Starting phenix.real_space_refine on Mon Jul 6 11:59:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2q_63589/07_2026/9m2q_63589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2q_63589/07_2026/9m2q_63589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m2q_63589/07_2026/9m2q_63589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2q_63589/07_2026/9m2q_63589.map" model { file = "/net/cci-nas-00/data/ceres_data/9m2q_63589/07_2026/9m2q_63589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2q_63589/07_2026/9m2q_63589.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 48 7.51 5 S 72 5.16 5 C 21888 2.51 5 N 6792 2.21 5 O 6648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35448 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "B" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "C" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "D" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "E" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "F" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "G" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "H" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "I" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "J" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "K" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "L" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "M" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "N" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "O" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "P" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "Q" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "R" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "S" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "T" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "U" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "V" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "W" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "X" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "M" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "O" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "Q" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "V" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "W" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "X" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3TR': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 8.66, per 1000 atoms: 0.24 Number of scatterers: 35448 At special positions: 0 Unit cell: (131.61, 131.61, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 48 24.99 S 72 16.00 O 6648 8.00 N 6792 7.00 C 21888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.9 seconds 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8448 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 72 sheets defined 40.5% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 72 through 92 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS A 135 " --> pdb=" O HIS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 174 through 194 Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 72 through 92 Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS B 135 " --> pdb=" O HIS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 162 Processing helix chain 'B' and resid 174 through 194 Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 72 through 92 Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS C 135 " --> pdb=" O HIS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 162 Processing helix chain 'C' and resid 174 through 194 Processing helix chain 'D' and resid 42 through 56 Processing helix chain 'D' and resid 72 through 92 Processing helix chain 'D' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS D 135 " --> pdb=" O HIS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 162 Processing helix chain 'D' and resid 174 through 194 Processing helix chain 'E' and resid 42 through 56 Processing helix chain 'E' and resid 72 through 92 Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.602A pdb=" N HIS E 135 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 162 Processing helix chain 'E' and resid 174 through 194 Processing helix chain 'F' and resid 42 through 56 Processing helix chain 'F' and resid 72 through 92 Processing helix chain 'F' and resid 130 through 135 removed outlier: 3.602A pdb=" N HIS F 135 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 162 Processing helix chain 'F' and resid 174 through 194 Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 72 through 92 Processing helix chain 'G' and resid 130 through 135 removed outlier: 3.602A pdb=" N HIS G 135 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 162 Processing helix chain 'G' and resid 174 through 194 Processing helix chain 'H' and resid 42 through 56 Processing helix chain 'H' and resid 72 through 92 Processing helix chain 'H' and resid 130 through 135 removed outlier: 3.602A pdb=" N HIS H 135 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 162 Processing helix chain 'H' and resid 174 through 194 Processing helix chain 'I' and resid 42 through 56 Processing helix chain 'I' and resid 72 through 92 Processing helix chain 'I' and resid 130 through 135 removed outlier: 3.602A pdb=" N HIS I 135 " --> pdb=" O HIS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 162 Processing helix chain 'I' and resid 174 through 194 Processing helix chain 'J' and resid 42 through 56 Processing helix chain 'J' and resid 72 through 92 Processing helix chain 'J' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 162 Processing helix chain 'J' and resid 174 through 194 Processing helix chain 'K' and resid 42 through 56 Processing helix chain 'K' and resid 72 through 92 Processing helix chain 'K' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS K 135 " --> pdb=" O HIS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 162 Processing helix chain 'K' and resid 174 through 194 Processing helix chain 'L' and resid 42 through 56 Processing helix chain 'L' and resid 72 through 92 Processing helix chain 'L' and resid 130 through 135 removed outlier: 3.602A pdb=" N HIS L 135 " --> pdb=" O HIS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 162 Processing helix chain 'L' and resid 174 through 194 Processing helix chain 'M' and resid 42 through 56 Processing helix chain 'M' and resid 72 through 92 Processing helix chain 'M' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS M 135 " --> pdb=" O HIS M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 162 Processing helix chain 'M' and resid 174 through 194 Processing helix chain 'N' and resid 42 through 56 Processing helix chain 'N' and resid 72 through 92 Processing helix chain 'N' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS N 135 " --> pdb=" O HIS N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 162 Processing helix chain 'N' and resid 174 through 194 Processing helix chain 'O' and resid 42 through 56 Processing helix chain 'O' and resid 72 through 92 Processing helix chain 'O' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS O 135 " --> pdb=" O HIS O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 162 Processing helix chain 'O' and resid 174 through 194 Processing helix chain 'P' and resid 42 through 56 Processing helix chain 'P' and resid 72 through 92 Processing helix chain 'P' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS P 135 " --> pdb=" O HIS P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 162 Processing helix chain 'P' and resid 174 through 194 Processing helix chain 'Q' and resid 42 through 56 Processing helix chain 'Q' and resid 72 through 92 Processing helix chain 'Q' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS Q 135 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 162 Processing helix chain 'Q' and resid 174 through 194 Processing helix chain 'R' and resid 42 through 56 Processing helix chain 'R' and resid 72 through 92 Processing helix chain 'R' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS R 135 " --> pdb=" O HIS R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 162 Processing helix chain 'R' and resid 174 through 194 Processing helix chain 'S' and resid 42 through 56 Processing helix chain 'S' and resid 72 through 92 Processing helix chain 'S' and resid 130 through 135 removed outlier: 3.602A pdb=" N HIS S 135 " --> pdb=" O HIS S 132 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 162 Processing helix chain 'S' and resid 174 through 194 Processing helix chain 'T' and resid 42 through 56 Processing helix chain 'T' and resid 72 through 92 Processing helix chain 'T' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS T 135 " --> pdb=" O HIS T 132 " (cutoff:3.500A) Processing helix chain 'T' and resid 149 through 162 Processing helix chain 'T' and resid 174 through 194 Processing helix chain 'U' and resid 42 through 56 Processing helix chain 'U' and resid 72 through 92 Processing helix chain 'U' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS U 135 " --> pdb=" O HIS U 132 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 162 Processing helix chain 'U' and resid 174 through 194 Processing helix chain 'V' and resid 42 through 56 Processing helix chain 'V' and resid 72 through 92 Processing helix chain 'V' and resid 130 through 135 removed outlier: 3.602A pdb=" N HIS V 135 " --> pdb=" O HIS V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 162 Processing helix chain 'V' and resid 174 through 194 Processing helix chain 'W' and resid 42 through 56 Processing helix chain 'W' and resid 72 through 92 Processing helix chain 'W' and resid 130 through 135 removed outlier: 3.601A pdb=" N HIS W 135 " --> pdb=" O HIS W 132 " (cutoff:3.500A) Processing helix chain 'W' and resid 149 through 162 Processing helix chain 'W' and resid 174 through 194 Processing helix chain 'X' and resid 42 through 56 Processing helix chain 'X' and resid 72 through 92 Processing helix chain 'X' and resid 130 through 135 removed outlier: 3.602A pdb=" N HIS X 135 " --> pdb=" O HIS X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 162 Processing helix chain 'X' and resid 174 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU A 111 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR A 123 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A 167 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 125 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 169 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR A 127 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR A 171 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 137 through 138 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 18 Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU B 111 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR B 123 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL B 167 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 125 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL B 169 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR B 127 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR B 171 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 18 Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU C 111 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR C 123 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL C 167 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 125 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL C 169 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR C 127 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR C 171 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 18 Processing sheet with id=AB2, first strand: chain 'D' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU D 111 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR D 123 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL D 167 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL D 125 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL D 169 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR D 127 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR D 171 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 137 through 138 Processing sheet with id=AB4, first strand: chain 'E' and resid 12 through 18 Processing sheet with id=AB5, first strand: chain 'E' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU E 111 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR E 123 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL E 167 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL E 125 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL E 169 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR E 127 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR E 171 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 137 through 138 Processing sheet with id=AB7, first strand: chain 'F' and resid 12 through 18 Processing sheet with id=AB8, first strand: chain 'F' and resid 100 through 107 removed outlier: 6.697A pdb=" N LEU F 111 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR F 123 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL F 167 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL F 125 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL F 169 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR F 127 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR F 171 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 137 through 138 Processing sheet with id=AC1, first strand: chain 'G' and resid 12 through 18 Processing sheet with id=AC2, first strand: chain 'G' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU G 111 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR G 123 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL G 167 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL G 125 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL G 169 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR G 127 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR G 171 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 137 through 138 Processing sheet with id=AC4, first strand: chain 'H' and resid 12 through 18 Processing sheet with id=AC5, first strand: chain 'H' and resid 100 through 107 removed outlier: 6.697A pdb=" N LEU H 111 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR H 123 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL H 167 " --> pdb=" O TYR H 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL H 125 " --> pdb=" O VAL H 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL H 169 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR H 127 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR H 171 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 137 through 138 Processing sheet with id=AC7, first strand: chain 'I' and resid 12 through 18 Processing sheet with id=AC8, first strand: chain 'I' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU I 111 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR I 123 " --> pdb=" O LEU I 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL I 167 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL I 125 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL I 169 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR I 127 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR I 171 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 137 through 138 Processing sheet with id=AD1, first strand: chain 'J' and resid 12 through 18 Processing sheet with id=AD2, first strand: chain 'J' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU J 111 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR J 123 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL J 167 " --> pdb=" O TYR J 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL J 125 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL J 169 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR J 127 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR J 171 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 137 through 138 Processing sheet with id=AD4, first strand: chain 'K' and resid 12 through 18 Processing sheet with id=AD5, first strand: chain 'K' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU K 111 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR K 123 " --> pdb=" O LEU K 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL K 167 " --> pdb=" O TYR K 123 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL K 125 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL K 169 " --> pdb=" O VAL K 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR K 127 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR K 171 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 137 through 138 Processing sheet with id=AD7, first strand: chain 'L' and resid 12 through 18 Processing sheet with id=AD8, first strand: chain 'L' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU L 111 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR L 123 " --> pdb=" O LEU L 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL L 167 " --> pdb=" O TYR L 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL L 125 " --> pdb=" O VAL L 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL L 169 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR L 127 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR L 171 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 137 through 138 Processing sheet with id=AE1, first strand: chain 'M' and resid 12 through 18 Processing sheet with id=AE2, first strand: chain 'M' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU M 111 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR M 123 " --> pdb=" O LEU M 165 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL M 167 " --> pdb=" O TYR M 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL M 125 " --> pdb=" O VAL M 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL M 169 " --> pdb=" O VAL M 125 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR M 127 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR M 171 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 137 through 138 Processing sheet with id=AE4, first strand: chain 'N' and resid 12 through 18 Processing sheet with id=AE5, first strand: chain 'N' and resid 100 through 107 removed outlier: 6.697A pdb=" N LEU N 111 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR N 123 " --> pdb=" O LEU N 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL N 167 " --> pdb=" O TYR N 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL N 125 " --> pdb=" O VAL N 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL N 169 " --> pdb=" O VAL N 125 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR N 127 " --> pdb=" O VAL N 169 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR N 171 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 137 through 138 Processing sheet with id=AE7, first strand: chain 'O' and resid 12 through 18 Processing sheet with id=AE8, first strand: chain 'O' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU O 111 " --> pdb=" O LEU O 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR O 123 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL O 167 " --> pdb=" O TYR O 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL O 125 " --> pdb=" O VAL O 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL O 169 " --> pdb=" O VAL O 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR O 127 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR O 171 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 137 through 138 Processing sheet with id=AF1, first strand: chain 'P' and resid 12 through 18 Processing sheet with id=AF2, first strand: chain 'P' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU P 111 " --> pdb=" O LEU P 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR P 123 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL P 167 " --> pdb=" O TYR P 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL P 125 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL P 169 " --> pdb=" O VAL P 125 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR P 127 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR P 171 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 137 through 138 Processing sheet with id=AF4, first strand: chain 'Q' and resid 12 through 18 Processing sheet with id=AF5, first strand: chain 'Q' and resid 100 through 107 removed outlier: 6.697A pdb=" N LEU Q 111 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR Q 123 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL Q 167 " --> pdb=" O TYR Q 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL Q 125 " --> pdb=" O VAL Q 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL Q 169 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR Q 127 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR Q 171 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 137 through 138 Processing sheet with id=AF7, first strand: chain 'R' and resid 12 through 18 Processing sheet with id=AF8, first strand: chain 'R' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU R 111 " --> pdb=" O LEU R 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR R 123 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL R 167 " --> pdb=" O TYR R 123 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL R 125 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL R 169 " --> pdb=" O VAL R 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR R 127 " --> pdb=" O VAL R 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR R 171 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 137 through 138 Processing sheet with id=AG1, first strand: chain 'S' and resid 12 through 18 Processing sheet with id=AG2, first strand: chain 'S' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU S 111 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR S 123 " --> pdb=" O LEU S 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL S 167 " --> pdb=" O TYR S 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL S 125 " --> pdb=" O VAL S 167 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL S 169 " --> pdb=" O VAL S 125 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR S 127 " --> pdb=" O VAL S 169 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR S 171 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 137 through 138 Processing sheet with id=AG4, first strand: chain 'T' and resid 12 through 18 Processing sheet with id=AG5, first strand: chain 'T' and resid 100 through 107 removed outlier: 6.697A pdb=" N LEU T 111 " --> pdb=" O LEU T 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR T 123 " --> pdb=" O LEU T 165 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL T 167 " --> pdb=" O TYR T 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL T 125 " --> pdb=" O VAL T 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL T 169 " --> pdb=" O VAL T 125 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR T 127 " --> pdb=" O VAL T 169 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR T 171 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 137 through 138 Processing sheet with id=AG7, first strand: chain 'U' and resid 12 through 18 Processing sheet with id=AG8, first strand: chain 'U' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU U 111 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR U 123 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL U 167 " --> pdb=" O TYR U 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL U 125 " --> pdb=" O VAL U 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL U 169 " --> pdb=" O VAL U 125 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR U 127 " --> pdb=" O VAL U 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR U 171 " --> pdb=" O THR U 127 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 137 through 138 Processing sheet with id=AH1, first strand: chain 'V' and resid 12 through 18 Processing sheet with id=AH2, first strand: chain 'V' and resid 100 through 107 removed outlier: 6.697A pdb=" N LEU V 111 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR V 123 " --> pdb=" O LEU V 165 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL V 167 " --> pdb=" O TYR V 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL V 125 " --> pdb=" O VAL V 167 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL V 169 " --> pdb=" O VAL V 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR V 127 " --> pdb=" O VAL V 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR V 171 " --> pdb=" O THR V 127 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 137 through 138 Processing sheet with id=AH4, first strand: chain 'W' and resid 12 through 18 Processing sheet with id=AH5, first strand: chain 'W' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU W 111 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR W 123 " --> pdb=" O LEU W 165 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL W 167 " --> pdb=" O TYR W 123 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL W 125 " --> pdb=" O VAL W 167 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL W 169 " --> pdb=" O VAL W 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR W 127 " --> pdb=" O VAL W 169 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR W 171 " --> pdb=" O THR W 127 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 137 through 138 Processing sheet with id=AH7, first strand: chain 'X' and resid 12 through 18 Processing sheet with id=AH8, first strand: chain 'X' and resid 100 through 107 removed outlier: 6.696A pdb=" N LEU X 111 " --> pdb=" O LEU X 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR X 123 " --> pdb=" O LEU X 165 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL X 167 " --> pdb=" O TYR X 123 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL X 125 " --> pdb=" O VAL X 167 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL X 169 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR X 127 " --> pdb=" O VAL X 169 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR X 171 " --> pdb=" O THR X 127 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 137 through 138 2232 hydrogen bonds defined for protein. 6264 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: 9.97 Time building geometry restraints manager: 4.32 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: 10670 1.34 - 1.46: 9003 1.46 - 1.58: 16327 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 36120 Sorted by residual: bond pdb=" C3 3TR O 303 " pdb=" N3A 3TR O 303 " ideal model delta sigma weight residual 1.371 1.423 -0.052 2.00e-02 2.50e+03 6.83e+00 bond pdb=" C3 3TR K 303 " pdb=" N3A 3TR K 303 " ideal model delta sigma weight residual 1.371 1.423 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" C3 3TR Q 303 " pdb=" N3A 3TR Q 303 " ideal model delta sigma weight residual 1.371 1.423 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" C3 3TR P 303 " pdb=" N3A 3TR P 303 " ideal model delta sigma weight residual 1.371 1.423 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C3 3TR C 303 " pdb=" N3A 3TR C 303 " ideal model delta sigma weight residual 1.371 1.423 -0.052 2.00e-02 2.50e+03 6.70e+00 ... (remaining 36115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 44897 1.69 - 3.39: 3891 3.39 - 5.08: 242 5.08 - 6.77: 49 6.77 - 8.47: 1 Bond angle restraints: 49080 Sorted by residual: angle pdb=" CA SER A 119 " pdb=" CB SER A 119 " pdb=" OG SER A 119 " ideal model delta sigma weight residual 111.10 102.63 8.47 2.00e+00 2.50e-01 1.79e+01 angle pdb=" N ARG R 99 " pdb=" CA ARG R 99 " pdb=" CB ARG R 99 " ideal model delta sigma weight residual 114.17 109.95 4.22 1.14e+00 7.69e-01 1.37e+01 angle pdb=" N ARG C 99 " pdb=" CA ARG C 99 " pdb=" CB ARG C 99 " ideal model delta sigma weight residual 114.17 109.95 4.22 1.14e+00 7.69e-01 1.37e+01 angle pdb=" N ARG B 99 " pdb=" CA ARG B 99 " pdb=" CB ARG B 99 " ideal model delta sigma weight residual 114.17 109.96 4.21 1.14e+00 7.69e-01 1.37e+01 angle pdb=" N ARG W 99 " pdb=" CA ARG W 99 " pdb=" CB ARG W 99 " ideal model delta sigma weight residual 114.17 109.96 4.21 1.14e+00 7.69e-01 1.36e+01 ... (remaining 49075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.93: 19557 13.93 - 27.86: 1355 27.86 - 41.79: 375 41.79 - 55.72: 121 55.72 - 69.65: 72 Dihedral angle restraints: 21480 sinusoidal: 8376 harmonic: 13104 Sorted by residual: dihedral pdb=" CA PHE Q 58 " pdb=" C PHE Q 58 " pdb=" N ASP Q 59 " pdb=" CA ASP Q 59 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE N 58 " pdb=" C PHE N 58 " pdb=" N ASP N 59 " pdb=" CA ASP N 59 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE E 58 " pdb=" C PHE E 58 " pdb=" N ASP E 59 " pdb=" CA ASP E 59 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 21477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2569 0.038 - 0.075: 1419 0.075 - 0.113: 1214 0.113 - 0.151: 270 0.151 - 0.188: 120 Chirality restraints: 5592 Sorted by residual: chirality pdb=" CA PRO B 175 " pdb=" N PRO B 175 " pdb=" C PRO B 175 " pdb=" CB PRO B 175 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA PRO Q 175 " pdb=" N PRO Q 175 " pdb=" C PRO Q 175 " pdb=" CB PRO Q 175 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA PRO U 175 " pdb=" N PRO U 175 " pdb=" C PRO U 175 " pdb=" CB PRO U 175 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 5589 not shown) Planarity restraints: 6528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG X 121 " 0.190 9.50e-02 1.11e+02 8.52e-02 4.76e+00 pdb=" NE ARG X 121 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG X 121 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG X 121 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG X 121 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG T 121 " 0.187 9.50e-02 1.11e+02 8.37e-02 4.46e+00 pdb=" NE ARG T 121 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG T 121 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG T 121 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG T 121 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 121 " -0.186 9.50e-02 1.11e+02 8.35e-02 4.45e+00 pdb=" NE ARG W 121 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG W 121 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG W 121 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG W 121 " -0.004 2.00e-02 2.50e+03 ... (remaining 6525 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 435 2.62 - 3.19: 29420 3.19 - 3.76: 55667 3.76 - 4.33: 80883 4.33 - 4.90: 137707 Nonbonded interactions: 304112 Sorted by model distance: nonbonded pdb=" NE2 HIS T 176 " pdb="MN MN T 302 " model vdw 2.055 3.140 nonbonded pdb=" NE2 HIS J 176 " pdb="MN MN J 302 " model vdw 2.055 3.140 nonbonded pdb=" NE2 HIS B 176 " pdb="MN MN B 302 " model vdw 2.055 3.140 nonbonded pdb=" NE2 HIS X 176 " pdb="MN MN X 302 " model vdw 2.055 3.140 nonbonded pdb=" NE2 HIS U 176 " pdb="MN MN U 302 " model vdw 2.055 3.140 ... (remaining 304107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 37.550 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 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 : 0.007 0.052 36120 Z= 0.490 Angle : 1.011 8.466 49080 Z= 0.698 Chirality : 0.066 0.188 5592 Planarity : 0.009 0.085 6528 Dihedral : 12.149 69.650 13032 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.18 % Allowed : 5.43 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 4512 helix: 1.26 (0.12), residues: 1848 sheet: -0.36 (0.13), residues: 1488 loop : -1.33 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG I 162 TYR 0.014 0.003 TYR N 183 PHE 0.013 0.003 PHE W 154 HIS 0.011 0.003 HIS N 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.49 (36120) covalent geometry : angle 1.01093 / 0.70 (49080) hydrogen bonds : bond 0.13895 / 9.89 ( 2232) hydrogen bonds : angle 5.48592 / 3.98 ( 6264) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 705 time to evaluate : 1.345 Fit side-chains REVERT: A 12 ARG cc_start: 0.5354 (mtt90) cc_final: 0.5046 (mpt-90) REVERT: A 14 ARG cc_start: 0.7186 (ttt90) cc_final: 0.6756 (ttt-90) REVERT: A 16 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6140 (tt0) REVERT: A 27 GLU cc_start: 0.6241 (mt-10) cc_final: 0.5424 (mp0) REVERT: A 61 THR cc_start: 0.6831 (m) cc_final: 0.6223 (p) REVERT: A 63 ARG cc_start: 0.6470 (ttt180) cc_final: 0.6040 (mtp180) REVERT: A 121 ARG cc_start: 0.6078 (mtt90) cc_final: 0.5598 (mtm-85) REVERT: A 131 ASP cc_start: 0.7410 (m-30) cc_final: 0.7121 (m-30) REVERT: A 134 GLN cc_start: 0.7358 (mt0) cc_final: 0.7042 (mt0) REVERT: A 162 ARG cc_start: 0.5752 (mtt180) cc_final: 0.5514 (mtp85) REVERT: B 12 ARG cc_start: 0.5351 (mtt90) cc_final: 0.5043 (mpt-90) REVERT: B 14 ARG cc_start: 0.7149 (ttt90) cc_final: 0.6693 (ttt-90) REVERT: B 16 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6139 (tt0) REVERT: B 27 GLU cc_start: 0.6297 (mt-10) cc_final: 0.5500 (mp0) REVERT: B 61 THR cc_start: 0.6939 (m) cc_final: 0.6341 (p) REVERT: B 63 ARG cc_start: 0.6588 (ttt180) cc_final: 0.6188 (mtp180) REVERT: B 131 ASP cc_start: 0.7407 (m-30) cc_final: 0.7122 (m-30) REVERT: B 134 GLN cc_start: 0.7356 (mt0) cc_final: 0.7038 (mt0) REVERT: B 162 ARG cc_start: 0.5819 (mtt180) cc_final: 0.5492 (mtp-110) REVERT: C 12 ARG cc_start: 0.5370 (mtt90) cc_final: 0.5069 (mpt-90) REVERT: C 14 ARG cc_start: 0.7145 (ttt90) cc_final: 0.6708 (ttt-90) REVERT: C 16 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6137 (tt0) REVERT: C 27 GLU cc_start: 0.6300 (mt-10) cc_final: 0.5502 (mp0) REVERT: C 61 THR cc_start: 0.6946 (m) cc_final: 0.6336 (p) REVERT: C 63 ARG cc_start: 0.6584 (ttt180) cc_final: 0.6198 (mtp180) REVERT: C 131 ASP cc_start: 0.7403 (m-30) cc_final: 0.7115 (m-30) REVERT: C 134 GLN cc_start: 0.7363 (mt0) cc_final: 0.7045 (mt0) REVERT: C 162 ARG cc_start: 0.5685 (mtt180) cc_final: 0.5450 (mtp-110) REVERT: D 12 ARG cc_start: 0.5349 (mtt90) cc_final: 0.5041 (mpt-90) REVERT: D 14 ARG cc_start: 0.7126 (ttt90) cc_final: 0.6924 (ttt-90) REVERT: D 16 GLU cc_start: 0.6533 (mt-10) cc_final: 0.6328 (tt0) REVERT: D 27 GLU cc_start: 0.6419 (mt-10) cc_final: 0.5631 (mp0) REVERT: D 61 THR cc_start: 0.6929 (m) cc_final: 0.6313 (p) REVERT: D 63 ARG cc_start: 0.6468 (ttt180) cc_final: 0.6036 (mtp180) REVERT: D 131 ASP cc_start: 0.7407 (m-30) cc_final: 0.7115 (m-30) REVERT: D 134 GLN cc_start: 0.7361 (mt0) cc_final: 0.7047 (mt0) REVERT: E 12 ARG cc_start: 0.5318 (mtt90) cc_final: 0.5006 (mpt-90) REVERT: E 14 ARG cc_start: 0.7164 (ttt90) cc_final: 0.6738 (ttt-90) REVERT: E 16 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6204 (tt0) REVERT: E 27 GLU cc_start: 0.6252 (mt-10) cc_final: 0.5428 (mp0) REVERT: E 61 THR cc_start: 0.6837 (m) cc_final: 0.6244 (p) REVERT: E 63 ARG cc_start: 0.6457 (ttt180) cc_final: 0.6029 (mtp180) REVERT: E 131 ASP cc_start: 0.7415 (m-30) cc_final: 0.7119 (m-30) REVERT: E 134 GLN cc_start: 0.7349 (mt0) cc_final: 0.7027 (mt0) REVERT: E 162 ARG cc_start: 0.5800 (mtt180) cc_final: 0.5463 (mtp-110) REVERT: F 12 ARG cc_start: 0.5358 (mtt90) cc_final: 0.5049 (mpt-90) REVERT: F 14 ARG cc_start: 0.7133 (ttt90) cc_final: 0.6674 (ttt-90) REVERT: F 16 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6146 (tt0) REVERT: F 27 GLU cc_start: 0.6455 (mt-10) cc_final: 0.5703 (mp0) REVERT: F 61 THR cc_start: 0.6842 (m) cc_final: 0.6231 (p) REVERT: F 63 ARG cc_start: 0.6603 (ttt180) cc_final: 0.6196 (mtp180) REVERT: F 131 ASP cc_start: 0.7415 (m-30) cc_final: 0.7123 (m-30) REVERT: F 134 GLN cc_start: 0.7355 (mt0) cc_final: 0.7032 (mt0) REVERT: F 162 ARG cc_start: 0.5930 (mtt180) cc_final: 0.5555 (mtp-110) REVERT: G 12 ARG cc_start: 0.5352 (mtt90) cc_final: 0.5044 (mpt-90) REVERT: G 14 ARG cc_start: 0.7146 (ttt90) cc_final: 0.6697 (ttt-90) REVERT: G 16 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6141 (tt0) REVERT: G 27 GLU cc_start: 0.6244 (mt-10) cc_final: 0.5430 (mp0) REVERT: G 61 THR cc_start: 0.6940 (m) cc_final: 0.6339 (p) REVERT: G 63 ARG cc_start: 0.6617 (ttt180) cc_final: 0.6209 (mtp180) REVERT: G 131 ASP cc_start: 0.7411 (m-30) cc_final: 0.7122 (m-30) REVERT: G 134 GLN cc_start: 0.7358 (mt0) cc_final: 0.7041 (mt0) REVERT: G 162 ARG cc_start: 0.5820 (mtt180) cc_final: 0.5481 (mtp-110) REVERT: H 12 ARG cc_start: 0.5353 (mtt90) cc_final: 0.5045 (mpt-90) REVERT: H 14 ARG cc_start: 0.7144 (ttt90) cc_final: 0.6626 (mtp-110) REVERT: H 16 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6120 (tt0) REVERT: H 27 GLU cc_start: 0.6305 (mt-10) cc_final: 0.5510 (mp0) REVERT: H 61 THR cc_start: 0.6937 (m) cc_final: 0.6335 (p) REVERT: H 63 ARG cc_start: 0.6475 (ttt180) cc_final: 0.6042 (mtp180) REVERT: H 131 ASP cc_start: 0.7409 (m-30) cc_final: 0.7119 (m-30) REVERT: H 134 GLN cc_start: 0.7354 (mt0) cc_final: 0.7032 (mt0) REVERT: I 12 ARG cc_start: 0.5352 (mtt90) cc_final: 0.5044 (mpt-90) REVERT: I 14 ARG cc_start: 0.7145 (ttt90) cc_final: 0.6714 (ttt-90) REVERT: I 16 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6140 (tt0) REVERT: I 27 GLU cc_start: 0.6310 (mt-10) cc_final: 0.5510 (mp0) REVERT: I 61 THR cc_start: 0.6935 (m) cc_final: 0.6334 (p) REVERT: I 63 ARG cc_start: 0.6476 (ttt180) cc_final: 0.6040 (mtp180) REVERT: I 131 ASP cc_start: 0.7412 (m-30) cc_final: 0.7118 (m-30) REVERT: I 134 GLN cc_start: 0.7355 (mt0) cc_final: 0.7031 (mt0) REVERT: J 12 ARG cc_start: 0.5354 (mtt90) cc_final: 0.5045 (mpt-90) REVERT: J 14 ARG cc_start: 0.7151 (ttt90) cc_final: 0.6687 (ttt-90) REVERT: J 16 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6187 (tt0) REVERT: J 27 GLU cc_start: 0.6306 (mt-10) cc_final: 0.5490 (mp0) REVERT: J 61 THR cc_start: 0.6955 (m) cc_final: 0.6332 (p) REVERT: J 63 ARG cc_start: 0.6598 (ttt180) cc_final: 0.6200 (mtp180) REVERT: J 131 ASP cc_start: 0.7411 (m-30) cc_final: 0.7126 (m-30) REVERT: J 134 GLN cc_start: 0.7353 (mt0) cc_final: 0.7033 (mt0) REVERT: J 162 ARG cc_start: 0.5758 (mtt180) cc_final: 0.5523 (mtp85) REVERT: K 12 ARG cc_start: 0.5373 (mtt90) cc_final: 0.5071 (mpt-90) REVERT: K 14 ARG cc_start: 0.7132 (ttt90) cc_final: 0.6921 (ttt-90) REVERT: K 16 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6426 (tt0) REVERT: K 27 GLU cc_start: 0.6413 (mt-10) cc_final: 0.5629 (mp0) REVERT: K 61 THR cc_start: 0.6929 (m) cc_final: 0.6313 (p) REVERT: K 63 ARG cc_start: 0.6594 (ttt180) cc_final: 0.6194 (mtp180) REVERT: K 131 ASP cc_start: 0.7405 (m-30) cc_final: 0.7120 (m-30) REVERT: K 134 GLN cc_start: 0.7359 (mt0) cc_final: 0.7040 (mt0) REVERT: L 12 ARG cc_start: 0.5347 (mtt90) cc_final: 0.5040 (mpt-90) REVERT: L 14 ARG cc_start: 0.7130 (ttt90) cc_final: 0.6604 (mtp-110) REVERT: L 16 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6091 (tt0) REVERT: L 27 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5444 (mp0) REVERT: L 61 THR cc_start: 0.6850 (m) cc_final: 0.6239 (p) REVERT: L 63 ARG cc_start: 0.6640 (ttt180) cc_final: 0.6216 (mtp180) REVERT: L 131 ASP cc_start: 0.7406 (m-30) cc_final: 0.7111 (m-30) REVERT: L 134 GLN cc_start: 0.7358 (mt0) cc_final: 0.7036 (mt0) REVERT: L 162 ARG cc_start: 0.5825 (mtt180) cc_final: 0.5478 (mtp-110) REVERT: M 12 ARG cc_start: 0.5351 (mtt90) cc_final: 0.5044 (mpt-90) REVERT: M 14 ARG cc_start: 0.7137 (ttt90) cc_final: 0.6659 (ttt-90) REVERT: M 16 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6143 (tt0) REVERT: M 27 GLU cc_start: 0.6470 (mt-10) cc_final: 0.5721 (mp0) REVERT: M 61 THR cc_start: 0.6957 (m) cc_final: 0.6344 (p) REVERT: M 63 ARG cc_start: 0.6598 (ttt180) cc_final: 0.6198 (mtp180) REVERT: M 131 ASP cc_start: 0.7410 (m-30) cc_final: 0.7120 (m-30) REVERT: M 134 GLN cc_start: 0.7360 (mt0) cc_final: 0.7042 (mt0) REVERT: M 162 ARG cc_start: 0.5653 (mtt180) cc_final: 0.5341 (mtp-110) REVERT: N 12 ARG cc_start: 0.5345 (mtt90) cc_final: 0.5039 (mpt-90) REVERT: N 14 ARG cc_start: 0.7133 (ttt90) cc_final: 0.6707 (ttt-90) REVERT: N 16 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6145 (tt0) REVERT: N 27 GLU cc_start: 0.6313 (mt-10) cc_final: 0.5513 (mp0) REVERT: N 61 THR cc_start: 0.6953 (m) cc_final: 0.6348 (p) REVERT: N 63 ARG cc_start: 0.6573 (ttt180) cc_final: 0.6197 (mtp180) REVERT: N 131 ASP cc_start: 0.7407 (m-30) cc_final: 0.7116 (m-30) REVERT: N 134 GLN cc_start: 0.7365 (mt0) cc_final: 0.7048 (mt0) REVERT: N 162 ARG cc_start: 0.5763 (mtt180) cc_final: 0.5483 (mtp-110) REVERT: O 12 ARG cc_start: 0.5345 (mtt90) cc_final: 0.5040 (mpt-90) REVERT: O 14 ARG cc_start: 0.7170 (ttt90) cc_final: 0.6770 (ttt-90) REVERT: O 16 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6232 (tt0) REVERT: O 27 GLU cc_start: 0.6365 (mt-10) cc_final: 0.5544 (mp0) REVERT: O 61 THR cc_start: 0.6830 (m) cc_final: 0.6211 (p) REVERT: O 63 ARG cc_start: 0.6467 (ttt180) cc_final: 0.6054 (mtp180) REVERT: O 131 ASP cc_start: 0.7403 (m-30) cc_final: 0.7087 (m-30) REVERT: O 134 GLN cc_start: 0.7360 (mt0) cc_final: 0.6994 (mt0) REVERT: O 162 ARG cc_start: 0.5869 (mtt180) cc_final: 0.5508 (mtp-110) REVERT: P 12 ARG cc_start: 0.5348 (mtt90) cc_final: 0.5041 (mpt-90) REVERT: P 14 ARG cc_start: 0.7147 (ttt90) cc_final: 0.6693 (ttt-90) REVERT: P 16 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6144 (tt0) REVERT: P 27 GLU cc_start: 0.6260 (mt-10) cc_final: 0.5443 (mp0) REVERT: P 61 THR cc_start: 0.6955 (m) cc_final: 0.6359 (p) REVERT: P 63 ARG cc_start: 0.6592 (ttt180) cc_final: 0.6196 (mtp180) REVERT: P 131 ASP cc_start: 0.7406 (m-30) cc_final: 0.7114 (m-30) REVERT: P 134 GLN cc_start: 0.7363 (mt0) cc_final: 0.7045 (mt0) REVERT: P 162 ARG cc_start: 0.5823 (mtt180) cc_final: 0.5475 (mtp-110) REVERT: Q 12 ARG cc_start: 0.5278 (mtt90) cc_final: 0.4968 (mpt-90) REVERT: Q 14 ARG cc_start: 0.7133 (ttt90) cc_final: 0.6681 (ttt-90) REVERT: Q 16 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6148 (tt0) REVERT: Q 27 GLU cc_start: 0.6471 (mt-10) cc_final: 0.5714 (mp0) REVERT: Q 61 THR cc_start: 0.6838 (m) cc_final: 0.6222 (p) REVERT: Q 63 ARG cc_start: 0.6600 (ttt180) cc_final: 0.6194 (mtp180) REVERT: Q 131 ASP cc_start: 0.7413 (m-30) cc_final: 0.7116 (m-30) REVERT: Q 134 GLN cc_start: 0.7357 (mt0) cc_final: 0.7036 (mt0) REVERT: Q 162 ARG cc_start: 0.5752 (mtt180) cc_final: 0.5536 (mtp-110) REVERT: R 12 ARG cc_start: 0.5347 (mtt90) cc_final: 0.5040 (mpt-90) REVERT: R 14 ARG cc_start: 0.7146 (ttt90) cc_final: 0.6698 (ttt-90) REVERT: R 16 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6142 (tt0) REVERT: R 27 GLU cc_start: 0.6306 (mt-10) cc_final: 0.5506 (mp0) REVERT: R 61 THR cc_start: 0.6950 (m) cc_final: 0.6346 (p) REVERT: R 63 ARG cc_start: 0.6621 (ttt180) cc_final: 0.6211 (mtp180) REVERT: R 131 ASP cc_start: 0.7404 (m-30) cc_final: 0.7111 (m-30) REVERT: R 134 GLN cc_start: 0.7357 (mt0) cc_final: 0.7035 (mt0) REVERT: R 162 ARG cc_start: 0.5796 (mtt180) cc_final: 0.5479 (mtp-110) REVERT: S 12 ARG cc_start: 0.5366 (mtt90) cc_final: 0.5064 (mpt-90) REVERT: S 14 ARG cc_start: 0.7098 (ttt90) cc_final: 0.6647 (ttt-90) REVERT: S 16 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6397 (tt0) REVERT: S 27 GLU cc_start: 0.6314 (mt-10) cc_final: 0.5514 (mp0) REVERT: S 61 THR cc_start: 0.6947 (m) cc_final: 0.6332 (p) REVERT: S 63 ARG cc_start: 0.6588 (ttt180) cc_final: 0.6204 (mtp180) REVERT: S 131 ASP cc_start: 0.7402 (m-30) cc_final: 0.7113 (m-30) REVERT: S 134 GLN cc_start: 0.7368 (mt0) cc_final: 0.7049 (mt0) REVERT: S 162 ARG cc_start: 0.5762 (mtt180) cc_final: 0.5406 (mtp-110) REVERT: T 12 ARG cc_start: 0.5343 (mtt90) cc_final: 0.5037 (mpt-90) REVERT: T 14 ARG cc_start: 0.7102 (ttt90) cc_final: 0.6659 (ttt-90) REVERT: T 16 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6273 (tt0) REVERT: T 27 GLU cc_start: 0.6320 (mt-10) cc_final: 0.5518 (mp0) REVERT: T 61 THR cc_start: 0.6953 (m) cc_final: 0.6343 (p) REVERT: T 63 ARG cc_start: 0.6577 (ttt180) cc_final: 0.6196 (mtp180) REVERT: T 131 ASP cc_start: 0.7405 (m-30) cc_final: 0.7112 (m-30) REVERT: T 134 GLN cc_start: 0.7360 (mt0) cc_final: 0.7034 (mt0) REVERT: T 162 ARG cc_start: 0.5793 (mtt180) cc_final: 0.5510 (mtp-110) REVERT: U 12 ARG cc_start: 0.5379 (mtt90) cc_final: 0.5074 (mpt-90) REVERT: U 14 ARG cc_start: 0.7148 (ttt90) cc_final: 0.6692 (ttt-90) REVERT: U 16 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6141 (tt0) REVERT: U 27 GLU cc_start: 0.6309 (mt-10) cc_final: 0.5512 (mp0) REVERT: U 61 THR cc_start: 0.6819 (m) cc_final: 0.6230 (p) REVERT: U 63 ARG cc_start: 0.6587 (ttt180) cc_final: 0.6189 (mtp180) REVERT: U 131 ASP cc_start: 0.7411 (m-30) cc_final: 0.7127 (m-30) REVERT: U 134 GLN cc_start: 0.7352 (mt0) cc_final: 0.7034 (mt0) REVERT: V 12 ARG cc_start: 0.5353 (mtt90) cc_final: 0.5045 (mpt-90) REVERT: V 14 ARG cc_start: 0.7148 (ttt90) cc_final: 0.6698 (ttt-90) REVERT: V 16 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6146 (tt0) REVERT: V 27 GLU cc_start: 0.6252 (mt-10) cc_final: 0.5430 (mp0) REVERT: V 61 THR cc_start: 0.6841 (m) cc_final: 0.6243 (p) REVERT: V 63 ARG cc_start: 0.6606 (ttt180) cc_final: 0.6202 (mtp180) REVERT: V 131 ASP cc_start: 0.7412 (m-30) cc_final: 0.7120 (m-30) REVERT: V 134 GLN cc_start: 0.7352 (mt0) cc_final: 0.7026 (mt0) REVERT: V 162 ARG cc_start: 0.5757 (mtt180) cc_final: 0.5470 (mtp-110) REVERT: W 12 ARG cc_start: 0.5372 (mtt90) cc_final: 0.5070 (mpt-90) REVERT: W 14 ARG cc_start: 0.7146 (ttt90) cc_final: 0.6712 (ttt-90) REVERT: W 16 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6138 (tt0) REVERT: W 27 GLU cc_start: 0.6314 (mt-10) cc_final: 0.5513 (mp0) REVERT: W 61 THR cc_start: 0.6933 (m) cc_final: 0.6323 (p) REVERT: W 63 ARG cc_start: 0.6479 (ttt180) cc_final: 0.6049 (mtp180) REVERT: W 131 ASP cc_start: 0.7405 (m-30) cc_final: 0.7116 (m-30) REVERT: W 134 GLN cc_start: 0.7365 (mt0) cc_final: 0.7049 (mt0) REVERT: X 12 ARG cc_start: 0.5308 (mtt90) cc_final: 0.5001 (mpt-90) REVERT: X 14 ARG cc_start: 0.7136 (ttt90) cc_final: 0.6676 (ttt-90) REVERT: X 16 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6145 (tt0) REVERT: X 27 GLU cc_start: 0.6464 (mt-10) cc_final: 0.5711 (mp0) REVERT: X 61 THR cc_start: 0.6850 (m) cc_final: 0.6229 (p) REVERT: X 63 ARG cc_start: 0.6613 (ttt180) cc_final: 0.6197 (mtp180) REVERT: X 131 ASP cc_start: 0.7404 (m-30) cc_final: 0.7110 (m-30) REVERT: X 134 GLN cc_start: 0.7360 (mt0) cc_final: 0.7037 (mt0) REVERT: X 162 ARG cc_start: 0.5768 (mtt180) cc_final: 0.5525 (mtp-110) outliers start: 43 outliers final: 43 residues processed: 748 average time/residue: 0.9947 time to fit residues: 849.4937 Evaluate side-chains 557 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 514 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 133 LEU Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 133 LEU Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 182 GLN B 74 HIS B 182 GLN C 74 HIS C 182 GLN D 74 HIS D 182 GLN E 74 HIS E 182 GLN F 74 HIS F 182 GLN G 74 HIS G 182 GLN H 74 HIS H 182 GLN I 74 HIS I 182 GLN J 74 HIS J 182 GLN K 74 HIS K 182 GLN L 74 HIS L 182 GLN M 74 HIS M 182 GLN N 74 HIS N 182 GLN O 74 HIS O 182 GLN P 74 HIS P 182 GLN Q 74 HIS Q 182 GLN R 74 HIS R 182 GLN S 74 HIS S 182 GLN T 74 HIS T 182 GLN U 74 HIS U 182 GLN V 74 HIS V 182 GLN W 74 HIS W 182 GLN X 74 HIS X 182 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.102038 restraints weight = 35736.746| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.72 r_work: 0.2848 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 36120 Z= 0.128 Angle : 0.519 8.634 49080 Z= 0.274 Chirality : 0.046 0.142 5592 Planarity : 0.004 0.025 6528 Dihedral : 5.679 43.205 5174 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.11 % Allowed : 11.79 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.13), residues: 4512 helix: 2.02 (0.12), residues: 1872 sheet: -0.48 (0.12), residues: 1488 loop : -1.42 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 121 TYR 0.008 0.001 TYR A 123 PHE 0.007 0.002 PHE D 104 HIS 0.005 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (36120) covalent geometry : angle 0.51856 / 0.27 (49080) hydrogen bonds : bond 0.03706 / 2.59 ( 2232) hydrogen bonds : angle 3.95730 / 2.87 ( 6264) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 599 time to evaluate : 1.299 Fit side-chains REVERT: A 12 ARG cc_start: 0.6582 (mtt90) cc_final: 0.6351 (mpt-90) REVERT: A 16 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6797 (tt0) REVERT: A 27 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7169 (mp0) REVERT: A 65 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7171 (p) REVERT: A 109 GLU cc_start: 0.8794 (pm20) cc_final: 0.8442 (pm20) REVERT: B 12 ARG cc_start: 0.6657 (mtt90) cc_final: 0.6430 (mpt-90) REVERT: B 14 ARG cc_start: 0.7989 (ttt90) cc_final: 0.7771 (ttt-90) REVERT: B 16 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6805 (tt0) REVERT: B 27 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7163 (mp0) REVERT: B 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7150 (p) REVERT: B 109 GLU cc_start: 0.8785 (pm20) cc_final: 0.8439 (pm20) REVERT: C 12 ARG cc_start: 0.6639 (mtt90) cc_final: 0.6408 (mpt-90) REVERT: C 27 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7172 (mp0) REVERT: C 65 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7146 (p) REVERT: C 109 GLU cc_start: 0.8783 (pm20) cc_final: 0.8579 (pm20) REVERT: D 12 ARG cc_start: 0.6600 (mtt90) cc_final: 0.6359 (mpt-90) REVERT: D 27 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7112 (mp0) REVERT: D 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7145 (p) REVERT: D 109 GLU cc_start: 0.8801 (pm20) cc_final: 0.8594 (pm20) REVERT: E 12 ARG cc_start: 0.6578 (mtt90) cc_final: 0.6363 (mpt-90) REVERT: E 16 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6793 (tt0) REVERT: E 27 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7148 (mp0) REVERT: E 65 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7182 (p) REVERT: E 71 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: E 109 GLU cc_start: 0.8797 (pm20) cc_final: 0.8442 (pm20) REVERT: F 12 ARG cc_start: 0.6586 (mtt90) cc_final: 0.6360 (mpt-90) REVERT: F 27 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7107 (mp0) REVERT: F 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7153 (p) REVERT: F 109 GLU cc_start: 0.8790 (pm20) cc_final: 0.8435 (pm20) REVERT: G 12 ARG cc_start: 0.6610 (mtt90) cc_final: 0.6382 (mpt-90) REVERT: G 16 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6796 (tt0) REVERT: G 27 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7189 (mp0) REVERT: G 65 THR cc_start: 0.7487 (OUTLIER) cc_final: 0.7150 (p) REVERT: G 109 GLU cc_start: 0.8793 (pm20) cc_final: 0.8449 (pm20) REVERT: H 12 ARG cc_start: 0.6606 (mtt90) cc_final: 0.6376 (mpt-90) REVERT: H 14 ARG cc_start: 0.8003 (ttt90) cc_final: 0.7787 (ttt-90) REVERT: H 16 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6784 (tt0) REVERT: H 27 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7159 (mp0) REVERT: H 65 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7163 (p) REVERT: H 109 GLU cc_start: 0.8798 (pm20) cc_final: 0.8452 (pm20) REVERT: I 12 ARG cc_start: 0.6597 (mtt90) cc_final: 0.6366 (mpt-90) REVERT: I 16 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6788 (tt0) REVERT: I 27 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7145 (mp0) REVERT: I 65 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7148 (p) REVERT: I 109 GLU cc_start: 0.8794 (pm20) cc_final: 0.8450 (pm20) REVERT: J 12 ARG cc_start: 0.6658 (mtt90) cc_final: 0.6424 (mpt-90) REVERT: J 27 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7155 (mp0) REVERT: J 65 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7172 (p) REVERT: J 109 GLU cc_start: 0.8790 (pm20) cc_final: 0.8443 (pm20) REVERT: K 12 ARG cc_start: 0.6624 (mtt90) cc_final: 0.6398 (mpt-90) REVERT: K 27 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7146 (mp0) REVERT: K 65 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7146 (p) REVERT: K 109 GLU cc_start: 0.8798 (pm20) cc_final: 0.8452 (pm20) REVERT: L 12 ARG cc_start: 0.6608 (mtt90) cc_final: 0.6373 (mpt-90) REVERT: L 16 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6779 (tt0) REVERT: L 27 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7171 (mp0) REVERT: L 65 THR cc_start: 0.7485 (OUTLIER) cc_final: 0.7138 (p) REVERT: L 109 GLU cc_start: 0.8793 (pm20) cc_final: 0.8435 (pm20) REVERT: M 12 ARG cc_start: 0.6646 (mtt90) cc_final: 0.6423 (mpt-90) REVERT: M 27 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7147 (mp0) REVERT: M 65 THR cc_start: 0.7493 (OUTLIER) cc_final: 0.7150 (p) REVERT: M 109 GLU cc_start: 0.8788 (pm20) cc_final: 0.8442 (pm20) REVERT: N 12 ARG cc_start: 0.6590 (mtt90) cc_final: 0.6359 (mpt-90) REVERT: N 16 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6800 (tt0) REVERT: N 27 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7187 (mp0) REVERT: N 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7134 (p) REVERT: N 109 GLU cc_start: 0.8787 (pm20) cc_final: 0.8435 (pm20) REVERT: O 12 ARG cc_start: 0.6566 (mtt90) cc_final: 0.6314 (mpt-90) REVERT: O 16 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6784 (tt0) REVERT: O 27 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7150 (mp0) REVERT: O 65 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7147 (p) REVERT: O 71 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: O 109 GLU cc_start: 0.8790 (pm20) cc_final: 0.8584 (pm20) REVERT: P 12 ARG cc_start: 0.6599 (mtt90) cc_final: 0.6376 (mpt-90) REVERT: P 14 ARG cc_start: 0.7957 (ttt90) cc_final: 0.7755 (ttt-90) REVERT: P 16 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6817 (tt0) REVERT: P 27 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7191 (mp0) REVERT: P 65 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7151 (p) REVERT: P 109 GLU cc_start: 0.8792 (pm20) cc_final: 0.8438 (pm20) REVERT: Q 12 ARG cc_start: 0.6599 (mtt90) cc_final: 0.6359 (mpt-90) REVERT: Q 27 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7103 (mp0) REVERT: Q 65 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.7144 (p) REVERT: Q 109 GLU cc_start: 0.8784 (pm20) cc_final: 0.8429 (pm20) REVERT: R 12 ARG cc_start: 0.6610 (mtt90) cc_final: 0.6383 (mpt-90) REVERT: R 27 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7170 (mp0) REVERT: R 65 THR cc_start: 0.7504 (OUTLIER) cc_final: 0.7157 (p) REVERT: R 109 GLU cc_start: 0.8797 (pm20) cc_final: 0.8589 (pm20) REVERT: S 12 ARG cc_start: 0.6633 (mtt90) cc_final: 0.6403 (mpt-90) REVERT: S 14 ARG cc_start: 0.7953 (ttt90) cc_final: 0.7751 (ttt-90) REVERT: S 27 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7206 (mp0) REVERT: S 65 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7156 (p) REVERT: S 109 GLU cc_start: 0.8795 (pm20) cc_final: 0.8590 (pm20) REVERT: T 12 ARG cc_start: 0.6650 (mtt90) cc_final: 0.6430 (mpt-90) REVERT: T 27 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7191 (mp0) REVERT: T 65 THR cc_start: 0.7470 (OUTLIER) cc_final: 0.7111 (p) REVERT: T 109 GLU cc_start: 0.8801 (pm20) cc_final: 0.8592 (pm20) REVERT: U 12 ARG cc_start: 0.6636 (mtt90) cc_final: 0.6404 (mpt-90) REVERT: U 14 ARG cc_start: 0.7976 (ttt90) cc_final: 0.7774 (ttt-90) REVERT: U 27 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7186 (mp0) REVERT: U 65 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7161 (p) REVERT: U 109 GLU cc_start: 0.8808 (pm20) cc_final: 0.8456 (pm20) REVERT: V 12 ARG cc_start: 0.6604 (mtt90) cc_final: 0.6375 (mpt-90) REVERT: V 16 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6810 (tt0) REVERT: V 27 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7189 (mp0) REVERT: V 65 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7148 (p) REVERT: V 109 GLU cc_start: 0.8799 (pm20) cc_final: 0.8448 (pm20) REVERT: W 12 ARG cc_start: 0.6610 (mtt90) cc_final: 0.6383 (mpt-90) REVERT: W 27 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7180 (mp0) REVERT: W 65 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.7126 (p) REVERT: W 71 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7545 (pt0) REVERT: W 109 GLU cc_start: 0.8787 (pm20) cc_final: 0.8435 (pm20) REVERT: X 12 ARG cc_start: 0.6615 (mtt90) cc_final: 0.6387 (mpt-90) REVERT: X 27 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7128 (mp0) REVERT: X 65 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7132 (p) REVERT: X 71 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7564 (pt0) REVERT: X 109 GLU cc_start: 0.8787 (pm20) cc_final: 0.8420 (pm20) outliers start: 77 outliers final: 5 residues processed: 652 average time/residue: 1.0736 time to fit residues: 790.5190 Evaluate side-chains 536 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 503 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 283 optimal weight: 10.0000 chunk 355 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 415 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN B 134 GLN ** C 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN D 134 GLN ** E 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN H 134 GLN ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN ** J 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN K 134 GLN ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN M 134 GLN ** N 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN O 134 GLN ** P 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 134 GLN Q 134 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 GLN ** S 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 GLN ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 GLN ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN V 134 GLN ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 134 GLN ** X 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.098743 restraints weight = 35573.115| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.55 r_work: 0.2801 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 36120 Z= 0.333 Angle : 0.694 9.940 49080 Z= 0.372 Chirality : 0.054 0.162 5592 Planarity : 0.008 0.054 6528 Dihedral : 5.314 20.171 5088 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.87 % Allowed : 19.65 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 4512 helix: 1.46 (0.12), residues: 1848 sheet: -0.27 (0.13), residues: 1320 loop : -1.47 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 14 TYR 0.008 0.002 TYR C 171 PHE 0.015 0.003 PHE J 154 HIS 0.010 0.002 HIS H 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.33 (36120) covalent geometry : angle 0.69376 / 0.37 (49080) hydrogen bonds : bond 0.05068 / 3.53 ( 2232) hydrogen bonds : angle 4.23374 / 3.08 ( 6264) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 442 time to evaluate : 1.294 Fit side-chains REVERT: A 27 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7277 (mp0) REVERT: A 65 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7165 (p) REVERT: B 14 ARG cc_start: 0.8196 (ttt90) cc_final: 0.7919 (ttt-90) REVERT: B 16 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6863 (tt0) REVERT: B 27 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7306 (mp0) REVERT: B 65 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7147 (p) REVERT: C 27 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7296 (mp0) REVERT: C 65 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7160 (p) REVERT: D 27 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7160 (mp0) REVERT: D 65 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7157 (p) REVERT: E 27 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7268 (mp0) REVERT: E 65 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7180 (p) REVERT: F 27 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7159 (mp0) REVERT: F 65 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7183 (p) REVERT: G 27 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7278 (mp0) REVERT: G 65 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7176 (p) REVERT: H 14 ARG cc_start: 0.8188 (ttt90) cc_final: 0.7907 (ttt-90) REVERT: H 27 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7310 (mp0) REVERT: H 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7170 (p) REVERT: I 27 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7296 (mp0) REVERT: I 65 THR cc_start: 0.7504 (OUTLIER) cc_final: 0.7183 (p) REVERT: J 27 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7249 (mp0) REVERT: J 65 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7179 (p) REVERT: K 27 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7158 (mp0) REVERT: K 65 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.7158 (p) REVERT: L 27 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7286 (mp0) REVERT: L 65 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7176 (p) REVERT: M 27 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7150 (mp0) REVERT: M 65 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7160 (p) REVERT: M 71 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: N 27 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7262 (mp0) REVERT: N 65 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7171 (p) REVERT: O 27 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7307 (mp0) REVERT: O 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7168 (p) REVERT: P 14 ARG cc_start: 0.8204 (ttt90) cc_final: 0.7913 (ttt-90) REVERT: P 16 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6893 (tt0) REVERT: P 27 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7292 (mp0) REVERT: P 65 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7163 (p) REVERT: Q 27 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7172 (mp0) REVERT: Q 65 THR cc_start: 0.7511 (OUTLIER) cc_final: 0.7194 (p) REVERT: R 27 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7300 (mp0) REVERT: R 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7166 (p) REVERT: S 27 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7345 (mp0) REVERT: S 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7159 (p) REVERT: T 27 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7265 (mp0) REVERT: T 65 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7154 (p) REVERT: U 27 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7273 (mp0) REVERT: U 65 THR cc_start: 0.7470 (OUTLIER) cc_final: 0.7151 (p) REVERT: V 27 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7270 (mp0) REVERT: V 65 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7175 (p) REVERT: W 27 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7300 (mp0) REVERT: W 65 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.7136 (p) REVERT: X 27 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7176 (mp0) REVERT: X 65 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7173 (p) outliers start: 141 outliers final: 52 residues processed: 578 average time/residue: 0.9124 time to fit residues: 608.5741 Evaluate side-chains 492 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 415 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 404 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 429 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 134 GLN B 74 HIS B 134 GLN C 74 HIS C 134 GLN D 134 GLN E 74 HIS E 134 GLN F 134 GLN G 74 HIS G 134 GLN H 74 HIS H 134 GLN I 74 HIS I 134 GLN J 74 HIS J 134 GLN K 134 GLN L 74 HIS L 134 GLN M 134 GLN N 74 HIS N 134 GLN O 74 HIS O 134 GLN P 74 HIS P 134 GLN Q 134 GLN R 74 HIS R 134 GLN S 74 HIS S 134 GLN T 74 HIS T 134 GLN U 74 HIS U 134 GLN V 74 HIS V 134 GLN W 74 HIS W 134 GLN X 74 HIS X 134 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.099199 restraints weight = 35323.541| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.73 r_work: 0.2878 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 36120 Z= 0.119 Angle : 0.505 8.062 49080 Z= 0.266 Chirality : 0.045 0.140 5592 Planarity : 0.004 0.034 6528 Dihedral : 4.586 19.496 5088 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.66 % Allowed : 21.24 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.13), residues: 4512 helix: 1.92 (0.12), residues: 1872 sheet: -0.37 (0.13), residues: 1488 loop : -1.24 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 14 TYR 0.006 0.001 TYR J 145 PHE 0.009 0.001 PHE F 44 HIS 0.005 0.001 HIS X 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (36120) covalent geometry : angle 0.50485 / 0.27 (49080) hydrogen bonds : bond 0.03393 / 2.37 ( 2232) hydrogen bonds : angle 3.77903 / 2.75 ( 6264) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 505 time to evaluate : 1.368 Fit side-chains REVERT: A 27 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7174 (mp0) REVERT: A 65 THR cc_start: 0.7417 (OUTLIER) cc_final: 0.7069 (p) REVERT: A 71 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7339 (pt0) REVERT: B 14 ARG cc_start: 0.8140 (ttt90) cc_final: 0.7832 (ttt-90) REVERT: B 16 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6792 (tt0) REVERT: B 27 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7248 (mp0) REVERT: B 65 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.6976 (p) REVERT: B 71 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: C 27 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7216 (mp0) REVERT: C 65 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.6958 (p) REVERT: C 71 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7341 (pt0) REVERT: D 27 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7081 (mp0) REVERT: D 65 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.6967 (p) REVERT: D 71 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7344 (pt0) REVERT: E 27 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7197 (mp0) REVERT: E 65 THR cc_start: 0.7443 (OUTLIER) cc_final: 0.7099 (p) REVERT: E 71 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: F 27 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7095 (mp0) REVERT: F 65 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.6990 (p) REVERT: F 71 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: G 27 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7197 (mp0) REVERT: G 65 THR cc_start: 0.7417 (OUTLIER) cc_final: 0.7072 (p) REVERT: G 71 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: H 27 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7210 (mp0) REVERT: H 65 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7062 (p) REVERT: H 71 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: I 27 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7187 (mp0) REVERT: I 65 THR cc_start: 0.7428 (OUTLIER) cc_final: 0.7076 (p) REVERT: I 71 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7330 (pt0) REVERT: J 27 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7173 (mp0) REVERT: J 65 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.6957 (p) REVERT: J 71 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: K 27 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7054 (mp0) REVERT: K 65 THR cc_start: 0.7279 (OUTLIER) cc_final: 0.6970 (p) REVERT: K 71 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: L 27 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7170 (mp0) REVERT: L 65 THR cc_start: 0.7443 (OUTLIER) cc_final: 0.7096 (p) REVERT: L 71 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: M 27 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7072 (mp0) REVERT: M 65 THR cc_start: 0.7288 (OUTLIER) cc_final: 0.6978 (p) REVERT: N 27 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7159 (mp0) REVERT: N 65 THR cc_start: 0.7234 (OUTLIER) cc_final: 0.6936 (p) REVERT: N 71 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: O 27 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7215 (mp0) REVERT: O 65 THR cc_start: 0.7411 (OUTLIER) cc_final: 0.7061 (p) REVERT: O 71 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: P 14 ARG cc_start: 0.8143 (ttt90) cc_final: 0.7829 (ttt-90) REVERT: P 16 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6825 (tt0) REVERT: P 27 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7190 (mp0) REVERT: P 65 THR cc_start: 0.7250 (OUTLIER) cc_final: 0.6953 (p) REVERT: P 71 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7338 (pt0) REVERT: Q 27 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7074 (mp0) REVERT: Q 65 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.6983 (p) REVERT: Q 71 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: R 27 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7167 (mp0) REVERT: R 65 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.6970 (p) REVERT: R 71 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7330 (pt0) REVERT: S 27 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7190 (mp0) REVERT: S 65 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.6989 (p) REVERT: S 69 GLU cc_start: 0.7076 (pm20) cc_final: 0.6750 (mp0) REVERT: S 71 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: T 27 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7184 (mp0) REVERT: T 65 THR cc_start: 0.7270 (OUTLIER) cc_final: 0.6958 (p) REVERT: T 71 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: U 27 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7176 (mp0) REVERT: U 65 THR cc_start: 0.7277 (OUTLIER) cc_final: 0.6969 (p) REVERT: U 71 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: V 27 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7187 (mp0) REVERT: V 65 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.6957 (p) REVERT: V 71 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: W 27 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7174 (mp0) REVERT: W 65 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.6951 (p) REVERT: W 71 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: X 27 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7062 (mp0) REVERT: X 65 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.6978 (p) REVERT: X 71 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7377 (pt0) outliers start: 97 outliers final: 26 residues processed: 583 average time/residue: 0.9552 time to fit residues: 637.7538 Evaluate side-chains 524 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 451 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 133 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 175 optimal weight: 0.8980 chunk 396 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 454 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 380 optimal weight: 20.0000 chunk 273 optimal weight: 9.9990 chunk 446 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 134 GLN J 134 GLN K 134 GLN ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN M 134 GLN N 134 GLN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** V 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 GLN W 134 GLN ** X 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101391 restraints weight = 34897.337| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.55 r_work: 0.2842 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 36120 Z= 0.164 Angle : 0.540 8.357 49080 Z= 0.284 Chirality : 0.046 0.138 5592 Planarity : 0.005 0.034 6528 Dihedral : 4.678 19.893 5088 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.36 % Allowed : 20.86 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.13), residues: 4512 helix: 1.95 (0.12), residues: 1872 sheet: -0.33 (0.13), residues: 1488 loop : -1.16 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 14 TYR 0.006 0.001 TYR S 145 PHE 0.009 0.002 PHE A 44 HIS 0.006 0.001 HIS N 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (36120) covalent geometry : angle 0.54019 / 0.28 (49080) hydrogen bonds : bond 0.03775 / 2.63 ( 2232) hydrogen bonds : angle 3.81071 / 2.77 ( 6264) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 439 time to evaluate : 1.302 Fit side-chains REVERT: A 27 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7163 (mp0) REVERT: A 65 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.7061 (p) REVERT: A 69 GLU cc_start: 0.7132 (pm20) cc_final: 0.6804 (mp0) REVERT: A 71 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: B 14 ARG cc_start: 0.8166 (ttt90) cc_final: 0.7870 (ttt-90) REVERT: B 16 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6792 (tt0) REVERT: B 27 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7271 (mp0) REVERT: B 65 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.7057 (p) REVERT: B 71 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: C 27 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7224 (mp0) REVERT: C 69 GLU cc_start: 0.7116 (pm20) cc_final: 0.6789 (mp0) REVERT: C 71 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: D 27 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7121 (mp0) REVERT: D 69 GLU cc_start: 0.7128 (pm20) cc_final: 0.6805 (mp0) REVERT: D 71 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: E 27 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7184 (mp0) REVERT: E 65 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.7032 (p) REVERT: E 71 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: F 27 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7079 (mp0) REVERT: F 65 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7071 (p) REVERT: F 71 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7422 (pt0) REVERT: G 27 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7222 (mp0) REVERT: G 65 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.7047 (p) REVERT: G 69 GLU cc_start: 0.7125 (pm20) cc_final: 0.6791 (mp0) REVERT: G 71 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: H 27 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7194 (mp0) REVERT: H 65 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7064 (p) REVERT: H 69 GLU cc_start: 0.7125 (pm20) cc_final: 0.6803 (mp0) REVERT: H 71 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: H 109 GLU cc_start: 0.8832 (pm20) cc_final: 0.8522 (pm20) REVERT: I 27 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7215 (mp0) REVERT: I 65 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7055 (p) REVERT: I 69 GLU cc_start: 0.7115 (pm20) cc_final: 0.6790 (mp0) REVERT: I 71 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: J 27 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7172 (mp0) REVERT: J 65 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7052 (p) REVERT: J 69 GLU cc_start: 0.7127 (pm20) cc_final: 0.6775 (mp0) REVERT: J 71 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: J 109 GLU cc_start: 0.8838 (pm20) cc_final: 0.8526 (pm20) REVERT: K 27 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7096 (mp0) REVERT: K 65 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7074 (p) REVERT: K 69 GLU cc_start: 0.7119 (pm20) cc_final: 0.6785 (mp0) REVERT: K 71 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7405 (pt0) REVERT: L 27 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7209 (mp0) REVERT: L 65 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7079 (p) REVERT: L 69 GLU cc_start: 0.7115 (pm20) cc_final: 0.6790 (mp0) REVERT: L 71 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: L 162 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7736 (mtt-85) REVERT: M 27 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7074 (mp0) REVERT: M 65 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7070 (p) REVERT: M 69 GLU cc_start: 0.7101 (pm20) cc_final: 0.6776 (mp0) REVERT: M 71 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: N 27 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7189 (mp0) REVERT: N 65 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.7029 (p) REVERT: N 69 GLU cc_start: 0.7114 (pm20) cc_final: 0.6781 (mp0) REVERT: N 71 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: O 27 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7225 (mp0) REVERT: O 65 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.7051 (p) REVERT: O 69 GLU cc_start: 0.7116 (pm20) cc_final: 0.6801 (mp0) REVERT: O 71 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: P 14 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7873 (ttt-90) REVERT: P 16 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6857 (tt0) REVERT: P 27 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7248 (mp0) REVERT: P 65 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7071 (p) REVERT: P 69 GLU cc_start: 0.7119 (pm20) cc_final: 0.6787 (mp0) REVERT: P 71 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: P 162 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: Q 27 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7077 (mp0) REVERT: Q 65 THR cc_start: 0.7378 (OUTLIER) cc_final: 0.7077 (p) REVERT: Q 69 GLU cc_start: 0.7132 (pm20) cc_final: 0.6784 (mp0) REVERT: Q 71 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: R 27 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7197 (mp0) REVERT: R 65 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.7072 (p) REVERT: R 71 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: S 27 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7256 (mp0) REVERT: S 69 GLU cc_start: 0.7134 (pm20) cc_final: 0.6800 (mp0) REVERT: S 71 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: T 27 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7199 (mp0) REVERT: T 65 THR cc_start: 0.7340 (OUTLIER) cc_final: 0.7034 (p) REVERT: T 69 GLU cc_start: 0.7093 (pm20) cc_final: 0.6764 (mp0) REVERT: T 71 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7403 (pt0) REVERT: T 109 GLU cc_start: 0.8830 (pm20) cc_final: 0.8520 (pm20) REVERT: U 27 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7198 (mp0) REVERT: U 65 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7052 (p) REVERT: U 69 GLU cc_start: 0.7131 (pm20) cc_final: 0.6776 (mp0) REVERT: U 71 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: U 109 GLU cc_start: 0.8832 (pm20) cc_final: 0.8528 (pm20) REVERT: V 27 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7179 (mp0) REVERT: V 65 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.7057 (p) REVERT: V 69 GLU cc_start: 0.7132 (pm20) cc_final: 0.6778 (mp0) REVERT: V 71 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: W 27 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7214 (mp0) REVERT: W 65 THR cc_start: 0.7362 (OUTLIER) cc_final: 0.7065 (p) REVERT: W 71 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: X 27 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7092 (mp0) REVERT: X 65 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7078 (p) REVERT: X 69 GLU cc_start: 0.7122 (pm20) cc_final: 0.6799 (mp0) REVERT: X 71 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7458 (pt0) outliers start: 159 outliers final: 76 residues processed: 597 average time/residue: 0.9231 time to fit residues: 630.9963 Evaluate side-chains 548 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 425 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain P residue 162 ARG Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 42 VAL Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 396 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 448 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 408 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 341 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 134 GLN J 134 GLN K 134 GLN ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN M 134 GLN N 134 GLN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** V 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 GLN W 134 GLN X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.102084 restraints weight = 35049.032| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.55 r_work: 0.2844 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36120 Z= 0.145 Angle : 0.527 8.194 49080 Z= 0.275 Chirality : 0.046 0.136 5592 Planarity : 0.005 0.034 6528 Dihedral : 4.577 19.705 5088 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.61 % Allowed : 20.56 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.13), residues: 4512 helix: 2.00 (0.12), residues: 1872 sheet: -0.35 (0.13), residues: 1488 loop : -1.09 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 14 TYR 0.005 0.001 TYR S 145 PHE 0.009 0.002 PHE U 44 HIS 0.006 0.001 HIS M 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (36120) covalent geometry : angle 0.52670 / 0.28 (49080) hydrogen bonds : bond 0.03545 / 2.48 ( 2232) hydrogen bonds : angle 3.77190 / 2.74 ( 6264) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 451 time to evaluate : 1.328 Fit side-chains REVERT: A 27 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7198 (mp0) REVERT: A 65 THR cc_start: 0.7396 (OUTLIER) cc_final: 0.7089 (p) REVERT: A 69 GLU cc_start: 0.7135 (pm20) cc_final: 0.6804 (mp0) REVERT: A 71 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: B 14 ARG cc_start: 0.8135 (ttt90) cc_final: 0.7930 (ttt-90) REVERT: B 16 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6887 (tt0) REVERT: B 27 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7286 (mp0) REVERT: B 65 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.7106 (p) REVERT: B 71 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: C 27 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7254 (mp0) REVERT: C 65 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7080 (p) REVERT: C 69 GLU cc_start: 0.7147 (pm20) cc_final: 0.6792 (mp0) REVERT: C 71 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7402 (pt0) REVERT: D 27 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7156 (mp0) REVERT: D 65 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7093 (p) REVERT: D 69 GLU cc_start: 0.7145 (pm20) cc_final: 0.6798 (mp0) REVERT: D 71 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: E 27 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7195 (mp0) REVERT: E 65 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7065 (p) REVERT: E 71 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7435 (pt0) REVERT: F 27 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7157 (mp0) REVERT: F 65 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7110 (p) REVERT: F 71 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: G 27 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7196 (mp0) REVERT: G 65 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7096 (p) REVERT: G 69 GLU cc_start: 0.7159 (pm20) cc_final: 0.6797 (mp0) REVERT: G 71 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: G 109 GLU cc_start: 0.8837 (pm20) cc_final: 0.8527 (pm20) REVERT: H 27 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7212 (mp0) REVERT: H 65 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7088 (p) REVERT: H 69 GLU cc_start: 0.7149 (pm20) cc_final: 0.6797 (mp0) REVERT: H 71 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: I 27 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7189 (mp0) REVERT: I 65 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.7105 (p) REVERT: I 69 GLU cc_start: 0.7146 (pm20) cc_final: 0.6792 (mp0) REVERT: I 71 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: I 109 GLU cc_start: 0.8840 (pm20) cc_final: 0.8545 (pm20) REVERT: J 27 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7190 (mp0) REVERT: J 65 THR cc_start: 0.7398 (OUTLIER) cc_final: 0.7090 (p) REVERT: J 69 GLU cc_start: 0.7086 (pm20) cc_final: 0.6798 (mp0) REVERT: J 71 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7433 (pt0) REVERT: K 27 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7085 (mp0) REVERT: K 65 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.7092 (p) REVERT: K 69 GLU cc_start: 0.7146 (pm20) cc_final: 0.6794 (mp0) REVERT: K 71 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: L 27 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7221 (mp0) REVERT: L 65 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.7107 (p) REVERT: L 69 GLU cc_start: 0.7106 (pm20) cc_final: 0.6790 (mp0) REVERT: L 71 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7401 (pt0) REVERT: M 27 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7144 (mp0) REVERT: M 65 THR cc_start: 0.7416 (OUTLIER) cc_final: 0.7112 (p) REVERT: M 69 GLU cc_start: 0.7111 (pm20) cc_final: 0.6792 (mp0) REVERT: M 71 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: N 27 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7174 (mp0) REVERT: N 65 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7072 (p) REVERT: N 69 GLU cc_start: 0.7144 (pm20) cc_final: 0.6783 (mp0) REVERT: N 71 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: O 27 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7238 (mp0) REVERT: O 65 THR cc_start: 0.7396 (OUTLIER) cc_final: 0.7094 (p) REVERT: O 69 GLU cc_start: 0.7124 (pm20) cc_final: 0.6801 (mp0) REVERT: O 71 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: P 14 ARG cc_start: 0.8188 (ttt90) cc_final: 0.7931 (ttt-90) REVERT: P 16 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6878 (tt0) REVERT: P 27 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7247 (mp0) REVERT: P 65 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7106 (p) REVERT: P 69 GLU cc_start: 0.7138 (pm20) cc_final: 0.6779 (mp0) REVERT: P 71 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: Q 27 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7140 (mp0) REVERT: Q 65 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.7090 (p) REVERT: Q 69 GLU cc_start: 0.7077 (pm20) cc_final: 0.6787 (mp0) REVERT: Q 71 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: R 27 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7254 (mp0) REVERT: R 65 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7101 (p) REVERT: R 71 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: S 27 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7244 (mp0) REVERT: S 65 THR cc_start: 0.7388 (OUTLIER) cc_final: 0.7075 (p) REVERT: S 69 GLU cc_start: 0.7090 (pm20) cc_final: 0.6790 (mp0) REVERT: S 71 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: S 109 GLU cc_start: 0.8831 (pm20) cc_final: 0.8541 (pm20) REVERT: T 27 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7234 (mp0) REVERT: T 65 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7085 (p) REVERT: T 69 GLU cc_start: 0.7076 (pm20) cc_final: 0.6784 (mp0) REVERT: T 71 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: U 27 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7217 (mp0) REVERT: U 65 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.7096 (p) REVERT: U 69 GLU cc_start: 0.7079 (pm20) cc_final: 0.6785 (mp0) REVERT: U 71 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: V 27 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7195 (mp0) REVERT: V 65 THR cc_start: 0.7395 (OUTLIER) cc_final: 0.7090 (p) REVERT: V 69 GLU cc_start: 0.7085 (pm20) cc_final: 0.6789 (mp0) REVERT: V 71 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: W 27 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7269 (mp0) REVERT: W 65 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7087 (p) REVERT: W 71 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: X 27 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7186 (mp0) REVERT: X 65 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7088 (p) REVERT: X 69 GLU cc_start: 0.7136 (pm20) cc_final: 0.6813 (mp0) REVERT: X 71 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7424 (pt0) outliers start: 168 outliers final: 74 residues processed: 613 average time/residue: 0.9030 time to fit residues: 638.9688 Evaluate side-chains 574 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 452 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 42 VAL Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 455 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 266 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 323 optimal weight: 20.0000 chunk 151 optimal weight: 0.7980 chunk 197 optimal weight: 8.9990 chunk 190 optimal weight: 20.0000 chunk 381 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** C 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN D 134 GLN ** E 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 134 GLN ** J 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN K 134 GLN ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN M 134 GLN ** N 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN ** O 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 GLN P 134 GLN Q 134 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 GLN ** S 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 GLN T 134 GLN ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** V 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 GLN ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 134 GLN ** X 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.099439 restraints weight = 35206.750| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.63 r_work: 0.2805 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 36120 Z= 0.207 Angle : 0.583 8.862 49080 Z= 0.306 Chirality : 0.048 0.142 5592 Planarity : 0.006 0.037 6528 Dihedral : 4.835 20.427 5088 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.37 % Allowed : 19.76 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.13), residues: 4512 helix: 1.79 (0.12), residues: 1872 sheet: -0.20 (0.13), residues: 1464 loop : -1.24 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 14 TYR 0.006 0.002 TYR M 123 PHE 0.010 0.002 PHE C 44 HIS 0.007 0.002 HIS S 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (36120) covalent geometry : angle 0.58297 / 0.31 (49080) hydrogen bonds : bond 0.04084 / 2.85 ( 2232) hydrogen bonds : angle 3.90709 / 2.84 ( 6264) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 424 time to evaluate : 1.399 Fit side-chains REVERT: A 27 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7146 (mp0) REVERT: A 65 THR cc_start: 0.7308 (OUTLIER) cc_final: 0.7003 (p) REVERT: A 69 GLU cc_start: 0.7116 (pm20) cc_final: 0.6765 (mp0) REVERT: A 71 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: B 14 ARG cc_start: 0.8162 (ttt90) cc_final: 0.7878 (ttt-90) REVERT: B 16 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6842 (tt0) REVERT: B 27 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7235 (mp0) REVERT: B 65 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.6982 (p) REVERT: B 71 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: C 27 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7199 (mp0) REVERT: C 65 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.6998 (p) REVERT: C 69 GLU cc_start: 0.7099 (pm20) cc_final: 0.6752 (mp0) REVERT: C 71 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: D 27 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7145 (mp0) REVERT: D 65 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.6990 (p) REVERT: D 69 GLU cc_start: 0.7099 (pm20) cc_final: 0.6764 (mp0) REVERT: D 71 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: E 27 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7190 (mp0) REVERT: E 65 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7011 (p) REVERT: E 71 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: F 27 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7129 (mp0) REVERT: F 65 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.7008 (p) REVERT: F 71 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: G 27 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7142 (mp0) REVERT: G 65 THR cc_start: 0.7303 (OUTLIER) cc_final: 0.6996 (p) REVERT: G 69 GLU cc_start: 0.7106 (pm20) cc_final: 0.6758 (mp0) REVERT: G 71 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: H 27 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7190 (mp0) REVERT: H 65 THR cc_start: 0.7311 (OUTLIER) cc_final: 0.7005 (p) REVERT: H 69 GLU cc_start: 0.7115 (pm20) cc_final: 0.6772 (mp0) REVERT: H 71 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7401 (pt0) REVERT: I 27 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7148 (mp0) REVERT: I 65 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7007 (p) REVERT: I 69 GLU cc_start: 0.7098 (pm20) cc_final: 0.6754 (mp0) REVERT: I 71 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: J 27 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7171 (mp0) REVERT: J 65 THR cc_start: 0.7303 (OUTLIER) cc_final: 0.6994 (p) REVERT: J 69 GLU cc_start: 0.7108 (pm20) cc_final: 0.6765 (mp0) REVERT: J 71 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: K 27 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7117 (mp0) REVERT: K 65 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.7003 (p) REVERT: K 69 GLU cc_start: 0.7108 (pm20) cc_final: 0.6755 (mp0) REVERT: K 71 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: L 27 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7141 (mp0) REVERT: L 65 THR cc_start: 0.7312 (OUTLIER) cc_final: 0.7008 (p) REVERT: L 69 GLU cc_start: 0.7090 (pm20) cc_final: 0.6745 (mp0) REVERT: L 71 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: L 162 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7494 (mtt-85) REVERT: M 27 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7119 (mp0) REVERT: M 65 THR cc_start: 0.7302 (OUTLIER) cc_final: 0.6990 (p) REVERT: M 69 GLU cc_start: 0.7105 (pm20) cc_final: 0.6746 (mp0) REVERT: M 71 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: N 27 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7144 (mp0) REVERT: N 65 THR cc_start: 0.7296 (OUTLIER) cc_final: 0.6990 (p) REVERT: N 69 GLU cc_start: 0.7101 (pm20) cc_final: 0.6752 (mp0) REVERT: N 71 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: O 27 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7158 (mp0) REVERT: O 65 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7011 (p) REVERT: O 69 GLU cc_start: 0.7110 (pm20) cc_final: 0.6768 (mp0) REVERT: O 71 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: P 14 ARG cc_start: 0.8219 (ttt90) cc_final: 0.7884 (ttt-90) REVERT: P 16 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6869 (tt0) REVERT: P 27 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7237 (mp0) REVERT: P 65 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.7018 (p) REVERT: P 69 GLU cc_start: 0.7096 (pm20) cc_final: 0.6745 (mp0) REVERT: P 71 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7427 (pt0) REVERT: P 162 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7500 (mtt-85) REVERT: Q 27 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7124 (mp0) REVERT: Q 65 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.6994 (p) REVERT: Q 69 GLU cc_start: 0.7103 (pm20) cc_final: 0.6764 (mp0) REVERT: Q 71 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: R 27 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7178 (mp0) REVERT: R 65 THR cc_start: 0.7306 (OUTLIER) cc_final: 0.6998 (p) REVERT: R 71 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: S 27 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7224 (mp0) REVERT: S 65 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.6991 (p) REVERT: S 69 GLU cc_start: 0.7123 (pm20) cc_final: 0.6772 (mp0) REVERT: S 71 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: T 27 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7152 (mp0) REVERT: T 65 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.6992 (p) REVERT: T 69 GLU cc_start: 0.7100 (pm20) cc_final: 0.6755 (mp0) REVERT: T 71 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: U 27 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7168 (mp0) REVERT: U 65 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.6988 (p) REVERT: U 69 GLU cc_start: 0.7099 (pm20) cc_final: 0.6755 (mp0) REVERT: U 71 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: V 27 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7130 (mp0) REVERT: V 65 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.6994 (p) REVERT: V 69 GLU cc_start: 0.7094 (pm20) cc_final: 0.6752 (mp0) REVERT: V 71 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: W 27 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7203 (mp0) REVERT: W 65 THR cc_start: 0.7303 (OUTLIER) cc_final: 0.6991 (p) REVERT: W 71 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: X 27 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7129 (mp0) REVERT: X 65 THR cc_start: 0.7303 (OUTLIER) cc_final: 0.6993 (p) REVERT: X 69 GLU cc_start: 0.7096 (pm20) cc_final: 0.6756 (mp0) REVERT: X 71 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7419 (pt0) outliers start: 196 outliers final: 91 residues processed: 619 average time/residue: 0.8879 time to fit residues: 636.5499 Evaluate side-chains 551 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 410 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain P residue 162 ARG Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 133 LEU Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 133 LEU Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 42 VAL Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 211 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 chunk 334 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** C 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN D 134 GLN ** E 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 134 GLN ** J 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN K 134 GLN ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN M 134 GLN ** N 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN ** O 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 GLN ** P 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 134 GLN Q 134 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 GLN ** S 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 GLN T 134 GLN ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** V 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 GLN ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 134 GLN ** X 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.100258 restraints weight = 35169.203| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.50 r_work: 0.2845 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 36120 Z= 0.162 Angle : 0.549 8.400 49080 Z= 0.287 Chirality : 0.046 0.137 5592 Planarity : 0.005 0.033 6528 Dihedral : 4.692 20.544 5088 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.28 % Allowed : 20.92 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 4512 helix: 1.88 (0.12), residues: 1872 sheet: -0.21 (0.13), residues: 1464 loop : -1.17 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 14 TYR 0.006 0.001 TYR A 145 PHE 0.009 0.002 PHE A 44 HIS 0.006 0.001 HIS M 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (36120) covalent geometry : angle 0.54921 / 0.29 (49080) hydrogen bonds : bond 0.03707 / 2.59 ( 2232) hydrogen bonds : angle 3.84130 / 2.79 ( 6264) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 403 time to evaluate : 1.444 Fit side-chains REVERT: A 27 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7204 (mp0) REVERT: A 65 THR cc_start: 0.7369 (OUTLIER) cc_final: 0.7073 (p) REVERT: A 69 GLU cc_start: 0.7120 (pm20) cc_final: 0.6803 (mp0) REVERT: A 71 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: B 14 ARG cc_start: 0.8146 (ttt90) cc_final: 0.7937 (ttt-90) REVERT: B 16 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6919 (tt0) REVERT: B 27 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7231 (mp0) REVERT: B 65 THR cc_start: 0.7360 (OUTLIER) cc_final: 0.7061 (p) REVERT: B 71 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: C 27 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7215 (mp0) REVERT: C 65 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7072 (p) REVERT: C 69 GLU cc_start: 0.7112 (pm20) cc_final: 0.6788 (mp0) REVERT: C 71 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7401 (pt0) REVERT: D 27 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7148 (mp0) REVERT: D 65 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.7057 (p) REVERT: D 69 GLU cc_start: 0.7108 (pm20) cc_final: 0.6783 (mp0) REVERT: D 71 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: E 27 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7221 (mp0) REVERT: E 65 THR cc_start: 0.7372 (OUTLIER) cc_final: 0.7081 (p) REVERT: E 71 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: F 27 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7129 (mp0) REVERT: F 65 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7080 (p) REVERT: F 71 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: G 27 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7219 (mp0) REVERT: G 65 THR cc_start: 0.7371 (OUTLIER) cc_final: 0.7075 (p) REVERT: G 69 GLU cc_start: 0.7173 (pm20) cc_final: 0.6801 (mp0) REVERT: G 71 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: H 27 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7196 (mp0) REVERT: H 65 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7076 (p) REVERT: H 69 GLU cc_start: 0.7173 (pm20) cc_final: 0.6813 (mp0) REVERT: H 71 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: I 27 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7200 (mp0) REVERT: I 65 THR cc_start: 0.7374 (OUTLIER) cc_final: 0.7074 (p) REVERT: I 69 GLU cc_start: 0.7159 (pm20) cc_final: 0.6794 (mp0) REVERT: I 71 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: J 27 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7157 (mp0) REVERT: J 65 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7072 (p) REVERT: J 69 GLU cc_start: 0.7156 (pm20) cc_final: 0.6799 (mp0) REVERT: J 71 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7425 (pt0) REVERT: J 109 GLU cc_start: 0.8835 (pm20) cc_final: 0.8520 (pm20) REVERT: K 27 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7127 (mp0) REVERT: K 65 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7071 (p) REVERT: K 69 GLU cc_start: 0.7132 (pm20) cc_final: 0.6796 (mp0) REVERT: K 71 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: L 27 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7177 (mp0) REVERT: L 65 THR cc_start: 0.7380 (OUTLIER) cc_final: 0.7082 (p) REVERT: L 69 GLU cc_start: 0.7099 (pm20) cc_final: 0.6789 (mp0) REVERT: L 71 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: L 162 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7481 (mtt-85) REVERT: M 27 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7113 (mp0) REVERT: M 65 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.7051 (p) REVERT: M 69 GLU cc_start: 0.7143 (pm20) cc_final: 0.6794 (mp0) REVERT: M 71 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: N 27 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7147 (mp0) REVERT: N 65 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.7058 (p) REVERT: N 69 GLU cc_start: 0.7155 (pm20) cc_final: 0.6788 (mp0) REVERT: N 71 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: O 27 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7193 (mp0) REVERT: O 65 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.7092 (p) REVERT: O 69 GLU cc_start: 0.7157 (pm20) cc_final: 0.6808 (mp0) REVERT: O 71 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: P 14 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7938 (ttt-90) REVERT: P 16 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6950 (tt0) REVERT: P 27 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7213 (mp0) REVERT: P 65 THR cc_start: 0.7372 (OUTLIER) cc_final: 0.7083 (p) REVERT: P 69 GLU cc_start: 0.7108 (pm20) cc_final: 0.6792 (mp0) REVERT: P 71 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: P 162 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7504 (mtt-85) REVERT: Q 27 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7096 (mp0) REVERT: Q 65 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7074 (p) REVERT: Q 69 GLU cc_start: 0.7107 (pm20) cc_final: 0.6793 (mp0) REVERT: Q 71 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: R 27 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7214 (mp0) REVERT: R 65 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.7076 (p) REVERT: R 71 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: S 27 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7228 (mp0) REVERT: S 65 THR cc_start: 0.7378 (OUTLIER) cc_final: 0.7072 (p) REVERT: S 69 GLU cc_start: 0.7129 (pm20) cc_final: 0.6802 (mp0) REVERT: S 71 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: T 27 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7194 (mp0) REVERT: T 65 THR cc_start: 0.7362 (OUTLIER) cc_final: 0.7064 (p) REVERT: T 69 GLU cc_start: 0.7133 (pm20) cc_final: 0.6775 (mp0) REVERT: T 71 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: U 27 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7199 (mp0) REVERT: U 65 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7072 (p) REVERT: U 69 GLU cc_start: 0.7154 (pm20) cc_final: 0.6790 (mp0) REVERT: U 71 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: V 27 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7233 (mp0) REVERT: V 65 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7075 (p) REVERT: V 69 GLU cc_start: 0.7145 (pm20) cc_final: 0.6806 (mp0) REVERT: V 71 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7422 (pt0) REVERT: W 27 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7209 (mp0) REVERT: W 65 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7067 (p) REVERT: W 71 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7435 (pt0) REVERT: X 27 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7159 (mp0) REVERT: X 65 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7072 (p) REVERT: X 69 GLU cc_start: 0.7105 (pm20) cc_final: 0.6798 (mp0) REVERT: X 71 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7424 (pt0) outliers start: 156 outliers final: 75 residues processed: 558 average time/residue: 0.9256 time to fit residues: 593.2149 Evaluate side-chains 524 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 399 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain P residue 162 ARG Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 42 VAL Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 226 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 425 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** C 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN D 134 GLN ** E 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN ** J 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN K 134 GLN ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN M 134 GLN ** N 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN ** O 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 GLN ** P 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 134 GLN Q 134 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 GLN ** S 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 GLN T 134 GLN ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** V 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 GLN ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 134 GLN ** X 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097126 restraints weight = 35321.043| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.58 r_work: 0.2806 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 36120 Z= 0.254 Angle : 0.629 9.451 49080 Z= 0.330 Chirality : 0.050 0.150 5592 Planarity : 0.006 0.045 6528 Dihedral : 5.019 21.544 5088 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.14 % Allowed : 20.97 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 4512 helix: 1.65 (0.12), residues: 1848 sheet: -0.15 (0.13), residues: 1320 loop : -1.19 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 188 TYR 0.007 0.002 TYR Q 171 PHE 0.012 0.003 PHE Q 154 HIS 0.007 0.002 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.25 (36120) covalent geometry : angle 0.62929 / 0.33 (49080) hydrogen bonds : bond 0.04430 / 3.09 ( 2232) hydrogen bonds : angle 4.03425 / 2.93 ( 6264) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 421 time to evaluate : 1.261 Fit side-chains REVERT: A 27 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7210 (mp0) REVERT: A 65 THR cc_start: 0.7341 (OUTLIER) cc_final: 0.7057 (p) REVERT: A 69 GLU cc_start: 0.7226 (pm20) cc_final: 0.6834 (mp0) REVERT: A 71 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: B 14 ARG cc_start: 0.8169 (ttt90) cc_final: 0.7884 (ttt-90) REVERT: B 16 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6819 (tt0) REVERT: B 27 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7243 (mp0) REVERT: B 65 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.7031 (p) REVERT: B 71 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: C 27 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7251 (mp0) REVERT: C 65 THR cc_start: 0.7319 (OUTLIER) cc_final: 0.7021 (p) REVERT: C 69 GLU cc_start: 0.7173 (pm20) cc_final: 0.6819 (mp0) REVERT: C 71 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: D 27 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7166 (mp0) REVERT: D 65 THR cc_start: 0.7319 (OUTLIER) cc_final: 0.7020 (p) REVERT: D 69 GLU cc_start: 0.7212 (pm20) cc_final: 0.6831 (mp0) REVERT: D 71 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: E 27 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7245 (mp0) REVERT: E 65 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7034 (p) REVERT: F 27 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7165 (mp0) REVERT: F 65 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.7038 (p) REVERT: F 71 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: G 27 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7248 (mp0) REVERT: G 65 THR cc_start: 0.7312 (OUTLIER) cc_final: 0.7023 (p) REVERT: G 69 GLU cc_start: 0.7217 (pm20) cc_final: 0.6828 (mp0) REVERT: G 71 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: H 27 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7220 (mp0) REVERT: H 65 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.7032 (p) REVERT: H 69 GLU cc_start: 0.7218 (pm20) cc_final: 0.6836 (mp0) REVERT: H 71 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: I 27 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7263 (mp0) REVERT: I 65 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.7038 (p) REVERT: I 69 GLU cc_start: 0.7198 (pm20) cc_final: 0.6817 (mp0) REVERT: I 71 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: J 27 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7207 (mp0) REVERT: J 65 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7026 (p) REVERT: J 69 GLU cc_start: 0.7212 (pm20) cc_final: 0.6830 (mp0) REVERT: J 71 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: K 27 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7152 (mp0) REVERT: K 65 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.7024 (p) REVERT: K 69 GLU cc_start: 0.7187 (pm20) cc_final: 0.6827 (mp0) REVERT: K 71 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: L 27 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7274 (mp0) REVERT: L 65 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.7038 (p) REVERT: L 69 GLU cc_start: 0.7200 (pm20) cc_final: 0.6815 (mp0) REVERT: L 71 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7386 (pt0) REVERT: L 162 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7478 (mtt-85) REVERT: M 27 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7136 (mp0) REVERT: M 65 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.7008 (p) REVERT: M 69 GLU cc_start: 0.7204 (pm20) cc_final: 0.6826 (mp0) REVERT: M 71 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: N 27 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7225 (mp0) REVERT: N 65 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.7015 (p) REVERT: N 69 GLU cc_start: 0.7203 (pm20) cc_final: 0.6815 (mp0) REVERT: N 71 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: O 27 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7259 (mp0) REVERT: O 65 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7068 (p) REVERT: O 69 GLU cc_start: 0.7200 (pm20) cc_final: 0.6828 (mp0) REVERT: P 14 ARG cc_start: 0.8241 (ttt90) cc_final: 0.7908 (ttt-90) REVERT: P 16 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6894 (tt0) REVERT: P 27 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7251 (mp0) REVERT: P 65 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.7041 (p) REVERT: P 69 GLU cc_start: 0.7206 (pm20) cc_final: 0.6814 (mp0) REVERT: P 71 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: P 162 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7486 (mtt-85) REVERT: Q 27 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7158 (mp0) REVERT: Q 65 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7033 (p) REVERT: Q 69 GLU cc_start: 0.7221 (pm20) cc_final: 0.6838 (mp0) REVERT: Q 71 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: R 27 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7272 (mp0) REVERT: R 65 THR cc_start: 0.7313 (OUTLIER) cc_final: 0.7021 (p) REVERT: R 71 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: S 27 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7212 (mp0) REVERT: S 65 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7016 (p) REVERT: S 69 GLU cc_start: 0.7192 (pm20) cc_final: 0.6831 (mp0) REVERT: S 71 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: T 27 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7228 (mp0) REVERT: T 65 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.7018 (p) REVERT: T 69 GLU cc_start: 0.7207 (pm20) cc_final: 0.6821 (mp0) REVERT: T 71 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: U 27 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7216 (mp0) REVERT: U 65 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.7016 (p) REVERT: U 69 GLU cc_start: 0.7215 (pm20) cc_final: 0.6831 (mp0) REVERT: U 71 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: V 27 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7228 (mp0) REVERT: V 65 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7023 (p) REVERT: V 69 GLU cc_start: 0.7211 (pm20) cc_final: 0.6826 (mp0) REVERT: V 71 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: W 27 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7238 (mp0) REVERT: W 65 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7025 (p) REVERT: X 27 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7170 (mp0) REVERT: X 65 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.7030 (p) REVERT: X 69 GLU cc_start: 0.7173 (pm20) cc_final: 0.6816 (mp0) outliers start: 151 outliers final: 87 residues processed: 572 average time/residue: 0.8659 time to fit residues: 570.4633 Evaluate side-chains 534 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 401 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain P residue 162 ARG Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 42 VAL Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 120 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 395 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 408 optimal weight: 1.9990 chunk 398 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** C 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN D 134 GLN ** E 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN ** J 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN K 134 GLN ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN M 134 GLN ** N 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN ** O 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 GLN ** P 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 134 GLN Q 134 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 GLN ** S 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 GLN T 134 GLN ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** V 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 GLN ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 134 GLN ** X 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.097537 restraints weight = 35301.738| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.72 r_work: 0.2837 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36120 Z= 0.151 Angle : 0.549 8.299 49080 Z= 0.284 Chirality : 0.046 0.137 5592 Planarity : 0.005 0.033 6528 Dihedral : 4.680 20.874 5088 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.59 % Allowed : 21.77 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4512 helix: 1.82 (0.12), residues: 1872 sheet: -0.33 (0.13), residues: 1488 loop : -1.08 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 14 TYR 0.005 0.001 TYR A 145 PHE 0.008 0.002 PHE C 44 HIS 0.006 0.001 HIS M 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (36120) covalent geometry : angle 0.54865 / 0.28 (49080) hydrogen bonds : bond 0.03626 / 2.54 ( 2232) hydrogen bonds : angle 3.84150 / 2.79 ( 6264) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 404 time to evaluate : 1.231 Fit side-chains REVERT: A 27 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7104 (mp0) REVERT: A 65 THR cc_start: 0.7296 (OUTLIER) cc_final: 0.6995 (p) REVERT: A 69 GLU cc_start: 0.7115 (pm20) cc_final: 0.6763 (mp0) REVERT: A 71 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: B 14 ARG cc_start: 0.8127 (ttt90) cc_final: 0.7894 (ttt-90) REVERT: B 16 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6889 (tt0) REVERT: B 27 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7167 (mp0) REVERT: B 65 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.6985 (p) REVERT: B 71 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: C 27 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7158 (mp0) REVERT: C 65 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.6990 (p) REVERT: C 69 GLU cc_start: 0.7031 (pm20) cc_final: 0.6692 (mp0) REVERT: C 71 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7343 (pt0) REVERT: D 27 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7058 (mp0) REVERT: D 65 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.6993 (p) REVERT: D 69 GLU cc_start: 0.7034 (pm20) cc_final: 0.6696 (mp0) REVERT: D 71 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7330 (pt0) REVERT: E 27 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7111 (mp0) REVERT: E 65 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6969 (p) REVERT: E 71 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7402 (pt0) REVERT: F 27 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7044 (mp0) REVERT: F 65 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.6998 (p) REVERT: F 71 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: G 27 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7139 (mp0) REVERT: G 65 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.7008 (p) REVERT: G 69 GLU cc_start: 0.7121 (pm20) cc_final: 0.6769 (mp0) REVERT: G 71 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: H 27 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7123 (mp0) REVERT: H 65 THR cc_start: 0.7294 (OUTLIER) cc_final: 0.6990 (p) REVERT: H 69 GLU cc_start: 0.7079 (pm20) cc_final: 0.6728 (mp0) REVERT: H 71 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: I 27 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7128 (mp0) REVERT: I 65 THR cc_start: 0.7294 (OUTLIER) cc_final: 0.6993 (p) REVERT: I 69 GLU cc_start: 0.7097 (pm20) cc_final: 0.6754 (mp0) REVERT: I 71 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7357 (pt0) REVERT: J 27 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7132 (mp0) REVERT: J 65 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.6993 (p) REVERT: J 69 GLU cc_start: 0.7048 (pm20) cc_final: 0.6708 (mp0) REVERT: J 71 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: K 27 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7053 (mp0) REVERT: K 65 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.6998 (p) REVERT: K 69 GLU cc_start: 0.7096 (pm20) cc_final: 0.6745 (mp0) REVERT: K 71 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: L 27 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7154 (mp0) REVERT: L 65 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.7002 (p) REVERT: L 69 GLU cc_start: 0.7065 (pm20) cc_final: 0.6715 (mp0) REVERT: L 71 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7351 (pt0) REVERT: M 27 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7033 (mp0) REVERT: M 65 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.6974 (p) REVERT: M 69 GLU cc_start: 0.7038 (pm20) cc_final: 0.6706 (mp0) REVERT: M 71 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: N 27 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7134 (mp0) REVERT: N 65 THR cc_start: 0.7294 (OUTLIER) cc_final: 0.6991 (p) REVERT: N 69 GLU cc_start: 0.7061 (pm20) cc_final: 0.6725 (mp0) REVERT: N 71 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: O 27 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7168 (mp0) REVERT: O 65 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.6999 (p) REVERT: O 69 GLU cc_start: 0.7032 (pm20) cc_final: 0.6719 (mp0) REVERT: O 71 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: P 14 ARG cc_start: 0.8136 (ttt90) cc_final: 0.7900 (ttt-90) REVERT: P 16 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6893 (tt0) REVERT: P 27 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7170 (mp0) REVERT: P 65 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.7013 (p) REVERT: P 69 GLU cc_start: 0.7098 (pm20) cc_final: 0.6750 (mp0) REVERT: P 71 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: Q 27 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7026 (mp0) REVERT: Q 65 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.6992 (p) REVERT: Q 69 GLU cc_start: 0.7100 (pm20) cc_final: 0.6731 (mp0) REVERT: Q 71 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: R 27 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7130 (mp0) REVERT: R 65 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.6999 (p) REVERT: R 71 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7348 (pt0) REVERT: S 27 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7210 (mp0) REVERT: S 65 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.6999 (p) REVERT: S 69 GLU cc_start: 0.7058 (pm20) cc_final: 0.6710 (mp0) REVERT: S 71 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7439 (pt0) REVERT: T 27 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7123 (mp0) REVERT: T 65 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.6986 (p) REVERT: T 69 GLU cc_start: 0.7039 (pm20) cc_final: 0.6701 (mp0) REVERT: T 71 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: U 27 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7184 (mp0) REVERT: U 65 THR cc_start: 0.7296 (OUTLIER) cc_final: 0.6991 (p) REVERT: U 69 GLU cc_start: 0.7074 (pm20) cc_final: 0.6719 (mp0) REVERT: U 71 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7320 (pt0) REVERT: V 27 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7136 (mp0) REVERT: V 65 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.6997 (p) REVERT: V 69 GLU cc_start: 0.7113 (pm20) cc_final: 0.6738 (mp0) REVERT: V 71 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: W 27 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7167 (mp0) REVERT: W 65 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.6996 (p) REVERT: W 71 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: X 27 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7043 (mp0) REVERT: X 65 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.6997 (p) REVERT: X 69 GLU cc_start: 0.7076 (pm20) cc_final: 0.6754 (mp0) REVERT: X 71 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7346 (pt0) outliers start: 131 outliers final: 66 residues processed: 534 average time/residue: 0.9084 time to fit residues: 555.1443 Evaluate side-chains 517 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 403 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 42 VAL Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 25 optimal weight: 6.9990 chunk 412 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 454 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** C 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN D 134 GLN ** E 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN ** J 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN K 134 GLN ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN M 134 GLN ** N 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN ** O 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 GLN ** P 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 134 GLN Q 134 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 GLN ** S 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 GLN ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 GLN ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** V 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 GLN ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 134 GLN ** X 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.129869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.097394 restraints weight = 35157.479| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.57 r_work: 0.2813 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 36120 Z= 0.238 Angle : 0.618 9.205 49080 Z= 0.323 Chirality : 0.049 0.148 5592 Planarity : 0.006 0.042 6528 Dihedral : 4.970 21.547 5088 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.67 % Allowed : 21.68 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 4512 helix: 1.58 (0.12), residues: 1872 sheet: -0.16 (0.13), residues: 1464 loop : -1.21 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 18 TYR 0.007 0.002 TYR N 171 PHE 0.011 0.002 PHE K 154 HIS 0.007 0.002 HIS N 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (36120) covalent geometry : angle 0.61767 / 0.32 (49080) hydrogen bonds : bond 0.04317 / 3.01 ( 2232) hydrogen bonds : angle 4.00807 / 2.91 ( 6264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13114.92 seconds wall clock time: 224 minutes 12.08 seconds (13452.08 seconds total)