-10) REVERT: P 100 ILE cc_start: 0.9435 (pt) cc_final: 0.8907 (pt) REVERT: Q 7 LYS cc_start: 0.9268 (mtpt) cc_final: 0.8716 (mtmt) REVERT: Q 31 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8573 (mmm-85) REVERT: Q 51 ARG cc_start: 0.8889 (ttp-170) cc_final: 0.8078 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7475 (mp0) REVERT: Q 87 GLU cc_start: 0.8739 (pm20) cc_final: 0.8169 (pm20) REVERT: Q 132 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8844 (mm) REVERT: R 70 PHE cc_start: 0.8826 (t80) cc_final: 0.6216 (t80) REVERT: R 74 ASP cc_start: 0.9324 (p0) cc_final: 0.9020 (p0) REVERT: R 76 ASP cc_start: 0.9198 (t0) cc_final: 0.8578 (t0) REVERT: R 98 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.6551 (m-10) REVERT: S 71 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8359 (mtmm) REVERT: S 81 GLN cc_start: 0.9019 (tm-30) cc_final: 0.7882 (tm-30) REVERT: S 82 ILE cc_start: 0.9453 (mt) cc_final: 0.9058 (mt) REVERT: S 85 ASP cc_start: 0.9097 (m-30) cc_final: 0.8640 (p0) REVERT: T 31 ARG cc_start: 0.9240 (ptm160) cc_final: 0.8809 (ptm-80) REVERT: T 71 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8054 (mtmm) REVERT: T 76 ASP cc_start: 0.8764 (t0) cc_final: 0.7227 (t0) REVERT: T 85 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8593 (p0) REVERT: T 92 GLN cc_start: 0.8954 (tt0) cc_final: 0.8738 (tt0) REVERT: T 98 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7120 (m-10) REVERT: U 5 ASN cc_start: 0.8596 (t0) cc_final: 0.8275 (t0) REVERT: U 24 ILE cc_start: 0.9161 (pt) cc_final: 0.8811 (tp) REVERT: U 51 ARG cc_start: 0.8943 (ttp-170) cc_final: 0.7975 (ttp-170) REVERT: U 92 GLN cc_start: 0.8727 (tt0) cc_final: 0.8522 (tt0) REVERT: U 132 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8838 (mm) REVERT: V 8 ASP cc_start: 0.8993 (m-30) cc_final: 0.8667 (m-30) REVERT: V 70 PHE cc_start: 0.8938 (t80) cc_final: 0.6079 (t80) REVERT: V 76 ASP cc_start: 0.9140 (t0) cc_final: 0.8333 (t0) REVERT: V 98 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.6531 (m-10) REVERT: W 81 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8513 (tm-30) REVERT: W 82 ILE cc_start: 0.9437 (mt) cc_final: 0.8833 (mt) REVERT: W 85 ASP cc_start: 0.9139 (m-30) cc_final: 0.8500 (p0) REVERT: W 111 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8064 (p0) REVERT: W 123 GLU cc_start: 0.8476 (mp0) cc_final: 0.7998 (mp0) REVERT: X 31 ARG cc_start: 0.9097 (ttm-80) cc_final: 0.8871 (ttm-80) REVERT: X 35 ASN cc_start: 0.9412 (OUTLIER) cc_final: 0.9080 (p0) REVERT: X 76 ASP cc_start: 0.8696 (t0) cc_final: 0.7287 (t0) REVERT: X 92 GLN cc_start: 0.9059 (tt0) cc_final: 0.8685 (tt0) REVERT: X 98 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.6521 (m-10) REVERT: X 126 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8507 (mmm) outliers start: 299 outliers final: 189 residues processed: 934 average time/residue: 0.3244 time to fit residues: 474.8142 Evaluate side-chains 958 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 739 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 117 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 87 GLU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 87 GLU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 117 ASN Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 117 ASN Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 109 SER Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 117 ASN Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 126 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 8.9990 chunk 271 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 102 GLN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23688 Z= 0.284 Angle : 0.803 9.623 31968 Z= 0.395 Chirality : 0.050 0.240 3576 Planarity : 0.004 0.039 4248 Dihedral : 5.660 25.350 3264 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 29.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 11.74 % Allowed : 25.88 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.14), residues: 3024 helix: -0.84 (0.24), residues: 456 sheet: -1.23 (0.13), residues: 1224 loop : -3.40 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 50 HIS 0.002 0.001 HIS O 116 PHE 0.025 0.002 PHE F 91 TYR 0.015 0.001 TYR H 122 ARG 0.008 0.001 ARG S 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 795 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9145 (mtmm) REVERT: D 51 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.7661 (ttp-170) REVERT: D 76 ASP cc_start: 0.9356 (t0) cc_final: 0.9084 (m-30) REVERT: B 8 ASP cc_start: 0.9012 (m-30) cc_final: 0.8721 (m-30) REVERT: B 74 ASP cc_start: 0.9229 (p0) cc_final: 0.8923 (p0) REVERT: B 76 ASP cc_start: 0.8744 (t0) cc_final: 0.7499 (t0) REVERT: B 98 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.5672 (m-10) REVERT: C 20 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: C 31 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7203 (ttt90) REVERT: C 81 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8246 (pp30) REVERT: C 82 ILE cc_start: 0.9404 (mt) cc_final: 0.9033 (mt) REVERT: C 87 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8409 (mt-10) REVERT: C 98 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.6999 (m-10) REVERT: C 111 ASP cc_start: 0.8531 (p0) cc_final: 0.8097 (p0) REVERT: A 76 ASP cc_start: 0.9032 (t0) cc_final: 0.8337 (t0) REVERT: A 85 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8478 (p0) REVERT: A 98 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.6881 (m-10) REVERT: A 122 TYR cc_start: 0.8127 (p90) cc_final: 0.7514 (p90) REVERT: E 31 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8525 (mmm-85) REVERT: E 51 ARG cc_start: 0.8827 (ttp-170) cc_final: 0.8014 (ttp-170) REVERT: E 52 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7502 (mp0) REVERT: F 70 PHE cc_start: 0.8824 (t80) cc_final: 0.6200 (t80) REVERT: F 74 ASP cc_start: 0.9335 (p0) cc_final: 0.8948 (p0) REVERT: F 76 ASP cc_start: 0.9171 (t0) cc_final: 0.8566 (t0) REVERT: F 98 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: F 126 MET cc_start: 0.8413 (mtp) cc_final: 0.8183 (mmm) REVERT: G 71 LYS cc_start: 0.8889 (mtmm) cc_final: 0.8278 (mtmm) REVERT: G 76 ASP cc_start: 0.9177 (t0) cc_final: 0.8933 (t0) REVERT: G 81 GLN cc_start: 0.9052 (tm-30) cc_final: 0.7366 (tm-30) REVERT: G 82 ILE cc_start: 0.9468 (mt) cc_final: 0.8462 (mt) REVERT: G 85 ASP cc_start: 0.9087 (m-30) cc_final: 0.8122 (p0) REVERT: G 87 GLU cc_start: 0.8692 (mt-10) cc_final: 0.7692 (mp0) REVERT: G 111 ASP cc_start: 0.8127 (p0) cc_final: 0.7347 (p0) REVERT: G 123 GLU cc_start: 0.8107 (mp0) cc_final: 0.7762 (mp0) REVERT: H 31 ARG cc_start: 0.9236 (ptm160) cc_final: 0.8788 (ptm-80) REVERT: H 71 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8100 (mtmm) REVERT: H 76 ASP cc_start: 0.8758 (t0) cc_final: 0.7275 (t0) REVERT: H 85 ASP cc_start: 0.9219 (OUTLIER) cc_final: 0.8633 (p0) REVERT: H 92 GLN cc_start: 0.9000 (tt0) cc_final: 0.8592 (tp40) REVERT: H 98 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7019 (m-10) REVERT: H 119 GLU cc_start: 0.9264 (pm20) cc_final: 0.8861 (pm20) REVERT: I 24 ILE cc_start: 0.9111 (pt) cc_final: 0.8817 (tp) REVERT: I 51 ARG cc_start: 0.8901 (ttp-170) cc_final: 0.8139 (ttp-170) REVERT: J 4 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8382 (mm-40) REVERT: J 8 ASP cc_start: 0.9037 (m-30) cc_final: 0.8702 (m-30) REVERT: J 70 PHE cc_start: 0.8933 (t80) cc_final: 0.6103 (t80) REVERT: J 76 ASP cc_start: 0.9132 (t0) cc_final: 0.8327 (t0) REVERT: J 98 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.6450 (m-10) REVERT: J 126 MET cc_start: 0.8482 (mtp) cc_final: 0.7986 (mmm) REVERT: K 81 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8179 (tm-30) REVERT: K 82 ILE cc_start: 0.9455 (mt) cc_final: 0.8316 (mt) REVERT: K 85 ASP cc_start: 0.9102 (m-30) cc_final: 0.7966 (p0) REVERT: K 87 GLU cc_start: 0.8967 (mt-10) cc_final: 0.7891 (mp0) REVERT: K 98 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: K 123 GLU cc_start: 0.8517 (mp0) cc_final: 0.7858 (mp0) REVERT: L 31 ARG cc_start: 0.9232 (ptm160) cc_final: 0.8827 (ptm-80) REVERT: L 35 ASN cc_start: 0.9427 (OUTLIER) cc_final: 0.9124 (p0) REVERT: L 71 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8189 (mtmm) REVERT: L 76 ASP cc_start: 0.8664 (t0) cc_final: 0.7237 (t0) REVERT: L 92 GLN cc_start: 0.9023 (tt0) cc_final: 0.8717 (tt0) REVERT: L 98 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: L 106 MET cc_start: 0.8446 (ptp) cc_final: 0.8159 (ptm) REVERT: L 126 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8448 (mmm) REVERT: M 7 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9146 (mtmm) REVERT: M 51 ARG cc_start: 0.8693 (ttp-170) cc_final: 0.7653 (ttp-170) REVERT: M 76 ASP cc_start: 0.9367 (t0) cc_final: 0.9099 (m-30) REVERT: N 8 ASP cc_start: 0.9014 (m-30) cc_final: 0.8719 (m-30) REVERT: N 74 ASP cc_start: 0.9183 (p0) cc_final: 0.8867 (p0) REVERT: N 76 ASP cc_start: 0.8885 (t0) cc_final: 0.7833 (t0) REVERT: N 98 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.5721 (m-10) REVERT: O 31 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7157 (ttt90) REVERT: O 76 ASP cc_start: 0.9316 (t0) cc_final: 0.8703 (t0) REVERT: O 81 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8288 (pp30) REVERT: O 82 ILE cc_start: 0.9401 (mt) cc_final: 0.9030 (mt) REVERT: O 87 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8413 (mt-10) REVERT: O 92 GLN cc_start: 0.9297 (tt0) cc_final: 0.8956 (tt0) REVERT: O 98 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7000 (m-10) REVERT: O 111 ASP cc_start: 0.8437 (p0) cc_final: 0.7799 (p0) REVERT: O 123 GLU cc_start: 0.8335 (mp0) cc_final: 0.7791 (mp0) REVERT: P 70 PHE cc_start: 0.8707 (t80) cc_final: 0.7824 (t80) REVERT: P 76 ASP cc_start: 0.8799 (t0) cc_final: 0.8368 (t0) REVERT: P 85 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8480 (p0) REVERT: P 92 GLN cc_start: 0.9078 (tt0) cc_final: 0.8787 (tp-100) REVERT: P 98 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.6669 (m-10) REVERT: P 100 ILE cc_start: 0.9394 (pt) cc_final: 0.8734 (pt) REVERT: Q 31 ARG cc_start: 0.8873 (mmm-85) cc_final: 0.8538 (mmm-85) REVERT: Q 51 ARG cc_start: 0.8882 (ttp-170) cc_final: 0.8404 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7503 (mp0) REVERT: R 70 PHE cc_start: 0.8825 (t80) cc_final: 0.6199 (t80) REVERT: R 74 ASP cc_start: 0.9329 (p0) cc_final: 0.8976 (p0) REVERT: R 76 ASP cc_start: 0.9183 (t0) cc_final: 0.8555 (t0) REVERT: R 98 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.6378 (m-10) REVERT: R 126 MET cc_start: 0.8408 (mtp) cc_final: 0.8182 (mmm) REVERT: S 71 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8282 (mtmm) REVERT: S 76 ASP cc_start: 0.9178 (t0) cc_final: 0.8943 (t0) REVERT: S 81 GLN cc_start: 0.9046 (tm-30) cc_final: 0.7539 (tm-30) REVERT: S 82 ILE cc_start: 0.9467 (mt) cc_final: 0.8978 (mt) REVERT: S 85 ASP cc_start: 0.9083 (m-30) cc_final: 0.8462 (p0) REVERT: S 87 GLU cc_start: 0.8690 (mt-10) cc_final: 0.7694 (mt-10) REVERT: S 111 ASP cc_start: 0.8169 (p0) cc_final: 0.7352 (p0) REVERT: S 123 GLU cc_start: 0.8105 (mp0) cc_final: 0.7754 (mp0) REVERT: T 31 ARG cc_start: 0.9231 (ptm160) cc_final: 0.8803 (ptm-80) REVERT: T 71 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8105 (mtmm) REVERT: T 76 ASP cc_start: 0.8763 (t0) cc_final: 0.7283 (t0) REVERT: T 85 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8593 (p0) REVERT: T 92 GLN cc_start: 0.8998 (tt0) cc_final: 0.8587 (tp40) REVERT: T 98 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7019 (m-10) REVERT: T 119 GLU cc_start: 0.9265 (pm20) cc_final: 0.8861 (pm20) REVERT: U 24 ILE cc_start: 0.9105 (pt) cc_final: 0.8790 (tp) REVERT: U 51 ARG cc_start: 0.8906 (ttp-170) cc_final: 0.8172 (ttp-170) REVERT: U 132 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8827 (mm) REVERT: V 8 ASP cc_start: 0.9005 (m-30) cc_final: 0.8703 (m-30) REVERT: V 60 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7991 (mtp85) REVERT: V 70 PHE cc_start: 0.8939 (t80) cc_final: 0.6204 (t80) REVERT: V 76 ASP cc_start: 0.9130 (t0) cc_final: 0.8353 (t0) REVERT: V 98 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.6328 (m-10) REVERT: W 81 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8176 (tm-30) REVERT: W 82 ILE cc_start: 0.9456 (mt) cc_final: 0.8314 (mt) REVERT: W 85 ASP cc_start: 0.9097 (m-30) cc_final: 0.7964 (p0) REVERT: W 87 GLU cc_start: 0.8965 (mt-10) cc_final: 0.7890 (mp0) REVERT: W 123 GLU cc_start: 0.8513 (mp0) cc_final: 0.7866 (mp0) REVERT: X 31 ARG cc_start: 0.9110 (ttm-80) cc_final: 0.8791 (ttm-80) REVERT: X 35 ASN cc_start: 0.9418 (OUTLIER) cc_final: 0.9130 (p0) REVERT: X 71 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8189 (mtmm) REVERT: X 76 ASP cc_start: 0.8662 (t0) cc_final: 0.7235 (t0) REVERT: X 92 GLN cc_start: 0.9063 (tt0) cc_final: 0.8703 (tt0) REVERT: X 98 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.6493 (m-10) REVERT: X 126 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8473 (mmm) outliers start: 279 outliers final: 191 residues processed: 942 average time/residue: 0.3490 time to fit residues: 521.3016 Evaluate side-chains 961 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 740 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 117 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 106 MET Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 117 ASN Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 117 ASN Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 109 SER Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 117 ASN Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 126 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 170 optimal weight: 0.0970 chunk 254 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 300 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23688 Z= 0.228 Angle : 0.815 9.553 31968 Z= 0.395 Chirality : 0.050 0.225 3576 Planarity : 0.004 0.043 4248 Dihedral : 5.492 26.140 3264 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 9.85 % Allowed : 28.66 % Favored : 61.49 % 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: -2.99 (0.14), residues: 3024 helix: -0.67 (0.24), residues: 456 sheet: -1.23 (0.14), residues: 1224 loop : -3.21 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 50 HIS 0.001 0.000 HIS O 116 PHE 0.028 0.002 PHE F 91 TYR 0.013 0.001 TYR A 122 ARG 0.006 0.000 ARG S 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 824 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9147 (mtmm) REVERT: D 51 ARG cc_start: 0.8729 (ttp-170) cc_final: 0.7803 (ttp-170) REVERT: D 60 ARG cc_start: 0.8846 (ptp-110) cc_final: 0.8436 (ptp90) REVERT: D 71 LYS cc_start: 0.8448 (mtmm) cc_final: 0.7821 (mtmm) REVERT: D 76 ASP cc_start: 0.9247 (t0) cc_final: 0.8962 (m-30) REVERT: D 122 TYR cc_start: 0.8466 (p90) cc_final: 0.7002 (p90) REVERT: B 4 GLN cc_start: 0.8722 (mm-40) cc_final: 0.7991 (mp10) REVERT: B 8 ASP cc_start: 0.8955 (m-30) cc_final: 0.8646 (m-30) REVERT: B 74 ASP cc_start: 0.9195 (p0) cc_final: 0.8894 (p0) REVERT: B 76 ASP cc_start: 0.8696 (t0) cc_final: 0.7445 (t0) REVERT: B 98 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.6294 (m-10) REVERT: C 31 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7344 (ttt90) REVERT: C 82 ILE cc_start: 0.9419 (mt) cc_final: 0.9137 (mt) REVERT: C 98 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: C 111 ASP cc_start: 0.8396 (p0) cc_final: 0.8095 (p0) REVERT: A 76 ASP cc_start: 0.9027 (t0) cc_final: 0.8246 (t0) REVERT: A 85 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8535 (p0) REVERT: A 92 GLN cc_start: 0.9050 (tt0) cc_final: 0.8784 (tp-100) REVERT: A 98 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: E 31 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8553 (mmm-85) REVERT: E 51 ARG cc_start: 0.8802 (ttp-170) cc_final: 0.8013 (ttp-170) REVERT: E 52 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7607 (mp0) REVERT: F 74 ASP cc_start: 0.9263 (p0) cc_final: 0.8935 (p0) REVERT: F 76 ASP cc_start: 0.9155 (t0) cc_final: 0.8479 (t0) REVERT: F 98 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: F 126 MET cc_start: 0.8346 (mtp) cc_final: 0.8119 (mmm) REVERT: G 71 LYS cc_start: 0.8851 (mtmm) cc_final: 0.8483 (mtmm) REVERT: G 76 ASP cc_start: 0.9152 (t0) cc_final: 0.8907 (t0) REVERT: G 81 GLN cc_start: 0.9060 (tm-30) cc_final: 0.7416 (tm-30) REVERT: G 82 ILE cc_start: 0.9474 (mt) cc_final: 0.8894 (mt) REVERT: G 85 ASP cc_start: 0.9027 (m-30) cc_final: 0.8396 (p0) REVERT: G 87 GLU cc_start: 0.8687 (mt-10) cc_final: 0.7913 (mt-10) REVERT: G 92 GLN cc_start: 0.9256 (tt0) cc_final: 0.8887 (tt0) REVERT: G 111 ASP cc_start: 0.8057 (p0) cc_final: 0.7232 (p0) REVERT: G 123 GLU cc_start: 0.8025 (mp0) cc_final: 0.7629 (mp0) REVERT: H 31 ARG cc_start: 0.9209 (ptm160) cc_final: 0.8747 (ptm-80) REVERT: H 71 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8100 (mtmm) REVERT: H 76 ASP cc_start: 0.8697 (t0) cc_final: 0.7214 (t0) REVERT: H 85 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8672 (p0) REVERT: H 98 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.6830 (m-10) REVERT: H 119 GLU cc_start: 0.9243 (pm20) cc_final: 0.8895 (pm20) REVERT: H 122 TYR cc_start: 0.8236 (p90) cc_final: 0.7637 (p90) REVERT: I 51 ARG cc_start: 0.8867 (ttp-170) cc_final: 0.8245 (ttp-170) REVERT: J 8 ASP cc_start: 0.8975 (m-30) cc_final: 0.8698 (m-30) REVERT: J 60 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7945 (mtp85) REVERT: J 70 PHE cc_start: 0.8882 (t80) cc_final: 0.8140 (t80) REVERT: J 76 ASP cc_start: 0.9110 (t0) cc_final: 0.8668 (t0) REVERT: J 98 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: K 81 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8137 (tm-30) REVERT: K 82 ILE cc_start: 0.9436 (mt) cc_final: 0.8381 (mt) REVERT: K 85 ASP cc_start: 0.9074 (m-30) cc_final: 0.7954 (p0) REVERT: K 87 GLU cc_start: 0.8967 (mt-10) cc_final: 0.7923 (mp0) REVERT: K 98 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.6568 (m-10) REVERT: K 106 MET cc_start: 0.8898 (tpp) cc_final: 0.8418 (tpp) REVERT: L 35 ASN cc_start: 0.9423 (OUTLIER) cc_final: 0.9132 (p0) REVERT: L 71 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8107 (mtmm) REVERT: L 76 ASP cc_start: 0.8705 (t0) cc_final: 0.7326 (t0) REVERT: L 92 GLN cc_start: 0.8972 (tt0) cc_final: 0.8761 (tt0) REVERT: L 106 MET cc_start: 0.8522 (ptp) cc_final: 0.8285 (ptm) REVERT: L 122 TYR cc_start: 0.7937 (p90) cc_final: 0.7237 (p90) REVERT: L 126 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8422 (mmm) REVERT: M 7 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9147 (mtmm) REVERT: M 51 ARG cc_start: 0.8711 (ttp-170) cc_final: 0.7769 (ttp-170) REVERT: M 60 ARG cc_start: 0.8845 (ptp-110) cc_final: 0.8435 (ptp90) REVERT: M 71 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7820 (mtmm) REVERT: M 76 ASP cc_start: 0.9282 (t0) cc_final: 0.8999 (m-30) REVERT: N 4 GLN cc_start: 0.8727 (mm-40) cc_final: 0.7988 (mp10) REVERT: N 8 ASP cc_start: 0.8961 (m-30) cc_final: 0.8651 (m-30) REVERT: N 70 PHE cc_start: 0.8546 (t80) cc_final: 0.8271 (t80) REVERT: N 74 ASP cc_start: 0.9141 (p0) cc_final: 0.8827 (p0) REVERT: N 98 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.6268 (m-10) REVERT: O 31 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7346 (ttt90) REVERT: O 76 ASP cc_start: 0.9289 (t0) cc_final: 0.8661 (t0) REVERT: O 82 ILE cc_start: 0.9421 (mt) cc_final: 0.9204 (mt) REVERT: O 92 GLN cc_start: 0.9246 (tt0) cc_final: 0.9033 (tt0) REVERT: O 98 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.6983 (m-10) REVERT: O 111 ASP cc_start: 0.8455 (p0) cc_final: 0.7901 (p0) REVERT: O 123 GLU cc_start: 0.8285 (mp0) cc_final: 0.7751 (mp0) REVERT: P 70 PHE cc_start: 0.8694 (t80) cc_final: 0.8422 (t80) REVERT: P 85 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8538 (p0) REVERT: P 92 GLN cc_start: 0.9048 (tt0) cc_final: 0.8768 (tp-100) REVERT: P 98 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.6638 (m-10) REVERT: P 100 ILE cc_start: 0.9357 (pt) cc_final: 0.8627 (pt) REVERT: Q 31 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8553 (mmm-85) REVERT: Q 51 ARG cc_start: 0.8792 (ttp-170) cc_final: 0.8000 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7598 (mp0) REVERT: R 74 ASP cc_start: 0.9273 (p0) cc_final: 0.8929 (p0) REVERT: R 76 ASP cc_start: 0.9154 (t0) cc_final: 0.8485 (t0) REVERT: R 98 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: S 71 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8485 (mtmm) REVERT: S 76 ASP cc_start: 0.9150 (t0) cc_final: 0.8900 (t0) REVERT: S 81 GLN cc_start: 0.9054 (tm-30) cc_final: 0.7406 (tm-30) REVERT: S 82 ILE cc_start: 0.9474 (mt) cc_final: 0.8891 (mt) REVERT: S 85 ASP cc_start: 0.9025 (m-30) cc_final: 0.8393 (p0) REVERT: S 87 GLU cc_start: 0.8683 (mt-10) cc_final: 0.7911 (mt-10) REVERT: S 92 GLN cc_start: 0.9256 (tt0) cc_final: 0.8885 (tt0) REVERT: S 111 ASP cc_start: 0.8097 (p0) cc_final: 0.7242 (p0) REVERT: S 123 GLU cc_start: 0.7996 (mp0) cc_final: 0.7585 (mp0) REVERT: T 20 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: T 31 ARG cc_start: 0.9207 (ptm160) cc_final: 0.8755 (ptm-80) REVERT: T 71 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8101 (mtmm) REVERT: T 76 ASP cc_start: 0.8713 (t0) cc_final: 0.7174 (t0) REVERT: T 85 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8612 (p0) REVERT: T 98 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.6824 (m-10) REVERT: T 119 GLU cc_start: 0.9241 (pm20) cc_final: 0.8889 (pm20) REVERT: T 122 TYR cc_start: 0.8219 (p90) cc_final: 0.7624 (p90) REVERT: U 132 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8878 (mm) REVERT: V 8 ASP cc_start: 0.8944 (m-30) cc_final: 0.8667 (m-30) REVERT: V 60 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8050 (mtp85) REVERT: V 70 PHE cc_start: 0.8891 (t80) cc_final: 0.8223 (t80) REVERT: V 76 ASP cc_start: 0.9106 (t0) cc_final: 0.8690 (t0) REVERT: V 98 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.6011 (m-10) REVERT: W 81 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8136 (tm-30) REVERT: W 82 ILE cc_start: 0.9437 (mt) cc_final: 0.8379 (mt) REVERT: W 85 ASP cc_start: 0.9073 (m-30) cc_final: 0.7955 (p0) REVERT: W 87 GLU cc_start: 0.8966 (mt-10) cc_final: 0.7916 (mp0) REVERT: W 106 MET cc_start: 0.8900 (tpp) cc_final: 0.8416 (tpp) REVERT: X 35 ASN cc_start: 0.9426 (OUTLIER) cc_final: 0.9168 (p0) REVERT: X 71 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8112 (mtmm) REVERT: X 76 ASP cc_start: 0.8701 (t0) cc_final: 0.7327 (t0) REVERT: X 92 GLN cc_start: 0.9010 (tt0) cc_final: 0.8769 (tt0) REVERT: X 98 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.6308 (m-10) REVERT: X 122 TYR cc_start: 0.7963 (p90) cc_final: 0.7279 (p90) REVERT: X 126 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8419 (mmm) outliers start: 234 outliers final: 165 residues processed: 942 average time/residue: 0.3348 time to fit residues: 489.2511 Evaluate side-chains 947 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 754 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 117 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 106 MET Chi-restraints excluded: chain P residue 117 ASN Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 126 MET Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 117 ASN Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 109 SER Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 117 ASN Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 126 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** U 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23688 Z= 0.304 Angle : 0.832 9.558 31968 Z= 0.410 Chirality : 0.050 0.191 3576 Planarity : 0.004 0.042 4248 Dihedral : 5.608 28.563 3264 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 30.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 10.06 % Allowed : 29.50 % Favored : 60.44 % 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: -2.95 (0.14), residues: 3024 helix: -0.68 (0.24), residues: 456 sheet: -1.23 (0.14), residues: 1224 loop : -3.13 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 50 HIS 0.002 0.000 HIS W 116 PHE 0.029 0.002 PHE F 91 TYR 0.013 0.001 TYR D 112 ARG 0.003 0.000 ARG G 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 761 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9165 (mtmm) REVERT: D 51 ARG cc_start: 0.8650 (ttp-170) cc_final: 0.7690 (ttp-170) REVERT: D 71 LYS cc_start: 0.8526 (mtmm) cc_final: 0.7944 (mtmm) REVERT: D 76 ASP cc_start: 0.9287 (t0) cc_final: 0.8949 (m-30) REVERT: B 4 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8106 (mp10) REVERT: B 8 ASP cc_start: 0.8993 (m-30) cc_final: 0.8660 (m-30) REVERT: B 74 ASP cc_start: 0.9229 (p0) cc_final: 0.8941 (p0) REVERT: B 76 ASP cc_start: 0.8765 (t0) cc_final: 0.7503 (t0) REVERT: B 98 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.5845 (m-10) REVERT: C 31 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7787 (ttt90) REVERT: C 81 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8792 (tm-30) REVERT: C 82 ILE cc_start: 0.9410 (mt) cc_final: 0.9205 (mt) REVERT: C 111 ASP cc_start: 0.8437 (p0) cc_final: 0.8199 (p0) REVERT: A 70 PHE cc_start: 0.8853 (t80) cc_final: 0.7498 (t80) REVERT: A 76 ASP cc_start: 0.9073 (t0) cc_final: 0.8433 (t0) REVERT: A 85 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8490 (p0) REVERT: A 98 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: A 119 GLU cc_start: 0.9392 (pm20) cc_final: 0.9015 (pm20) REVERT: E 31 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8563 (mmm-85) REVERT: E 51 ARG cc_start: 0.8818 (ttp-170) cc_final: 0.7990 (ttp-170) REVERT: E 52 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7921 (mt-10) REVERT: E 70 PHE cc_start: 0.8774 (t80) cc_final: 0.8473 (t80) REVERT: F 70 PHE cc_start: 0.8847 (t80) cc_final: 0.6042 (t80) REVERT: F 74 ASP cc_start: 0.9330 (p0) cc_final: 0.8961 (p0) REVERT: F 76 ASP cc_start: 0.9181 (t0) cc_final: 0.8549 (t0) REVERT: F 98 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.6324 (m-10) REVERT: G 71 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8411 (mtmm) REVERT: G 81 GLN cc_start: 0.9067 (tm-30) cc_final: 0.7928 (tm-30) REVERT: G 82 ILE cc_start: 0.9470 (mt) cc_final: 0.8926 (mt) REVERT: G 85 ASP cc_start: 0.9076 (m-30) cc_final: 0.8394 (p0) REVERT: G 87 GLU cc_start: 0.8670 (mt-10) cc_final: 0.7157 (mt-10) REVERT: G 92 GLN cc_start: 0.9294 (tt0) cc_final: 0.8927 (tt0) REVERT: H 31 ARG cc_start: 0.9238 (ptm160) cc_final: 0.8650 (ptm-80) REVERT: H 71 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8017 (mtmm) REVERT: H 76 ASP cc_start: 0.8721 (t0) cc_final: 0.8437 (t0) REVERT: H 85 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8745 (p0) REVERT: H 98 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.6854 (m-10) REVERT: H 119 GLU cc_start: 0.9260 (pm20) cc_final: 0.8927 (pm20) REVERT: I 51 ARG cc_start: 0.8888 (ttp-170) cc_final: 0.8198 (ttp-170) REVERT: J 8 ASP cc_start: 0.8994 (m-30) cc_final: 0.8693 (m-30) REVERT: J 60 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8037 (mtp85) REVERT: J 70 PHE cc_start: 0.8932 (t80) cc_final: 0.6133 (t80) REVERT: J 76 ASP cc_start: 0.9164 (t0) cc_final: 0.8376 (t0) REVERT: J 98 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7161 (m-10) REVERT: J 126 MET cc_start: 0.8512 (mtp) cc_final: 0.7945 (mmm) REVERT: K 81 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8159 (tm-30) REVERT: K 82 ILE cc_start: 0.9440 (mt) cc_final: 0.8332 (mt) REVERT: K 85 ASP cc_start: 0.9084 (m-30) cc_final: 0.7932 (p0) REVERT: K 87 GLU cc_start: 0.8971 (mt-10) cc_final: 0.7859 (mp0) REVERT: K 98 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.6676 (m-10) REVERT: L 35 ASN cc_start: 0.9437 (OUTLIER) cc_final: 0.9174 (p0) REVERT: L 71 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8072 (mtmm) REVERT: L 76 ASP cc_start: 0.8735 (t0) cc_final: 0.7400 (t0) REVERT: L 106 MET cc_start: 0.8523 (ptp) cc_final: 0.8310 (ptm) REVERT: L 122 TYR cc_start: 0.8120 (p90) cc_final: 0.7060 (p90) REVERT: L 126 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8364 (mmm) REVERT: M 7 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9167 (mtmm) REVERT: M 51 ARG cc_start: 0.8660 (ttp-170) cc_final: 0.7702 (ttp-170) REVERT: M 71 LYS cc_start: 0.8527 (mtmm) cc_final: 0.7942 (mtmm) REVERT: M 76 ASP cc_start: 0.9298 (t0) cc_final: 0.8961 (m-30) REVERT: N 4 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8102 (mp10) REVERT: N 8 ASP cc_start: 0.8997 (m-30) cc_final: 0.8664 (m-30) REVERT: N 74 ASP cc_start: 0.9175 (p0) cc_final: 0.8855 (p0) REVERT: N 76 ASP cc_start: 0.8919 (t0) cc_final: 0.8058 (t0) REVERT: N 98 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.5831 (m-10) REVERT: N 126 MET cc_start: 0.8659 (mtp) cc_final: 0.8446 (mtp) REVERT: O 31 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7790 (ttt90) REVERT: O 76 ASP cc_start: 0.9285 (t0) cc_final: 0.8541 (t0) REVERT: O 92 GLN cc_start: 0.9302 (tt0) cc_final: 0.9089 (tt0) REVERT: O 111 ASP cc_start: 0.8413 (p0) cc_final: 0.7865 (p0) REVERT: O 123 GLU cc_start: 0.8247 (mp0) cc_final: 0.7744 (mp0) REVERT: P 85 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8503 (p0) REVERT: P 92 GLN cc_start: 0.9105 (tt0) cc_final: 0.8850 (tp-100) REVERT: P 98 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.6731 (m-10) REVERT: P 100 ILE cc_start: 0.9385 (pt) cc_final: 0.8701 (pt) REVERT: P 119 GLU cc_start: 0.9377 (pm20) cc_final: 0.8968 (pm20) REVERT: Q 31 ARG cc_start: 0.8923 (mmm-85) cc_final: 0.8584 (mmm-85) REVERT: Q 51 ARG cc_start: 0.8815 (ttp-170) cc_final: 0.7998 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7953 (mt-10) REVERT: Q 70 PHE cc_start: 0.8768 (t80) cc_final: 0.8469 (t80) REVERT: Q 132 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8819 (mm) REVERT: R 70 PHE cc_start: 0.8851 (t80) cc_final: 0.6066 (t80) REVERT: R 74 ASP cc_start: 0.9328 (p0) cc_final: 0.8958 (p0) REVERT: R 76 ASP cc_start: 0.9184 (t0) cc_final: 0.8556 (t0) REVERT: R 98 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.6402 (m-10) REVERT: S 71 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8414 (mtmm) REVERT: S 81 GLN cc_start: 0.9060 (tm-30) cc_final: 0.7918 (tm-30) REVERT: S 82 ILE cc_start: 0.9469 (mt) cc_final: 0.8923 (mt) REVERT: S 85 ASP cc_start: 0.9071 (m-30) cc_final: 0.8389 (p0) REVERT: S 87 GLU cc_start: 0.8669 (mt-10) cc_final: 0.7157 (mt-10) REVERT: S 92 GLN cc_start: 0.9293 (tt0) cc_final: 0.8923 (tt0) REVERT: T 31 ARG cc_start: 0.9235 (ptm160) cc_final: 0.8751 (ptm-80) REVERT: T 71 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8007 (mtmm) REVERT: T 76 ASP cc_start: 0.8741 (t0) cc_final: 0.7358 (t0) REVERT: T 85 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8620 (p0) REVERT: T 98 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.6844 (m-10) REVERT: T 119 GLU cc_start: 0.9258 (pm20) cc_final: 0.8914 (pm20) REVERT: U 132 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8785 (mm) REVERT: V 8 ASP cc_start: 0.8961 (m-30) cc_final: 0.8658 (m-30) REVERT: V 60 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8077 (mtp85) REVERT: V 70 PHE cc_start: 0.8943 (t80) cc_final: 0.6249 (t80) REVERT: V 76 ASP cc_start: 0.9166 (t0) cc_final: 0.8405 (t0) REVERT: V 98 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.6260 (m-10) REVERT: W 81 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8154 (tm-30) REVERT: W 82 ILE cc_start: 0.9437 (mt) cc_final: 0.8254 (mt) REVERT: W 85 ASP cc_start: 0.9082 (m-30) cc_final: 0.7929 (p0) REVERT: W 87 GLU cc_start: 0.8974 (mt-10) cc_final: 0.7853 (mp0) REVERT: X 35 ASN cc_start: 0.9443 (OUTLIER) cc_final: 0.9197 (p0) REVERT: X 71 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8071 (mtmm) REVERT: X 76 ASP cc_start: 0.8741 (t0) cc_final: 0.7398 (t0) REVERT: X 98 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.6634 (m-10) REVERT: X 122 TYR cc_start: 0.8131 (p90) cc_final: 0.7457 (p90) REVERT: X 126 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8399 (mmm) outliers start: 239 outliers final: 176 residues processed: 891 average time/residue: 0.3271 time to fit residues: 455.7449 Evaluate side-chains 934 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 731 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 117 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 106 MET Chi-restraints excluded: chain P residue 117 ASN Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 117 ASN Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 117 ASN Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 126 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 10.0000 chunk 288 optimal weight: 0.8980 chunk 262 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 265 optimal weight: 0.5980 chunk 279 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN C 102 GLN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN H 102 GLN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** U 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 23688 Z= 0.395 Angle : 0.861 9.495 31968 Z= 0.431 Chirality : 0.050 0.210 3576 Planarity : 0.004 0.043 4248 Dihedral : 5.861 31.405 3264 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 33.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 10.31 % Allowed : 29.50 % Favored : 60.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.93 (0.14), residues: 3024 helix: -0.75 (0.24), residues: 456 sheet: -1.12 (0.14), residues: 1200 loop : -3.17 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 50 HIS 0.002 0.001 HIS O 116 PHE 0.032 0.002 PHE I 91 TYR 0.015 0.001 TYR T 122 ARG 0.004 0.001 ARG S 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 733 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9134 (mtmm) REVERT: D 51 ARG cc_start: 0.8542 (ttp-170) cc_final: 0.7594 (ttp-170) REVERT: D 52 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 71 LYS cc_start: 0.8540 (mtmm) cc_final: 0.7954 (mtmm) REVERT: D 76 ASP cc_start: 0.9371 (t0) cc_final: 0.9052 (m-30) REVERT: D 111 ASP cc_start: 0.8521 (p0) cc_final: 0.7959 (p0) REVERT: B 4 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8042 (mp10) REVERT: B 8 ASP cc_start: 0.9027 (m-30) cc_final: 0.8664 (m-30) REVERT: B 74 ASP cc_start: 0.9262 (p0) cc_final: 0.8978 (p0) REVERT: B 76 ASP cc_start: 0.8781 (t0) cc_final: 0.7475 (t0) REVERT: B 98 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.6290 (m-10) REVERT: C 31 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7739 (ttt90) REVERT: C 76 ASP cc_start: 0.9229 (t0) cc_final: 0.8861 (t0) REVERT: C 81 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8902 (tm-30) REVERT: C 98 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.6468 (m-10) REVERT: A 76 ASP cc_start: 0.9059 (t0) cc_final: 0.8307 (t0) REVERT: A 85 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8523 (p0) REVERT: A 98 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: A 119 GLU cc_start: 0.9428 (pm20) cc_final: 0.9082 (pm20) REVERT: E 31 ARG cc_start: 0.8991 (mmm-85) cc_final: 0.8573 (mmm-85) REVERT: E 51 ARG cc_start: 0.8860 (ttp-170) cc_final: 0.7805 (ttp-170) REVERT: F 8 ASP cc_start: 0.8968 (m-30) cc_final: 0.8656 (m-30) REVERT: F 70 PHE cc_start: 0.8957 (t80) cc_final: 0.6577 (t80) REVERT: F 74 ASP cc_start: 0.9311 (p0) cc_final: 0.8976 (p0) REVERT: F 76 ASP cc_start: 0.9214 (t0) cc_final: 0.8626 (t0) REVERT: F 98 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.6712 (m-10) REVERT: G 31 ARG cc_start: 0.8279 (tpp80) cc_final: 0.8028 (ttt90) REVERT: G 71 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8386 (mtmm) REVERT: G 76 ASP cc_start: 0.9115 (t0) cc_final: 0.8730 (t0) REVERT: G 81 GLN cc_start: 0.9022 (tm-30) cc_final: 0.7988 (tm-30) REVERT: G 82 ILE cc_start: 0.9463 (mt) cc_final: 0.9075 (mt) REVERT: G 85 ASP cc_start: 0.9094 (m-30) cc_final: 0.8521 (p0) REVERT: G 92 GLN cc_start: 0.9340 (tt0) cc_final: 0.8975 (tt0) REVERT: H 20 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: H 31 ARG cc_start: 0.9181 (ptm160) cc_final: 0.8778 (ptm-80) REVERT: H 71 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8040 (mtmm) REVERT: H 76 ASP cc_start: 0.8733 (t0) cc_final: 0.8480 (t0) REVERT: H 98 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: H 119 GLU cc_start: 0.9247 (pm20) cc_final: 0.8937 (pm20) REVERT: I 51 ARG cc_start: 0.8907 (ttp-170) cc_final: 0.8214 (ttp-170) REVERT: I 92 GLN cc_start: 0.8969 (mt0) cc_final: 0.8675 (mt0) REVERT: J 8 ASP cc_start: 0.9079 (m-30) cc_final: 0.8782 (m-30) REVERT: J 70 PHE cc_start: 0.8990 (t80) cc_final: 0.6443 (t80) REVERT: J 76 ASP cc_start: 0.9195 (t0) cc_final: 0.8509 (t0) REVERT: J 98 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7088 (m-10) REVERT: J 126 MET cc_start: 0.8557 (mtp) cc_final: 0.7958 (mmm) REVERT: K 76 ASP cc_start: 0.9250 (t0) cc_final: 0.8919 (t0) REVERT: K 81 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8334 (tm-30) REVERT: K 82 ILE cc_start: 0.9424 (mt) cc_final: 0.8196 (mt) REVERT: K 85 ASP cc_start: 0.9156 (m-30) cc_final: 0.7989 (p0) REVERT: K 87 GLU cc_start: 0.8922 (mt-10) cc_final: 0.7679 (mp0) REVERT: K 98 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: L 35 ASN cc_start: 0.9443 (OUTLIER) cc_final: 0.9210 (p0) REVERT: L 71 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8026 (mtmm) REVERT: L 76 ASP cc_start: 0.8781 (t0) cc_final: 0.7471 (t0) REVERT: L 122 TYR cc_start: 0.7698 (p90) cc_final: 0.7406 (p90) REVERT: L 126 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8463 (mmm) REVERT: M 7 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9135 (mtmm) REVERT: M 51 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.7566 (ttp-170) REVERT: M 71 LYS cc_start: 0.8572 (mtmm) cc_final: 0.7990 (mtmm) REVERT: M 76 ASP cc_start: 0.9373 (t0) cc_final: 0.9052 (m-30) REVERT: N 4 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8021 (mp10) REVERT: N 8 ASP cc_start: 0.9029 (m-30) cc_final: 0.8662 (m-30) REVERT: N 74 ASP cc_start: 0.9201 (p0) cc_final: 0.8892 (p0) REVERT: N 76 ASP cc_start: 0.8981 (t0) cc_final: 0.8092 (t0) REVERT: N 98 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.6307 (m-10) REVERT: O 31 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7712 (ttt90) REVERT: O 76 ASP cc_start: 0.9285 (t0) cc_final: 0.8548 (t0) REVERT: O 81 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8335 (pp30) REVERT: O 92 GLN cc_start: 0.9279 (tt0) cc_final: 0.9047 (tt0) REVERT: O 98 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.6931 (m-10) REVERT: O 111 ASP cc_start: 0.8523 (p0) cc_final: 0.8204 (p0) REVERT: O 123 GLU cc_start: 0.8306 (mp0) cc_final: 0.7929 (mp0) REVERT: P 85 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8526 (p0) REVERT: P 92 GLN cc_start: 0.9156 (tt0) cc_final: 0.8821 (tp-100) REVERT: P 98 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.6831 (m-10) REVERT: P 100 ILE cc_start: 0.9395 (pt) cc_final: 0.8735 (pt) REVERT: P 119 GLU cc_start: 0.9433 (pm20) cc_final: 0.9056 (pm20) REVERT: Q 31 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8604 (mmm-85) REVERT: Q 51 ARG cc_start: 0.8835 (ttp-170) cc_final: 0.8245 (ttp-170) REVERT: Q 132 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8833 (mm) REVERT: R 8 ASP cc_start: 0.8963 (m-30) cc_final: 0.8652 (m-30) REVERT: R 70 PHE cc_start: 0.8954 (t80) cc_final: 0.6587 (t80) REVERT: R 74 ASP cc_start: 0.9326 (p0) cc_final: 0.9003 (p0) REVERT: R 76 ASP cc_start: 0.9218 (t0) cc_final: 0.8627 (t0) REVERT: R 98 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.6747 (m-10) REVERT: S 31 ARG cc_start: 0.8274 (tpp80) cc_final: 0.8032 (ttt90) REVERT: S 71 LYS cc_start: 0.8839 (mtmm) cc_final: 0.8388 (mtmm) REVERT: S 76 ASP cc_start: 0.9147 (t0) cc_final: 0.8796 (t0) REVERT: S 81 GLN cc_start: 0.9015 (tm-30) cc_final: 0.7602 (tm-30) REVERT: S 82 ILE cc_start: 0.9462 (mt) cc_final: 0.8972 (mt) REVERT: S 85 ASP cc_start: 0.9086 (m-30) cc_final: 0.8366 (p0) REVERT: S 87 GLU cc_start: 0.8685 (mt-10) cc_final: 0.7103 (mt-10) REVERT: S 92 GLN cc_start: 0.9338 (tt0) cc_final: 0.8973 (tt0) REVERT: T 31 ARG cc_start: 0.9255 (ptm160) cc_final: 0.8788 (ptm-80) REVERT: T 71 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8039 (mtmm) REVERT: T 76 ASP cc_start: 0.8767 (t0) cc_final: 0.7389 (t0) REVERT: T 85 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.8736 (p0) REVERT: T 98 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.6985 (m-10) REVERT: T 119 GLU cc_start: 0.9238 (pm20) cc_final: 0.8923 (pm20) REVERT: U 31 ARG cc_start: 0.9223 (ttp80) cc_final: 0.8379 (mmm-85) REVERT: U 92 GLN cc_start: 0.8995 (mt0) cc_final: 0.8648 (mt0) REVERT: U 132 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8842 (mm) REVERT: V 8 ASP cc_start: 0.9047 (m-30) cc_final: 0.8726 (m-30) REVERT: V 60 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8098 (mtp85) REVERT: V 70 PHE cc_start: 0.8997 (t80) cc_final: 0.6523 (t80) REVERT: V 76 ASP cc_start: 0.9197 (t0) cc_final: 0.8532 (t0) REVERT: V 98 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.6447 (m-10) REVERT: W 76 ASP cc_start: 0.9245 (t0) cc_final: 0.8913 (t0) REVERT: W 81 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8327 (tm-30) REVERT: W 82 ILE cc_start: 0.9424 (mt) cc_final: 0.8195 (mt) REVERT: W 85 ASP cc_start: 0.9141 (m-30) cc_final: 0.7979 (p0) REVERT: W 87 GLU cc_start: 0.8920 (mt-10) cc_final: 0.7674 (mp0) REVERT: X 35 ASN cc_start: 0.9445 (OUTLIER) cc_final: 0.9221 (p0) REVERT: X 71 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8032 (mtmm) REVERT: X 76 ASP cc_start: 0.8778 (t0) cc_final: 0.7476 (t0) REVERT: X 98 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.6394 (m-10) REVERT: X 126 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8452 (mmm) outliers start: 245 outliers final: 194 residues processed: 868 average time/residue: 0.3235 time to fit residues: 441.4495 Evaluate side-chains 945 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 722 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 117 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 117 ASN Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 126 MET Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 117 ASN Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 109 SER Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 94 ILE Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 117 ASN Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 126 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN C 20 GLN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN K 4 GLN K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 GLN ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN V 92 GLN W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 23688 Z= 0.460 Angle : 0.916 14.016 31968 Z= 0.461 Chirality : 0.052 0.231 3576 Planarity : 0.005 0.047 4248 Dihedral : 6.118 30.713 3264 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 37.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 10.65 % Allowed : 29.42 % Favored : 59.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.99 (0.14), residues: 3024 helix: -0.83 (0.24), residues: 456 sheet: -1.14 (0.14), residues: 1200 loop : -3.22 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 50 HIS 0.003 0.001 HIS C 116 PHE 0.052 0.002 PHE B 91 TYR 0.016 0.001 TYR C 112 ARG 0.007 0.001 ARG W 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 721 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9041 (mtmm) REVERT: D 51 ARG cc_start: 0.8470 (ttp-170) cc_final: 0.7667 (ttp-170) REVERT: D 71 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8272 (mtmm) REVERT: B 8 ASP cc_start: 0.9019 (m-30) cc_final: 0.8708 (m-30) REVERT: B 74 ASP cc_start: 0.9287 (p0) cc_final: 0.9001 (p0) REVERT: B 76 ASP cc_start: 0.8779 (t0) cc_final: 0.7178 (t0) REVERT: B 98 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.6407 (m-10) REVERT: C 31 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7722 (ttt90) REVERT: C 76 ASP cc_start: 0.9262 (t0) cc_final: 0.8917 (t0) REVERT: C 81 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8808 (tm-30) REVERT: C 98 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.6679 (m-10) REVERT: A 70 PHE cc_start: 0.8883 (t80) cc_final: 0.7513 (t80) REVERT: A 76 ASP cc_start: 0.9098 (t0) cc_final: 0.8387 (t0) REVERT: A 85 ASP cc_start: 0.9260 (OUTLIER) cc_final: 0.8544 (p0) REVERT: A 92 GLN cc_start: 0.8981 (tt0) cc_final: 0.8611 (tp40) REVERT: A 98 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.6729 (m-10) REVERT: A 119 GLU cc_start: 0.9436 (pm20) cc_final: 0.9140 (pm20) REVERT: E 31 ARG cc_start: 0.9020 (mmm-85) cc_final: 0.8593 (mmm-85) REVERT: E 51 ARG cc_start: 0.8834 (ttp-170) cc_final: 0.8150 (ttp-170) REVERT: E 132 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8833 (mm) REVERT: F 8 ASP cc_start: 0.8961 (m-30) cc_final: 0.8675 (m-30) REVERT: F 70 PHE cc_start: 0.8997 (t80) cc_final: 0.6646 (t80) REVERT: F 74 ASP cc_start: 0.9392 (p0) cc_final: 0.9033 (p0) REVERT: F 76 ASP cc_start: 0.9239 (t0) cc_final: 0.8638 (t0) REVERT: F 98 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: G 7 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9087 (mtmt) REVERT: G 31 ARG cc_start: 0.8313 (tpp80) cc_final: 0.8033 (ttt90) REVERT: G 76 ASP cc_start: 0.9127 (t0) cc_final: 0.8650 (t0) REVERT: G 81 GLN cc_start: 0.9012 (tm-30) cc_final: 0.7693 (tm-30) REVERT: G 82 ILE cc_start: 0.9467 (mt) cc_final: 0.9053 (mt) REVERT: G 85 ASP cc_start: 0.9109 (m-30) cc_final: 0.8583 (p0) REVERT: H 31 ARG cc_start: 0.9304 (ptm160) cc_final: 0.8800 (ptm-80) REVERT: H 71 LYS cc_start: 0.8534 (mtmt) cc_final: 0.7969 (mtmm) REVERT: H 76 ASP cc_start: 0.8734 (t0) cc_final: 0.7363 (t0) REVERT: H 98 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7003 (m-10) REVERT: H 119 GLU cc_start: 0.9339 (pm20) cc_final: 0.9048 (pm20) REVERT: I 51 ARG cc_start: 0.8860 (ttp-170) cc_final: 0.7982 (ttp-170) REVERT: I 76 ASP cc_start: 0.9198 (m-30) cc_final: 0.8545 (m-30) REVERT: J 8 ASP cc_start: 0.9099 (m-30) cc_final: 0.8805 (m-30) REVERT: J 70 PHE cc_start: 0.9033 (t80) cc_final: 0.6646 (t80) REVERT: J 76 ASP cc_start: 0.9223 (t0) cc_final: 0.8703 (t0) REVERT: J 98 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.7114 (m-10) REVERT: J 126 MET cc_start: 0.8656 (mtp) cc_final: 0.8036 (mmm) REVERT: K 76 ASP cc_start: 0.9295 (t0) cc_final: 0.8986 (t0) REVERT: K 81 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8336 (tm-30) REVERT: K 82 ILE cc_start: 0.9414 (mt) cc_final: 0.8185 (mt) REVERT: K 85 ASP cc_start: 0.9173 (m-30) cc_final: 0.7976 (p0) REVERT: K 87 GLU cc_start: 0.8954 (mt-10) cc_final: 0.7527 (mp0) REVERT: K 98 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: L 35 ASN cc_start: 0.9456 (OUTLIER) cc_final: 0.9239 (p0) REVERT: L 71 LYS cc_start: 0.8397 (mtmt) cc_final: 0.7937 (mtmm) REVERT: L 76 ASP cc_start: 0.8817 (t0) cc_final: 0.7511 (t0) REVERT: L 126 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8409 (mmm) REVERT: M 7 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9042 (mtmm) REVERT: M 51 ARG cc_start: 0.8475 (ttp-170) cc_final: 0.7586 (ttp-170) REVERT: M 71 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8265 (mtmm) REVERT: N 8 ASP cc_start: 0.9016 (m-30) cc_final: 0.8707 (m-30) REVERT: N 74 ASP cc_start: 0.9269 (p0) cc_final: 0.8958 (p0) REVERT: N 76 ASP cc_start: 0.8984 (t0) cc_final: 0.8000 (t0) REVERT: N 98 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.6326 (m-10) REVERT: O 31 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7421 (ttt90) REVERT: O 76 ASP cc_start: 0.9341 (t0) cc_final: 0.8582 (t0) REVERT: O 81 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8699 (tm-30) REVERT: O 92 GLN cc_start: 0.9377 (tt0) cc_final: 0.9112 (tt0) REVERT: O 98 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: O 111 ASP cc_start: 0.8554 (p0) cc_final: 0.8239 (p0) REVERT: O 123 GLU cc_start: 0.8349 (mp0) cc_final: 0.7919 (mp0) REVERT: P 37 GLU cc_start: 0.8776 (pm20) cc_final: 0.8510 (pm20) REVERT: P 85 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8544 (p0) REVERT: P 92 GLN cc_start: 0.9127 (tt0) cc_final: 0.8778 (tp-100) REVERT: P 98 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: P 100 ILE cc_start: 0.9392 (pt) cc_final: 0.8639 (pt) REVERT: P 119 GLU cc_start: 0.9415 (pm20) cc_final: 0.9086 (pm20) REVERT: Q 31 ARG cc_start: 0.9026 (mmm-85) cc_final: 0.8615 (mmm-85) REVERT: Q 51 ARG cc_start: 0.8812 (ttp-170) cc_final: 0.8069 (ttp-170) REVERT: Q 132 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8841 (mm) REVERT: R 8 ASP cc_start: 0.8958 (m-30) cc_final: 0.8670 (m-30) REVERT: R 70 PHE cc_start: 0.8995 (t80) cc_final: 0.6640 (t80) REVERT: R 74 ASP cc_start: 0.9386 (p0) cc_final: 0.9043 (p0) REVERT: R 76 ASP cc_start: 0.9245 (t0) cc_final: 0.8644 (t0) REVERT: R 98 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.6942 (m-10) REVERT: S 7 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9084 (mtmt) REVERT: S 31 ARG cc_start: 0.8305 (tpp80) cc_final: 0.8037 (ttt90) REVERT: S 76 ASP cc_start: 0.9162 (t0) cc_final: 0.8756 (t0) REVERT: S 81 GLN cc_start: 0.9010 (tm-30) cc_final: 0.7693 (tm-30) REVERT: S 82 ILE cc_start: 0.9468 (mt) cc_final: 0.9055 (mt) REVERT: S 85 ASP cc_start: 0.9104 (m-30) cc_final: 0.8582 (p0) REVERT: S 106 MET cc_start: 0.7816 (pmm) cc_final: 0.7570 (pmm) REVERT: S 111 ASP cc_start: 0.8259 (p0) cc_final: 0.7492 (p0) REVERT: T 31 ARG cc_start: 0.9301 (ptm160) cc_final: 0.8806 (ptm-80) REVERT: T 71 LYS cc_start: 0.8530 (mtmt) cc_final: 0.7970 (mtmm) REVERT: T 76 ASP cc_start: 0.8754 (t0) cc_final: 0.8494 (t0) REVERT: T 98 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7010 (m-10) REVERT: T 119 GLU cc_start: 0.9315 (pm20) cc_final: 0.9023 (pm20) REVERT: U 51 ARG cc_start: 0.8841 (ttp-170) cc_final: 0.8043 (ttp-110) REVERT: U 132 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8838 (mm) REVERT: V 8 ASP cc_start: 0.9091 (m-30) cc_final: 0.8794 (m-30) REVERT: V 60 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8040 (mtp85) REVERT: V 70 PHE cc_start: 0.9038 (t80) cc_final: 0.6696 (t80) REVERT: V 76 ASP cc_start: 0.9228 (t0) cc_final: 0.8719 (t0) REVERT: V 98 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.6368 (m-10) REVERT: W 76 ASP cc_start: 0.9293 (t0) cc_final: 0.8982 (t0) REVERT: W 81 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8334 (tm-30) REVERT: W 82 ILE cc_start: 0.9417 (mt) cc_final: 0.8183 (mt) REVERT: W 85 ASP cc_start: 0.9166 (m-30) cc_final: 0.7970 (p0) REVERT: W 87 GLU cc_start: 0.8949 (mt-10) cc_final: 0.7520 (mp0) REVERT: X 35 ASN cc_start: 0.9453 (OUTLIER) cc_final: 0.9245 (p0) REVERT: X 71 LYS cc_start: 0.8395 (mtmt) cc_final: 0.7937 (mtmm) REVERT: X 76 ASP cc_start: 0.8819 (t0) cc_final: 0.7501 (t0) REVERT: X 98 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.6216 (m-10) REVERT: X 126 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8364 (mmm) outliers start: 253 outliers final: 206 residues processed: 870 average time/residue: 0.3163 time to fit residues: 434.9253 Evaluate side-chains 943 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 707 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 117 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 117 ASN Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 92 GLN Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 117 ASN Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 81 GLN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 100 ILE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 20 GLN Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 100 ILE Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 109 SER Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 117 ASN Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 126 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 247 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 254 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN C 35 ASN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN H 20 GLN I 20 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 GLN ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN T 20 GLN U 20 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.053322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.046002 restraints weight = 112049.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.047621 restraints weight = 58325.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048725 restraints weight = 35343.478| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23688 Z= 0.249 Angle : 0.889 11.987 31968 Z= 0.432 Chirality : 0.051 0.194 3576 Planarity : 0.004 0.054 4248 Dihedral : 5.804 28.366 3264 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 30.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 9.43 % Allowed : 30.60 % Favored : 59.97 % 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: -2.90 (0.15), residues: 3024 helix: -0.76 (0.23), residues: 456 sheet: -1.30 (0.14), residues: 1224 loop : -2.93 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 50 HIS 0.002 0.000 HIS W 116 PHE 0.041 0.002 PHE N 91 TYR 0.015 0.001 TYR T 122 ARG 0.007 0.001 ARG W 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7445.93 seconds wall clock time: 132 minutes 58.88 seconds (7978.88 seconds total)