Starting phenix.real_space_refine on Tue Aug 26 08:59:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2q_63589/08_2025/9m2q_63589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2q_63589/08_2025/9m2q_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 { model { file = "/net/cci-nas-00/data/ceres_data/9m2q_63589/08_2025/9m2q_63589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2q_63589/08_2025/9m2q_63589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m2q_63589/08_2025/9m2q_63589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2q_63589/08_2025/9m2q_63589.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MN': 2, '3TR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.83, per 1000 atoms: 0.19 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: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.35 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: 6.92 Time building geometry restraints manager: 3.54 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 2.400 nonbonded pdb=" NE2 HIS J 176 " pdb="MN MN J 302 " model vdw 2.055 2.400 nonbonded pdb=" NE2 HIS B 176 " pdb="MN MN B 302 " model vdw 2.055 2.400 nonbonded pdb=" NE2 HIS X 176 " pdb="MN MN X 302 " model vdw 2.055 2.400 nonbonded pdb=" NE2 HIS U 176 " pdb="MN MN U 302 " model vdw 2.055 2.400 ... (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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 28.830 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 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 aren 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 covalent geometry : bond 0.00736 (36120) covalent geometry : angle 1.01093 (49080) hydrogen bonds : bond 0.13895 ( 2232) hydrogen bonds : angle 5.48592 ( 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 : 1.260 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: 0.7165 (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: 0.6305 (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: 0.6597 (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: 0.5443 (mp0) REVERT: L 61 THR cc_start: 0.6850 (m) cc_final: 0.6240 (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: 0.6706 (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: 0.5868 (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: 0.6694 (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: 0.6197 (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: 0.6313 (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: 0.5307 (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: 0.9000 time to fit residues: 766.1529 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 : 1.383 ------------------------------------------------------------------------------- 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: 5.9990 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: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN C 182 GLN D 182 GLN E 182 GLN F 182 GLN G 182 GLN J 182 GLN K 182 GLN L 182 GLN M 182 GLN O 182 GLN Q 182 GLN R 182 GLN S 182 GLN U 182 GLN V 182 GLN W 182 GLN X 182 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.095445 restraints weight = 37347.859| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.85 r_work: 0.2789 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 36120 Z= 0.159 Angle : 0.548 8.906 49080 Z= 0.292 Chirality : 0.047 0.141 5592 Planarity : 0.004 0.024 6528 Dihedral : 5.821 43.486 5174 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.43 % Allowed : 10.14 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.13), residues: 4512 helix: 1.84 (0.12), residues: 1872 sheet: -0.43 (0.13), residues: 1488 loop : -1.43 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 121 TYR 0.008 0.001 TYR C 123 PHE 0.008 0.002 PHE I 104 HIS 0.007 0.001 HIS O 176 Details of bonding type rmsd covalent geometry : bond 0.00364 (36120) covalent geometry : angle 0.54816 (49080) hydrogen bonds : bond 0.03884 ( 2232) hydrogen bonds : angle 4.02843 ( 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 707 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 582 time to evaluate : 1.200 Fit side-chains REVERT: A 12 ARG cc_start: 0.6660 (mtt90) cc_final: 0.6456 (mpt-90) REVERT: A 14 ARG cc_start: 0.8089 (ttt90) cc_final: 0.7838 (ttt-90) REVERT: A 16 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6767 (tt0) REVERT: A 27 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7088 (mp0) REVERT: A 65 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.7117 (p) REVERT: A 71 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: A 109 GLU cc_start: 0.8817 (pm20) cc_final: 0.8449 (pm20) REVERT: B 12 ARG cc_start: 0.6594 (mtt90) cc_final: 0.6348 (mpt-90) REVERT: B 14 ARG cc_start: 0.8075 (ttt90) cc_final: 0.7807 (ttt-90) REVERT: B 16 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6781 (tt0) REVERT: B 27 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7073 (mp0) REVERT: B 65 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.7090 (p) REVERT: B 71 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: C 12 ARG cc_start: 0.6596 (mtt90) cc_final: 0.6353 (mpt-90) REVERT: C 14 ARG cc_start: 0.8100 (ttt90) cc_final: 0.7829 (ttt-90) REVERT: C 16 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6770 (tt0) REVERT: C 27 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7096 (mp0) REVERT: C 65 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7111 (p) REVERT: C 71 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: C 109 GLU cc_start: 0.8813 (pm20) cc_final: 0.8438 (pm20) REVERT: D 12 ARG cc_start: 0.6550 (mtt90) cc_final: 0.6319 (mpt-90) REVERT: D 27 GLU cc_start: 0.7617 (mt-10) cc_final: 0.6996 (mp0) REVERT: D 65 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7077 (p) REVERT: D 71 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: D 109 GLU cc_start: 0.8827 (pm20) cc_final: 0.8458 (pm20) REVERT: E 12 ARG cc_start: 0.6656 (mtt90) cc_final: 0.6452 (mpt-90) REVERT: E 14 ARG cc_start: 0.8084 (ttt90) cc_final: 0.7828 (ttt-90) REVERT: E 16 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6797 (tt0) REVERT: E 27 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7093 (mp0) REVERT: E 65 THR cc_start: 0.7421 (OUTLIER) cc_final: 0.7103 (p) REVERT: E 71 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: E 109 GLU cc_start: 0.8813 (pm20) cc_final: 0.8450 (pm20) REVERT: F 27 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7061 (mp0) REVERT: F 65 THR cc_start: 0.7448 (OUTLIER) cc_final: 0.7116 (p) REVERT: F 71 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: F 109 GLU cc_start: 0.8807 (pm20) cc_final: 0.8438 (pm20) REVERT: G 12 ARG cc_start: 0.6571 (mtt90) cc_final: 0.6354 (mpt-90) REVERT: G 14 ARG cc_start: 0.8040 (ttt90) cc_final: 0.7826 (ttt-90) REVERT: G 16 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6764 (tt0) REVERT: G 27 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7093 (mp0) REVERT: G 65 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.7100 (p) REVERT: G 71 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: G 109 GLU cc_start: 0.8815 (pm20) cc_final: 0.8451 (pm20) REVERT: H 12 ARG cc_start: 0.6573 (mtt90) cc_final: 0.6355 (mpt-90) REVERT: H 14 ARG cc_start: 0.8085 (ttt90) cc_final: 0.7811 (ttt-90) REVERT: H 16 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6764 (tt0) REVERT: H 27 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7086 (mp0) REVERT: H 65 THR cc_start: 0.7417 (OUTLIER) cc_final: 0.7090 (p) REVERT: H 71 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: H 109 GLU cc_start: 0.8829 (pm20) cc_final: 0.8456 (pm20) REVERT: I 12 ARG cc_start: 0.6550 (mtt90) cc_final: 0.6336 (mpt-90) REVERT: I 14 ARG cc_start: 0.8100 (ttt90) cc_final: 0.7840 (ttt-90) REVERT: I 16 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6789 (tt0) REVERT: I 27 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7083 (mp0) REVERT: I 65 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.7084 (p) REVERT: I 71 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: I 109 GLU cc_start: 0.8824 (pm20) cc_final: 0.8456 (pm20) REVERT: J 12 ARG cc_start: 0.6603 (mtt90) cc_final: 0.6356 (mpt-90) REVERT: J 14 ARG cc_start: 0.8001 (ttt90) cc_final: 0.7745 (ttt-90) REVERT: J 16 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6811 (tt0) REVERT: J 27 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7089 (mp0) REVERT: J 65 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7136 (p) REVERT: J 71 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: J 109 GLU cc_start: 0.8802 (pm20) cc_final: 0.8424 (pm20) REVERT: K 12 ARG cc_start: 0.6578 (mtt90) cc_final: 0.6333 (mpt-90) REVERT: K 27 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7021 (mp0) REVERT: K 65 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7130 (p) REVERT: K 71 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: K 109 GLU cc_start: 0.8817 (pm20) cc_final: 0.8448 (pm20) REVERT: L 12 ARG cc_start: 0.6586 (mtt90) cc_final: 0.6370 (mpt-90) REVERT: L 14 ARG cc_start: 0.8087 (ttt90) cc_final: 0.7821 (ttt-90) REVERT: L 16 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6783 (tt0) REVERT: L 27 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7086 (mp0) REVERT: L 65 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.7077 (p) REVERT: L 71 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: L 109 GLU cc_start: 0.8812 (pm20) cc_final: 0.8434 (pm20) REVERT: M 12 ARG cc_start: 0.6608 (mtt90) cc_final: 0.6367 (mpt-90) REVERT: M 27 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7071 (mp0) REVERT: M 65 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7124 (p) REVERT: N 12 ARG cc_start: 0.6552 (mtt90) cc_final: 0.6339 (mpt-90) REVERT: N 14 ARG cc_start: 0.8042 (ttt90) cc_final: 0.7818 (ttt-90) REVERT: N 16 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6780 (tt0) REVERT: N 27 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7121 (mp0) REVERT: N 65 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.7126 (p) REVERT: N 71 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: N 109 GLU cc_start: 0.8812 (pm20) cc_final: 0.8436 (pm20) REVERT: O 12 ARG cc_start: 0.6576 (mtt90) cc_final: 0.6359 (mpt-90) REVERT: O 14 ARG cc_start: 0.8105 (ttt90) cc_final: 0.7843 (ttt-90) REVERT: O 16 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6788 (tt0) REVERT: O 27 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7094 (mp0) REVERT: O 65 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.7064 (p) REVERT: O 71 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: O 109 GLU cc_start: 0.8819 (pm20) cc_final: 0.8447 (pm20) REVERT: P 12 ARG cc_start: 0.6558 (mtt90) cc_final: 0.6345 (mpt-90) REVERT: P 14 ARG cc_start: 0.8041 (ttt90) cc_final: 0.7819 (ttt-90) REVERT: P 16 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6790 (tt0) REVERT: P 27 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7117 (mp0) REVERT: P 65 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.7098 (p) REVERT: P 71 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: P 109 GLU cc_start: 0.8819 (pm20) cc_final: 0.8446 (pm20) REVERT: Q 27 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7013 (mp0) REVERT: Q 65 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7105 (p) REVERT: Q 71 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: Q 109 GLU cc_start: 0.8802 (pm20) cc_final: 0.8436 (pm20) REVERT: R 12 ARG cc_start: 0.6575 (mtt90) cc_final: 0.6354 (mpt-90) REVERT: R 14 ARG cc_start: 0.8087 (ttt90) cc_final: 0.7817 (ttt-90) REVERT: R 16 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6796 (tt0) REVERT: R 27 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7078 (mp0) REVERT: R 63 ARG cc_start: 0.7682 (ttt180) cc_final: 0.7482 (mtp180) REVERT: R 65 THR cc_start: 0.7424 (OUTLIER) cc_final: 0.7080 (p) REVERT: R 71 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7617 (pt0) REVERT: R 109 GLU cc_start: 0.8811 (pm20) cc_final: 0.8429 (pm20) REVERT: S 12 ARG cc_start: 0.6590 (mtt90) cc_final: 0.6348 (mpt-90) REVERT: S 14 ARG cc_start: 0.7995 (ttt90) cc_final: 0.7731 (ttt-90) REVERT: S 27 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7096 (mp0) REVERT: S 63 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7474 (mtp180) REVERT: S 65 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7106 (p) REVERT: S 71 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7576 (pt0) REVERT: S 109 GLU cc_start: 0.8805 (pm20) cc_final: 0.8436 (pm20) REVERT: T 12 ARG cc_start: 0.6606 (mtt90) cc_final: 0.6368 (mpt-90) REVERT: T 14 ARG cc_start: 0.7990 (ttt90) cc_final: 0.7732 (ttt-90) REVERT: T 16 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6811 (tt0) REVERT: T 27 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7097 (mp0) REVERT: T 65 THR cc_start: 0.7472 (OUTLIER) cc_final: 0.7129 (p) REVERT: T 71 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: T 109 GLU cc_start: 0.8818 (pm20) cc_final: 0.8449 (pm20) REVERT: U 12 ARG cc_start: 0.6577 (mtt90) cc_final: 0.6330 (mpt-90) REVERT: U 14 ARG cc_start: 0.8031 (ttt90) cc_final: 0.7808 (ttt-90) REVERT: U 27 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7093 (mp0) REVERT: U 63 ARG cc_start: 0.7620 (ttt180) cc_final: 0.7399 (mtp180) REVERT: U 65 THR cc_start: 0.7413 (OUTLIER) cc_final: 0.7085 (p) REVERT: U 71 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: U 109 GLU cc_start: 0.8821 (pm20) cc_final: 0.8446 (pm20) REVERT: V 12 ARG cc_start: 0.6559 (mtt90) cc_final: 0.6343 (mpt-90) REVERT: V 14 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7826 (ttt-90) REVERT: V 16 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6812 (tt0) REVERT: V 27 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7094 (mp0) REVERT: V 65 THR cc_start: 0.7434 (OUTLIER) cc_final: 0.7097 (p) REVERT: V 71 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: V 109 GLU cc_start: 0.8816 (pm20) cc_final: 0.8445 (pm20) REVERT: W 12 ARG cc_start: 0.6602 (mtt90) cc_final: 0.6355 (mpt-90) REVERT: W 14 ARG cc_start: 0.8101 (ttt90) cc_final: 0.7831 (ttt-90) REVERT: W 16 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6766 (tt0) REVERT: W 27 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7086 (mp0) REVERT: W 65 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.7071 (p) REVERT: W 71 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7572 (pt0) REVERT: W 109 GLU cc_start: 0.8810 (pm20) cc_final: 0.8438 (pm20) REVERT: X 12 ARG cc_start: 0.6577 (mtt90) cc_final: 0.6358 (mpt-90) REVERT: X 27 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7015 (mp0) REVERT: X 65 THR cc_start: 0.7438 (OUTLIER) cc_final: 0.7092 (p) REVERT: X 71 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: X 109 GLU cc_start: 0.8802 (pm20) cc_final: 0.8419 (pm20) outliers start: 125 outliers final: 48 residues processed: 683 average time/residue: 0.9687 time to fit residues: 748.5938 Evaluate side-chains 626 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 531 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 152 HIS 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 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 283 optimal weight: 8.9990 chunk 355 optimal weight: 6.9990 chunk 351 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 189 optimal weight: 0.0770 chunk 164 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 415 optimal weight: 6.9990 chunk 56 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 overall best weight: 4.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 182 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN H 182 GLN I 134 GLN I 182 GLN J 134 GLN K 134 GLN L 134 GLN M 134 GLN N 134 GLN N 182 GLN O 134 GLN P 134 GLN P 182 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN T 182 GLN U 134 GLN V 134 GLN W 134 GLN X 134 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.093880 restraints weight = 37796.205| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.63 r_work: 0.2769 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36120 Z= 0.189 Angle : 0.562 8.951 49080 Z= 0.299 Chirality : 0.048 0.138 5592 Planarity : 0.005 0.032 6528 Dihedral : 5.161 26.080 5136 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.45 % Allowed : 17.46 % Favored : 79.08 % 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 aren not related in a simple way. whole: 0.38 (0.13), residues: 4512 helix: 1.71 (0.12), residues: 1872 sheet: -0.23 (0.13), residues: 1464 loop : -1.39 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 121 TYR 0.006 0.001 TYR O 123 PHE 0.009 0.002 PHE W 44 HIS 0.007 0.001 HIS O 176 Details of bonding type rmsd covalent geometry : bond 0.00442 (36120) covalent geometry : angle 0.56177 (49080) hydrogen bonds : bond 0.04109 ( 2232) hydrogen bonds : angle 3.93586 ( 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 629 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 503 time to evaluate : 1.370 Fit side-chains REVERT: A 14 ARG cc_start: 0.8170 (ttt90) cc_final: 0.7900 (ttt-90) REVERT: A 16 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6804 (tt0) REVERT: A 27 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7332 (mp0) REVERT: A 71 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: B 14 ARG cc_start: 0.8153 (ttt90) cc_final: 0.7892 (ttt-90) REVERT: B 16 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6846 (tt0) REVERT: B 27 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7282 (mp0) REVERT: B 71 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: C 14 ARG cc_start: 0.8187 (ttt90) cc_final: 0.7918 (ttt-90) REVERT: C 16 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6811 (tt0) REVERT: C 27 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7376 (mp0) REVERT: C 71 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7513 (pt0) REVERT: D 27 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7070 (mp0) REVERT: D 71 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7521 (pt0) REVERT: E 14 ARG cc_start: 0.8138 (ttt90) cc_final: 0.7894 (ttt-90) REVERT: E 27 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7353 (mp0) REVERT: E 71 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: F 27 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7162 (mp0) REVERT: F 71 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: G 14 ARG cc_start: 0.8147 (ttt90) cc_final: 0.7899 (ttt-90) REVERT: G 27 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7352 (mp0) REVERT: G 71 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: H 14 ARG cc_start: 0.8155 (ttt90) cc_final: 0.7921 (ttt-90) REVERT: H 16 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6834 (tt0) REVERT: H 27 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7276 (mp0) REVERT: H 71 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: I 14 ARG cc_start: 0.8178 (ttt90) cc_final: 0.7915 (ttt-90) REVERT: I 16 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6879 (tt0) REVERT: I 27 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7366 (mp0) REVERT: I 71 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: J 14 ARG cc_start: 0.8176 (ttt90) cc_final: 0.7908 (ttt-90) REVERT: J 16 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6888 (tt0) REVERT: J 27 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7405 (mp0) REVERT: J 71 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: K 27 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7098 (mp0) REVERT: K 71 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: L 14 ARG cc_start: 0.8160 (ttt90) cc_final: 0.7895 (ttt-90) REVERT: L 16 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6864 (tt0) REVERT: L 27 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7286 (mp0) REVERT: L 71 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: M 27 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7118 (mp0) REVERT: N 14 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7913 (ttt-90) REVERT: N 16 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6854 (tt0) REVERT: N 27 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7298 (mp0) REVERT: N 71 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: O 14 ARG cc_start: 0.8172 (ttt90) cc_final: 0.7913 (ttt-90) REVERT: O 16 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6899 (tt0) REVERT: O 27 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7382 (mp0) REVERT: O 71 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: P 14 ARG cc_start: 0.8175 (ttt90) cc_final: 0.7906 (ttt-90) REVERT: P 16 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6901 (tt0) REVERT: P 27 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7370 (mp0) REVERT: P 71 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: Q 27 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7085 (mp0) REVERT: Q 71 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: R 14 ARG cc_start: 0.8134 (ttt90) cc_final: 0.7892 (ttt-90) REVERT: R 27 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7360 (mp0) REVERT: R 71 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: S 27 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7352 (mp0) REVERT: S 69 GLU cc_start: 0.7133 (pm20) cc_final: 0.6826 (mp0) REVERT: S 71 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: T 14 ARG cc_start: 0.8183 (ttt90) cc_final: 0.7910 (ttt-90) REVERT: T 16 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6795 (tt0) REVERT: T 27 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7384 (mp0) REVERT: T 71 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: U 27 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7388 (mp0) REVERT: U 71 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7573 (pt0) REVERT: V 14 ARG cc_start: 0.8143 (ttt90) cc_final: 0.7894 (ttt-90) REVERT: V 27 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7392 (mp0) REVERT: V 71 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: W 14 ARG cc_start: 0.8152 (ttt90) cc_final: 0.7912 (ttt-90) REVERT: W 27 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7404 (mp0) REVERT: W 71 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: X 27 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7203 (mp0) REVERT: X 71 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7524 (pt0) outliers start: 126 outliers final: 72 residues processed: 609 average time/residue: 0.9198 time to fit residues: 640.0612 Evaluate side-chains 545 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 450 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 152 HIS 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 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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 71 GLU 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: 9.9990 chunk 170 optimal weight: 4.9990 chunk 271 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 429 optimal weight: 0.0030 chunk 8 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 overall best weight: 6.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN 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 134 GLN 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 = 0.3375 r_free = 0.3375 target = 0.128292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.095255 restraints weight = 37476.891| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.65 r_work: 0.2768 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 36120 Z= 0.269 Angle : 0.634 9.456 49080 Z= 0.337 Chirality : 0.051 0.151 5592 Planarity : 0.007 0.046 6528 Dihedral : 5.473 26.992 5136 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.63 % Allowed : 18.80 % Favored : 76.56 % 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 aren not related in a simple way. whole: 0.20 (0.13), residues: 4512 helix: 1.49 (0.12), residues: 1848 sheet: -0.18 (0.13), residues: 1320 loop : -1.36 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 14 TYR 0.007 0.002 TYR E 171 PHE 0.012 0.003 PHE W 154 HIS 0.009 0.002 HIS V 176 Details of bonding type rmsd covalent geometry : bond 0.00637 (36120) covalent geometry : angle 0.63368 (49080) hydrogen bonds : bond 0.04606 ( 2232) hydrogen bonds : angle 4.10954 ( 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 635 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 466 time to evaluate : 0.983 Fit side-chains REVERT: A 14 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7905 (ttt-90) REVERT: A 16 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6824 (tt0) REVERT: A 27 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7282 (mp0) REVERT: A 65 THR cc_start: 0.7450 (OUTLIER) cc_final: 0.7125 (p) REVERT: B 14 ARG cc_start: 0.8221 (ttt90) cc_final: 0.7910 (ttt-90) REVERT: B 16 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6812 (tt0) REVERT: B 27 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7317 (mp0) REVERT: B 65 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7145 (p) REVERT: C 14 ARG cc_start: 0.8220 (ttt90) cc_final: 0.7907 (ttt-90) REVERT: C 16 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6871 (tt0) REVERT: C 27 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7319 (mp0) REVERT: C 65 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7131 (p) REVERT: D 27 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7201 (mp0) REVERT: D 65 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.7123 (p) REVERT: E 27 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7298 (mp0) REVERT: E 65 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7154 (p) REVERT: F 27 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7175 (mp0) REVERT: F 65 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7182 (p) REVERT: G 27 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7303 (mp0) REVERT: G 65 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7114 (p) REVERT: H 14 ARG cc_start: 0.8217 (ttt90) cc_final: 0.7910 (ttt-90) REVERT: H 16 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6821 (tt0) REVERT: H 27 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7314 (mp0) REVERT: H 65 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7124 (p) REVERT: I 14 ARG cc_start: 0.8222 (ttt90) cc_final: 0.7908 (ttt-90) REVERT: I 16 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6880 (tt0) REVERT: I 27 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7317 (mp0) REVERT: I 65 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7130 (p) REVERT: J 14 ARG cc_start: 0.8213 (ttt90) cc_final: 0.7897 (ttt-90) REVERT: J 16 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6877 (tt0) REVERT: J 27 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7280 (mp0) REVERT: J 65 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7158 (p) REVERT: K 27 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7122 (mp0) REVERT: K 65 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7120 (p) REVERT: L 14 ARG cc_start: 0.8233 (ttt90) cc_final: 0.7921 (ttt-90) REVERT: L 16 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6850 (tt0) REVERT: L 27 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7315 (mp0) REVERT: L 65 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7137 (p) REVERT: M 27 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7132 (mp0) REVERT: M 65 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.7123 (p) REVERT: N 14 ARG cc_start: 0.8234 (ttt90) cc_final: 0.7921 (ttt-90) REVERT: N 16 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6866 (tt0) REVERT: N 27 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7312 (mp0) REVERT: N 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7153 (p) REVERT: O 14 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7909 (ttt-90) REVERT: O 16 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6837 (tt0) REVERT: O 27 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7325 (mp0) REVERT: O 65 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7144 (p) REVERT: P 14 ARG cc_start: 0.8235 (ttt90) cc_final: 0.7919 (ttt-90) REVERT: P 16 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6883 (tt0) REVERT: P 27 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7302 (mp0) REVERT: P 65 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7159 (p) REVERT: Q 27 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7135 (mp0) REVERT: Q 65 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7161 (p) REVERT: R 27 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7323 (mp0) REVERT: R 65 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.7103 (p) REVERT: S 27 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7305 (mp0) REVERT: S 65 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.7109 (p) REVERT: S 69 GLU cc_start: 0.7144 (pm20) cc_final: 0.6815 (mp0) REVERT: T 14 ARG cc_start: 0.8225 (ttt90) cc_final: 0.7911 (ttt-90) REVERT: T 16 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6895 (tt0) REVERT: T 27 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7306 (mp0) REVERT: T 65 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7123 (p) REVERT: U 27 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7268 (mp0) REVERT: U 65 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7113 (p) REVERT: V 27 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7309 (mp0) REVERT: V 65 THR cc_start: 0.7479 (OUTLIER) cc_final: 0.7154 (p) REVERT: W 27 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7311 (mp0) REVERT: W 65 THR cc_start: 0.7419 (OUTLIER) cc_final: 0.7083 (p) REVERT: X 27 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7194 (mp0) REVERT: X 65 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.7135 (p) outliers start: 169 outliers final: 93 residues processed: 620 average time/residue: 0.8584 time to fit residues: 609.5660 Evaluate side-chains 573 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 456 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR 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 57 SER Chi-restraints excluded: chain B residue 61 THR 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 57 SER Chi-restraints excluded: chain C residue 61 THR 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 57 SER Chi-restraints excluded: chain D residue 61 THR 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 57 SER Chi-restraints excluded: chain E residue 61 THR 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 61 THR 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 57 SER Chi-restraints excluded: chain G residue 61 THR 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 57 SER Chi-restraints excluded: chain H residue 61 THR 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 57 SER Chi-restraints excluded: chain I residue 61 THR 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 57 SER Chi-restraints excluded: chain J residue 61 THR 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 57 SER Chi-restraints excluded: chain K residue 61 THR 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 57 SER Chi-restraints excluded: chain L residue 61 THR 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 152 HIS Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR 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 57 SER Chi-restraints excluded: chain O residue 61 THR 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 61 THR 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 57 SER Chi-restraints excluded: chain Q residue 61 THR 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 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 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 57 SER Chi-restraints excluded: chain T residue 61 THR 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 57 SER Chi-restraints excluded: chain U residue 61 THR 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 57 SER Chi-restraints excluded: chain V residue 61 THR 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 57 SER Chi-restraints excluded: chain W residue 61 THR 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 61 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 175 optimal weight: 8.9990 chunk 396 optimal weight: 6.9990 chunk 75 optimal weight: 0.0770 chunk 454 optimal weight: 0.9990 chunk 388 optimal weight: 8.9990 chunk 380 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 446 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN 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 134 GLN 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 = 0.3404 r_free = 0.3404 target = 0.130689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.098874 restraints weight = 37219.805| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.57 r_work: 0.2814 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36120 Z= 0.136 Angle : 0.519 8.244 49080 Z= 0.273 Chirality : 0.046 0.137 5592 Planarity : 0.005 0.037 6528 Dihedral : 4.998 25.521 5136 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.61 % Allowed : 19.46 % Favored : 75.93 % 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 aren not related in a simple way. whole: 0.51 (0.13), residues: 4512 helix: 1.79 (0.12), residues: 1872 sheet: -0.18 (0.13), residues: 1464 loop : -1.26 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 14 TYR 0.005 0.001 TYR T 145 PHE 0.008 0.002 PHE N 44 HIS 0.006 0.001 HIS F 176 Details of bonding type rmsd covalent geometry : bond 0.00310 (36120) covalent geometry : angle 0.51851 (49080) hydrogen bonds : bond 0.03545 ( 2232) hydrogen bonds : angle 3.83457 ( 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 671 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 503 time to evaluate : 1.432 Fit side-chains REVERT: A 14 ARG cc_start: 0.8186 (ttt90) cc_final: 0.7876 (ttt-90) REVERT: A 16 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6843 (tt0) REVERT: A 27 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7284 (mp0) REVERT: A 65 THR cc_start: 0.7504 (OUTLIER) cc_final: 0.7168 (p) REVERT: A 71 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: B 14 ARG cc_start: 0.8189 (ttt90) cc_final: 0.7880 (ttt-90) REVERT: B 16 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6832 (tt0) REVERT: B 27 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7309 (mp0) REVERT: B 65 THR cc_start: 0.7359 (OUTLIER) cc_final: 0.7065 (p) REVERT: B 71 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: C 14 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7890 (ttt-90) REVERT: C 16 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6838 (tt0) REVERT: C 27 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7317 (mp0) REVERT: C 65 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7052 (p) REVERT: C 71 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: C 109 GLU cc_start: 0.8797 (pm20) cc_final: 0.8497 (pm20) REVERT: D 27 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7199 (mp0) REVERT: D 65 THR cc_start: 0.7374 (OUTLIER) cc_final: 0.7090 (p) REVERT: D 71 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: E 27 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7234 (mp0) REVERT: E 65 THR cc_start: 0.7339 (OUTLIER) cc_final: 0.7046 (p) REVERT: E 71 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: F 27 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7194 (mp0) REVERT: F 65 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7099 (p) REVERT: F 71 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: F 109 GLU cc_start: 0.8803 (pm20) cc_final: 0.8503 (pm20) REVERT: G 27 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7255 (mp0) REVERT: G 65 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7081 (p) REVERT: G 71 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7473 (pt0) REVERT: H 14 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7897 (ttt-90) REVERT: H 16 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6843 (tt0) REVERT: H 27 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7318 (mp0) REVERT: H 65 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.7072 (p) REVERT: H 71 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: I 14 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7890 (ttt-90) REVERT: I 16 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6855 (tt0) REVERT: I 27 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7307 (mp0) REVERT: I 65 THR cc_start: 0.7371 (OUTLIER) cc_final: 0.7079 (p) REVERT: I 71 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: I 109 GLU cc_start: 0.8815 (pm20) cc_final: 0.8526 (pm20) REVERT: J 14 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7872 (ttt-90) REVERT: J 16 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6874 (tt0) REVERT: J 27 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7272 (mp0) REVERT: J 65 THR cc_start: 0.7384 (OUTLIER) cc_final: 0.7087 (p) REVERT: J 71 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: K 27 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7114 (mp0) REVERT: K 65 THR cc_start: 0.7349 (OUTLIER) cc_final: 0.7057 (p) REVERT: K 71 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: L 14 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7893 (ttt-90) REVERT: L 16 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6871 (tt0) REVERT: L 27 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7312 (mp0) REVERT: L 65 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.7075 (p) REVERT: L 71 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: M 27 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7149 (mp0) REVERT: M 65 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7091 (p) REVERT: N 14 ARG cc_start: 0.8203 (ttt90) cc_final: 0.7894 (ttt-90) REVERT: N 16 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6861 (tt0) REVERT: N 27 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7299 (mp0) REVERT: N 65 THR cc_start: 0.7356 (OUTLIER) cc_final: 0.7066 (p) REVERT: N 71 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7452 (pt0) REVERT: O 14 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7896 (ttt-90) REVERT: O 16 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6850 (tt0) REVERT: O 27 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7320 (mp0) REVERT: O 65 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.7077 (p) REVERT: O 71 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: O 109 GLU cc_start: 0.8790 (pm20) cc_final: 0.8501 (pm20) REVERT: P 14 ARG cc_start: 0.8204 (ttt90) cc_final: 0.7892 (ttt-90) REVERT: P 16 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6885 (tt0) REVERT: P 27 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7288 (mp0) REVERT: P 65 THR cc_start: 0.7371 (OUTLIER) cc_final: 0.7080 (p) REVERT: P 71 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: Q 27 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7184 (mp0) REVERT: Q 65 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.7092 (p) REVERT: Q 71 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: Q 109 GLU cc_start: 0.8798 (pm20) cc_final: 0.8504 (pm20) REVERT: R 27 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7272 (mp0) REVERT: R 65 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7041 (p) REVERT: R 71 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: S 27 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7287 (mp0) REVERT: S 65 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7074 (p) REVERT: S 69 GLU cc_start: 0.7110 (pm20) cc_final: 0.6806 (mp0) REVERT: S 71 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: T 14 ARG cc_start: 0.8195 (ttt90) cc_final: 0.7884 (ttt-90) REVERT: T 16 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6869 (tt0) REVERT: T 27 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7290 (mp0) REVERT: T 65 THR cc_start: 0.7362 (OUTLIER) cc_final: 0.7066 (p) REVERT: T 71 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: U 27 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7247 (mp0) REVERT: U 65 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7041 (p) REVERT: U 71 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: V 27 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7224 (mp0) REVERT: V 65 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.7078 (p) REVERT: V 71 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: V 109 GLU cc_start: 0.8808 (pm20) cc_final: 0.8516 (pm20) REVERT: W 27 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7266 (mp0) REVERT: W 65 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7038 (p) REVERT: W 71 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: X 27 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7190 (mp0) REVERT: X 65 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.7063 (p) REVERT: X 71 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7407 (pt0) outliers start: 168 outliers final: 72 residues processed: 655 average time/residue: 0.9777 time to fit residues: 732.9237 Evaluate side-chains 611 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 492 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 133 LEU 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 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 M residue 57 SER Chi-restraints excluded: chain M residue 65 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 396 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 448 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 408 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 341 optimal weight: 0.2980 chunk 125 optimal weight: 10.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN 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 134 GLN 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 = 0.3402 r_free = 0.3402 target = 0.130487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.097427 restraints weight = 37169.362| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.66 r_work: 0.2783 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36120 Z= 0.178 Angle : 0.561 8.714 49080 Z= 0.293 Chirality : 0.047 0.138 5592 Planarity : 0.005 0.038 6528 Dihedral : 5.099 26.142 5136 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.51 % Allowed : 18.64 % Favored : 75.85 % 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 aren not related in a simple way. whole: 0.49 (0.13), residues: 4512 helix: 1.74 (0.12), residues: 1872 sheet: -0.19 (0.13), residues: 1464 loop : -1.19 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 14 TYR 0.005 0.001 TYR I 123 PHE 0.010 0.002 PHE V 44 HIS 0.006 0.001 HIS V 176 Details of bonding type rmsd covalent geometry : bond 0.00415 (36120) covalent geometry : angle 0.56067 (49080) hydrogen bonds : bond 0.03898 ( 2232) hydrogen bonds : angle 3.87952 ( 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 665 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 464 time to evaluate : 1.360 Fit side-chains REVERT: A 14 ARG cc_start: 0.8215 (ttt90) cc_final: 0.7900 (ttt-90) REVERT: A 16 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6841 (tt0) REVERT: A 27 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7250 (mp0) REVERT: A 65 THR cc_start: 0.7339 (OUTLIER) cc_final: 0.7031 (p) REVERT: A 71 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: B 14 ARG cc_start: 0.8220 (ttt90) cc_final: 0.7904 (ttt-90) REVERT: B 16 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6886 (tt0) REVERT: B 27 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7261 (mp0) REVERT: B 65 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7019 (p) REVERT: B 71 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: C 14 ARG cc_start: 0.8228 (ttt90) cc_final: 0.7910 (ttt-90) REVERT: C 16 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6879 (tt0) REVERT: C 27 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7291 (mp0) REVERT: C 65 THR cc_start: 0.7340 (OUTLIER) cc_final: 0.7039 (p) REVERT: C 71 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: D 27 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7184 (mp0) REVERT: D 65 THR cc_start: 0.7338 (OUTLIER) cc_final: 0.7028 (p) REVERT: D 71 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: E 27 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7229 (mp0) REVERT: E 65 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.7044 (p) REVERT: E 71 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: E 162 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7224 (mtt-85) REVERT: F 27 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7158 (mp0) REVERT: F 65 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7073 (p) REVERT: F 71 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: F 109 GLU cc_start: 0.8838 (pm20) cc_final: 0.8522 (pm20) REVERT: G 27 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7222 (mp0) REVERT: G 65 THR cc_start: 0.7335 (OUTLIER) cc_final: 0.7025 (p) REVERT: G 71 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7452 (pt0) REVERT: G 162 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7291 (mtt-85) REVERT: H 14 ARG cc_start: 0.8222 (ttt90) cc_final: 0.7908 (ttt-90) REVERT: H 16 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6835 (tt0) REVERT: H 27 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7287 (mp0) REVERT: H 65 THR cc_start: 0.7337 (OUTLIER) cc_final: 0.7028 (p) REVERT: H 71 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: I 14 ARG cc_start: 0.8223 (ttt90) cc_final: 0.7902 (ttt-90) REVERT: I 16 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6849 (tt0) REVERT: I 27 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7254 (mp0) REVERT: I 65 THR cc_start: 0.7343 (OUTLIER) cc_final: 0.7027 (p) REVERT: I 71 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: I 109 GLU cc_start: 0.8833 (pm20) cc_final: 0.8527 (pm20) REVERT: J 14 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7893 (ttt-90) REVERT: J 16 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6912 (tt0) REVERT: J 27 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7238 (mp0) REVERT: J 65 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.7042 (p) REVERT: J 71 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: K 27 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7145 (mp0) REVERT: K 65 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.7024 (p) REVERT: K 71 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: L 14 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7912 (ttt-90) REVERT: L 16 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6900 (tt0) REVERT: L 27 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7279 (mp0) REVERT: L 65 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7038 (p) REVERT: L 71 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: L 162 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7505 (mtt-85) REVERT: M 27 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7162 (mp0) REVERT: M 65 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.7056 (p) REVERT: N 14 ARG cc_start: 0.8236 (ttt90) cc_final: 0.7915 (ttt-90) REVERT: N 16 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6889 (tt0) REVERT: N 27 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7251 (mp0) REVERT: N 65 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.7030 (p) REVERT: N 71 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: O 14 ARG cc_start: 0.8226 (ttt90) cc_final: 0.7911 (ttt-90) REVERT: O 16 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6853 (tt0) REVERT: O 27 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7297 (mp0) REVERT: O 65 THR cc_start: 0.7349 (OUTLIER) cc_final: 0.7042 (p) REVERT: O 71 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: O 162 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7315 (mtt-85) REVERT: P 14 ARG cc_start: 0.8235 (ttt90) cc_final: 0.7911 (ttt-90) REVERT: P 16 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6915 (tt0) REVERT: P 27 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7255 (mp0) REVERT: P 65 THR cc_start: 0.7338 (OUTLIER) cc_final: 0.7040 (p) REVERT: P 71 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: P 162 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7521 (mtt-85) REVERT: Q 27 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7151 (mp0) REVERT: Q 65 THR cc_start: 0.7365 (OUTLIER) cc_final: 0.7057 (p) REVERT: Q 71 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: Q 109 GLU cc_start: 0.8827 (pm20) cc_final: 0.8522 (pm20) REVERT: R 27 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7221 (mp0) REVERT: R 65 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7002 (p) REVERT: R 71 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: R 162 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7295 (mtt-85) REVERT: S 27 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7240 (mp0) REVERT: S 65 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.7000 (p) REVERT: S 69 GLU cc_start: 0.7123 (pm20) cc_final: 0.6782 (mp0) REVERT: S 71 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: S 162 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7317 (mtt-85) REVERT: T 14 ARG cc_start: 0.8227 (ttt90) cc_final: 0.7907 (ttt-90) REVERT: T 16 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6895 (tt0) REVERT: T 27 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7243 (mp0) REVERT: T 65 THR cc_start: 0.7337 (OUTLIER) cc_final: 0.7028 (p) REVERT: T 71 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: U 27 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7210 (mp0) REVERT: U 65 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7024 (p) REVERT: U 71 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7428 (pt0) REVERT: V 27 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7227 (mp0) REVERT: V 65 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7040 (p) REVERT: V 71 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: V 162 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7294 (mtt-85) REVERT: W 27 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7211 (mp0) REVERT: W 65 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.6985 (p) REVERT: W 71 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: X 27 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7172 (mp0) REVERT: X 65 THR cc_start: 0.7323 (OUTLIER) cc_final: 0.7013 (p) REVERT: X 71 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: X 162 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7301 (mtt-85) outliers start: 201 outliers final: 96 residues processed: 665 average time/residue: 1.0193 time to fit residues: 774.9300 Evaluate side-chains 604 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 452 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 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 133 LEU 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 E residue 162 ARG 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 136 THR 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 G residue 162 ARG 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 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 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 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 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 133 LEU 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 O residue 162 ARG 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 R residue 162 ARG 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 S residue 162 ARG 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 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 133 LEU Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain V residue 162 ARG 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 133 LEU Chi-restraints excluded: chain X residue 152 HIS Chi-restraints excluded: chain X residue 162 ARG 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: 9.9990 chunk 264 optimal weight: 9.9990 chunk 266 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 381 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN 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 134 GLN 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 = 0.3363 r_free = 0.3363 target = 0.127427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094954 restraints weight = 37441.013| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.59 r_work: 0.2768 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 36120 Z= 0.312 Angle : 0.675 9.478 49080 Z= 0.355 Chirality : 0.053 0.159 5592 Planarity : 0.007 0.047 6528 Dihedral : 5.556 27.098 5136 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.93 % Allowed : 18.97 % 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 aren not related in a simple way. whole: 0.22 (0.13), residues: 4512 helix: 1.43 (0.12), residues: 1848 sheet: -0.14 (0.13), residues: 1320 loop : -1.26 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 14 TYR 0.007 0.002 TYR U 171 PHE 0.013 0.003 PHE V 154 HIS 0.009 0.002 HIS I 176 Details of bonding type rmsd covalent geometry : bond 0.00742 (36120) covalent geometry : angle 0.67535 (49080) hydrogen bonds : bond 0.04868 ( 2232) hydrogen bonds : angle 4.18961 ( 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 644 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 464 time to evaluate : 1.466 Fit side-chains REVERT: A 14 ARG cc_start: 0.8242 (ttt90) cc_final: 0.8003 (ttt-90) REVERT: A 16 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6897 (tt0) REVERT: A 27 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7304 (mp0) REVERT: A 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7150 (p) REVERT: B 14 ARG cc_start: 0.8251 (ttt90) cc_final: 0.8013 (ttt-90) REVERT: B 16 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6913 (tt0) REVERT: B 27 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7327 (mp0) REVERT: B 65 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7132 (p) REVERT: C 14 ARG cc_start: 0.8249 (ttt90) cc_final: 0.8012 (ttt-90) REVERT: C 16 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6920 (tt0) REVERT: C 27 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7359 (mp0) REVERT: C 65 THR cc_start: 0.7331 (OUTLIER) cc_final: 0.7034 (p) REVERT: D 27 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7224 (mp0) REVERT: D 65 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7154 (p) REVERT: E 27 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7285 (mp0) REVERT: E 65 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7161 (p) REVERT: F 27 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7212 (mp0) REVERT: F 65 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7180 (p) REVERT: G 27 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7277 (mp0) REVERT: G 65 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7153 (p) REVERT: H 14 ARG cc_start: 0.8241 (ttt90) cc_final: 0.8008 (ttt-90) REVERT: H 16 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6899 (tt0) REVERT: H 27 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7327 (mp0) REVERT: H 65 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7128 (p) REVERT: H 69 GLU cc_start: 0.7220 (pm20) cc_final: 0.6846 (mp0) REVERT: I 14 ARG cc_start: 0.8242 (ttt90) cc_final: 0.8004 (ttt-90) REVERT: I 16 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6898 (tt0) REVERT: I 27 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7327 (mp0) REVERT: I 65 THR cc_start: 0.7493 (OUTLIER) cc_final: 0.7150 (p) REVERT: J 14 ARG cc_start: 0.8247 (ttt90) cc_final: 0.8007 (ttt-90) REVERT: J 16 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6924 (tt0) REVERT: J 27 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7311 (mp0) REVERT: J 65 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.7031 (p) REVERT: K 27 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7244 (mp0) REVERT: K 65 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.7025 (p) REVERT: L 14 ARG cc_start: 0.8259 (ttt90) cc_final: 0.8018 (ttt-90) REVERT: L 16 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6925 (tt0) REVERT: L 27 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7366 (mp0) REVERT: L 65 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.7025 (p) REVERT: L 162 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7468 (mtt-85) REVERT: M 27 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7208 (mp0) REVERT: M 65 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7155 (p) REVERT: N 14 ARG cc_start: 0.8260 (ttt90) cc_final: 0.8023 (ttt-90) REVERT: N 16 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6907 (tt0) REVERT: N 27 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7358 (mp0) REVERT: N 65 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.7030 (p) REVERT: O 14 ARG cc_start: 0.8242 (ttt90) cc_final: 0.8008 (ttt-90) REVERT: O 16 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6922 (tt0) REVERT: O 27 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7372 (mp0) REVERT: O 65 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7033 (p) REVERT: P 14 ARG cc_start: 0.8259 (ttt90) cc_final: 0.8016 (ttt-90) REVERT: P 16 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6926 (tt0) REVERT: P 27 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7351 (mp0) REVERT: P 65 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7040 (p) REVERT: P 162 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7477 (mtt-85) REVERT: Q 27 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7196 (mp0) REVERT: Q 65 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7157 (p) REVERT: R 27 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7297 (mp0) REVERT: R 65 THR cc_start: 0.7472 (OUTLIER) cc_final: 0.7137 (p) REVERT: S 27 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7302 (mp0) REVERT: S 65 THR cc_start: 0.7356 (OUTLIER) cc_final: 0.7067 (p) REVERT: S 69 GLU cc_start: 0.7225 (pm20) cc_final: 0.6854 (mp0) REVERT: T 14 ARG cc_start: 0.8254 (ttt90) cc_final: 0.8019 (ttt-90) REVERT: T 16 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6912 (tt0) REVERT: T 27 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7342 (mp0) REVERT: T 65 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.7032 (p) REVERT: U 27 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7248 (mp0) REVERT: U 65 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7036 (p) REVERT: V 27 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7266 (mp0) REVERT: V 65 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7153 (p) REVERT: W 27 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7295 (mp0) REVERT: W 65 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7137 (p) REVERT: X 27 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7245 (mp0) REVERT: X 65 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7164 (p) outliers start: 180 outliers final: 119 residues processed: 630 average time/residue: 1.0285 time to fit residues: 742.1921 Evaluate side-chains 592 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 447 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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 136 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 211 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 406 optimal weight: 8.9990 chunk 334 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN 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 134 GLN 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 = 0.3373 r_free = 0.3373 target = 0.128282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.095292 restraints weight = 37326.938| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.65 r_work: 0.2776 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2096 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= 0.253 Angle : 0.626 9.319 49080 Z= 0.329 Chirality : 0.050 0.146 5592 Planarity : 0.006 0.044 6528 Dihedral : 5.436 26.956 5136 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.32 % Allowed : 19.11 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.13), residues: 4512 helix: 1.35 (0.12), residues: 1872 sheet: -0.10 (0.13), residues: 1464 loop : -1.27 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 14 TYR 0.006 0.002 TYR B 171 PHE 0.011 0.002 PHE S 44 HIS 0.008 0.002 HIS F 176 Details of bonding type rmsd covalent geometry : bond 0.00599 (36120) covalent geometry : angle 0.62575 (49080) hydrogen bonds : bond 0.04416 ( 2232) hydrogen bonds : angle 4.11080 ( 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 658 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 464 time to evaluate : 2.045 Fit side-chains REVERT: A 14 ARG cc_start: 0.8242 (ttt90) cc_final: 0.7977 (ttt-90) REVERT: A 16 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6906 (tt0) REVERT: A 27 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7328 (mp0) REVERT: A 65 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7144 (p) REVERT: B 14 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7990 (ttt-90) REVERT: B 16 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6916 (tt0) REVERT: B 27 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7334 (mp0) REVERT: B 65 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7114 (p) REVERT: C 14 ARG cc_start: 0.8194 (ttt90) cc_final: 0.7985 (ttt-90) REVERT: C 16 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6907 (tt0) REVERT: C 27 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7359 (mp0) REVERT: C 65 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7153 (p) REVERT: D 27 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7262 (mp0) REVERT: D 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7151 (p) REVERT: E 27 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7284 (mp0) REVERT: E 65 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.7142 (p) REVERT: F 27 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7227 (mp0) REVERT: F 65 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7160 (p) REVERT: G 27 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7273 (mp0) REVERT: G 65 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7148 (p) REVERT: H 14 ARG cc_start: 0.8241 (ttt90) cc_final: 0.7987 (ttt-90) REVERT: H 16 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6909 (tt0) REVERT: H 27 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7340 (mp0) REVERT: H 65 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7128 (p) REVERT: H 69 GLU cc_start: 0.7224 (pm20) cc_final: 0.6812 (mp0) REVERT: I 14 ARG cc_start: 0.8239 (ttt90) cc_final: 0.7980 (ttt-90) REVERT: I 16 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6879 (tt0) REVERT: I 27 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7332 (mp0) REVERT: I 65 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7148 (p) REVERT: J 14 ARG cc_start: 0.8193 (ttt90) cc_final: 0.7976 (ttt-90) REVERT: J 16 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6918 (tt0) REVERT: J 27 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7307 (mp0) REVERT: J 65 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7123 (p) REVERT: K 27 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7223 (mp0) REVERT: K 65 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7138 (p) REVERT: L 14 ARG cc_start: 0.8251 (ttt90) cc_final: 0.7991 (ttt-90) REVERT: L 16 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6921 (tt0) REVERT: L 27 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7321 (mp0) REVERT: L 65 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7135 (p) REVERT: L 162 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7460 (mtt-85) REVERT: M 27 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7224 (mp0) REVERT: M 65 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7149 (p) REVERT: N 14 ARG cc_start: 0.8206 (ttt90) cc_final: 0.8000 (ttt-90) REVERT: N 16 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6901 (tt0) REVERT: N 27 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7325 (mp0) REVERT: N 65 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7121 (p) REVERT: O 14 ARG cc_start: 0.8236 (ttt90) cc_final: 0.7983 (ttt-90) REVERT: O 16 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6928 (tt0) REVERT: O 27 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7336 (mp0) REVERT: O 65 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7124 (p) REVERT: O 69 GLU cc_start: 0.7208 (pm20) cc_final: 0.6828 (mp0) REVERT: P 14 ARG cc_start: 0.8203 (ttt90) cc_final: 0.7991 (ttt-90) REVERT: P 16 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6917 (tt0) REVERT: P 27 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7328 (mp0) REVERT: P 65 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7134 (p) REVERT: P 162 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7475 (mtt-85) REVERT: Q 27 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7235 (mp0) REVERT: Q 65 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7150 (p) REVERT: R 27 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7290 (mp0) REVERT: R 65 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7129 (p) REVERT: S 27 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7291 (mp0) REVERT: S 65 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7152 (p) REVERT: S 69 GLU cc_start: 0.7193 (pm20) cc_final: 0.6831 (mp0) REVERT: S 71 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: T 14 ARG cc_start: 0.8247 (ttt90) cc_final: 0.7987 (ttt-90) REVERT: T 16 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6904 (tt0) REVERT: T 27 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7344 (mp0) REVERT: T 65 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.7125 (p) REVERT: U 27 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7260 (mp0) REVERT: U 65 THR cc_start: 0.7464 (OUTLIER) cc_final: 0.7130 (p) REVERT: V 27 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7283 (mp0) REVERT: V 65 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7136 (p) REVERT: W 27 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7296 (mp0) REVERT: W 65 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7124 (p) REVERT: X 27 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7250 (mp0) REVERT: X 65 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7155 (p) outliers start: 194 outliers final: 138 residues processed: 645 average time/residue: 0.9534 time to fit residues: 705.9150 Evaluate side-chains 610 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 445 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain B residue 136 THR 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 136 THR 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 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 133 LEU Chi-restraints excluded: chain E residue 136 THR 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 136 THR 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 136 THR 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 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 136 THR 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 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 133 LEU Chi-restraints excluded: chain K residue 136 THR 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 136 THR 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 133 LEU Chi-restraints excluded: chain M residue 136 THR 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 133 LEU Chi-restraints excluded: chain N residue 136 THR 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 136 THR 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 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 133 LEU Chi-restraints excluded: chain Q residue 136 THR 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 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 133 LEU Chi-restraints excluded: chain S residue 136 THR 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 136 THR 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 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 133 LEU 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 133 LEU Chi-restraints excluded: chain W residue 136 THR 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 136 THR 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: 2.9990 chunk 49 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 384 optimal weight: 1.9990 chunk 425 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN 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 134 GLN 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 = 0.3383 r_free = 0.3383 target = 0.129124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.097237 restraints weight = 37160.101| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.56 r_work: 0.2799 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36120 Z= 0.186 Angle : 0.577 8.711 49080 Z= 0.302 Chirality : 0.047 0.136 5592 Planarity : 0.005 0.031 6528 Dihedral : 5.200 26.500 5136 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.04 % Allowed : 19.68 % Favored : 75.27 % 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 aren not related in a simple way. whole: 0.43 (0.13), residues: 4512 helix: 1.59 (0.12), residues: 1872 sheet: -0.12 (0.13), residues: 1464 loop : -1.18 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 14 TYR 0.006 0.001 TYR H 145 PHE 0.009 0.002 PHE W 44 HIS 0.007 0.001 HIS S 176 Details of bonding type rmsd covalent geometry : bond 0.00436 (36120) covalent geometry : angle 0.57728 (49080) hydrogen bonds : bond 0.03984 ( 2232) hydrogen bonds : angle 3.97702 ( 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 622 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 438 time to evaluate : 1.222 Fit side-chains REVERT: A 16 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6927 (tt0) REVERT: A 27 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7288 (mp0) REVERT: A 65 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7140 (p) REVERT: A 69 GLU cc_start: 0.7182 (pm20) cc_final: 0.6794 (mp0) REVERT: A 71 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: B 16 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6977 (tt0) REVERT: B 27 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7293 (mp0) REVERT: B 65 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.7008 (p) REVERT: B 71 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: C 16 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6961 (tt0) REVERT: C 27 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7298 (mp0) REVERT: C 65 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7032 (p) REVERT: C 69 GLU cc_start: 0.7184 (pm20) cc_final: 0.6803 (mp0) REVERT: C 71 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: D 27 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7202 (mp0) REVERT: D 65 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.7141 (p) REVERT: D 69 GLU cc_start: 0.7184 (pm20) cc_final: 0.6808 (mp0) REVERT: D 71 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: E 27 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7253 (mp0) REVERT: E 65 THR cc_start: 0.7470 (OUTLIER) cc_final: 0.7140 (p) REVERT: E 71 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: F 27 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7188 (mp0) REVERT: F 65 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.7140 (p) REVERT: F 71 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: G 27 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7249 (mp0) REVERT: G 65 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.7029 (p) REVERT: G 69 GLU cc_start: 0.7193 (pm20) cc_final: 0.6823 (mp0) REVERT: G 71 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: H 16 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6916 (tt0) REVERT: H 27 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7304 (mp0) REVERT: H 65 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.7012 (p) REVERT: H 69 GLU cc_start: 0.7176 (pm20) cc_final: 0.6819 (mp0) REVERT: H 71 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: I 16 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6928 (tt0) REVERT: I 27 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7293 (mp0) REVERT: I 65 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.7020 (p) REVERT: I 69 GLU cc_start: 0.7183 (pm20) cc_final: 0.6818 (mp0) REVERT: I 71 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7432 (pt0) REVERT: J 14 ARG cc_start: 0.8176 (ttt90) cc_final: 0.7959 (ttt-90) REVERT: J 16 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6991 (tt0) REVERT: J 27 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7281 (mp0) REVERT: J 65 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.7053 (p) REVERT: J 69 GLU cc_start: 0.7171 (pm20) cc_final: 0.6795 (mp0) REVERT: J 71 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7432 (pt0) REVERT: K 27 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7169 (mp0) REVERT: K 65 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.7021 (p) REVERT: K 69 GLU cc_start: 0.7178 (pm20) cc_final: 0.6835 (mp0) REVERT: K 71 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: L 16 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7005 (tt0) REVERT: L 27 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7311 (mp0) REVERT: L 65 THR cc_start: 0.7335 (OUTLIER) cc_final: 0.7024 (p) REVERT: L 69 GLU cc_start: 0.7168 (pm20) cc_final: 0.6786 (mp0) REVERT: L 71 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7423 (pt0) REVERT: L 162 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7450 (mtt-85) REVERT: M 27 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7202 (mp0) REVERT: M 65 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.7031 (p) REVERT: M 69 GLU cc_start: 0.7140 (pm20) cc_final: 0.6791 (mp0) REVERT: N 16 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6964 (tt0) REVERT: N 27 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7302 (mp0) REVERT: N 65 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.7005 (p) REVERT: N 69 GLU cc_start: 0.7196 (pm20) cc_final: 0.6805 (mp0) REVERT: N 71 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7433 (pt0) REVERT: O 16 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6960 (tt0) REVERT: O 27 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7306 (mp0) REVERT: O 65 THR cc_start: 0.7326 (OUTLIER) cc_final: 0.7025 (p) REVERT: O 69 GLU cc_start: 0.7216 (pm20) cc_final: 0.6828 (mp0) REVERT: O 71 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: P 16 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6987 (tt0) REVERT: P 27 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7296 (mp0) REVERT: P 65 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.7031 (p) REVERT: P 69 GLU cc_start: 0.7174 (pm20) cc_final: 0.6795 (mp0) REVERT: P 71 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: P 162 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7512 (mtt-85) REVERT: Q 27 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7192 (mp0) REVERT: Q 65 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.7132 (p) REVERT: Q 69 GLU cc_start: 0.7176 (pm20) cc_final: 0.6807 (mp0) REVERT: Q 71 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: R 27 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7254 (mp0) REVERT: R 65 THR cc_start: 0.7470 (OUTLIER) cc_final: 0.7126 (p) REVERT: R 71 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7462 (pt0) REVERT: S 27 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7271 (mp0) REVERT: S 65 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.7033 (p) REVERT: S 69 GLU cc_start: 0.7213 (pm20) cc_final: 0.6840 (mp0) REVERT: S 71 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: T 16 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6970 (tt0) REVERT: T 27 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7291 (mp0) REVERT: T 65 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.7022 (p) REVERT: T 69 GLU cc_start: 0.7176 (pm20) cc_final: 0.6796 (mp0) REVERT: T 71 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: U 27 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7228 (mp0) REVERT: U 65 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.7013 (p) REVERT: U 69 GLU cc_start: 0.7194 (pm20) cc_final: 0.6855 (mp0) REVERT: U 71 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: V 27 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7254 (mp0) REVERT: V 65 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7135 (p) REVERT: V 69 GLU cc_start: 0.7179 (pm20) cc_final: 0.6801 (mp0) REVERT: V 71 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7439 (pt0) REVERT: W 27 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7268 (mp0) REVERT: W 65 THR cc_start: 0.7451 (OUTLIER) cc_final: 0.7108 (p) REVERT: W 71 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: X 27 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7198 (mp0) REVERT: X 65 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7143 (p) REVERT: X 69 GLU cc_start: 0.7181 (pm20) cc_final: 0.6805 (mp0) REVERT: X 71 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7419 (pt0) outliers start: 184 outliers final: 116 residues processed: 608 average time/residue: 0.9747 time to fit residues: 677.3218 Evaluate side-chains 592 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 427 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain B residue 136 THR 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 136 THR 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 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 133 LEU Chi-restraints excluded: chain E residue 136 THR 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 136 THR 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 136 THR 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 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 136 THR 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 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 133 LEU Chi-restraints excluded: chain K residue 136 THR 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 136 THR 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 133 LEU Chi-restraints excluded: chain M residue 136 THR 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 133 LEU Chi-restraints excluded: chain N residue 136 THR 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 136 THR 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 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 133 LEU Chi-restraints excluded: chain Q residue 136 THR 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 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 133 LEU Chi-restraints excluded: chain S residue 136 THR 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 136 THR 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 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 133 LEU 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 133 LEU Chi-restraints excluded: chain W residue 136 THR 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 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: 9.9990 chunk 395 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 408 optimal weight: 0.9980 chunk 398 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN 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 134 GLN 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 = 0.3368 r_free = 0.3368 target = 0.127954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.095555 restraints weight = 37539.206| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.60 r_work: 0.2774 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 36120 Z= 0.245 Angle : 0.630 9.376 49080 Z= 0.330 Chirality : 0.050 0.147 5592 Planarity : 0.007 0.062 6528 Dihedral : 5.385 26.735 5136 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.63 % Allowed : 20.34 % Favored : 75.03 % 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 aren not related in a simple way. whole: 0.33 (0.13), residues: 4512 helix: 1.47 (0.12), residues: 1872 sheet: -0.10 (0.13), residues: 1464 loop : -1.26 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 14 TYR 0.006 0.002 TYR U 171 PHE 0.012 0.002 PHE G 44 HIS 0.008 0.002 HIS F 47 Details of bonding type rmsd covalent geometry : bond 0.00581 (36120) covalent geometry : angle 0.62969 (49080) hydrogen bonds : bond 0.04418 ( 2232) hydrogen bonds : angle 4.08811 ( 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 583 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 414 time to evaluate : 1.184 Fit side-chains REVERT: A 16 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6676 (tt0) REVERT: A 27 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7314 (mp0) REVERT: A 65 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.7029 (p) REVERT: A 69 GLU cc_start: 0.7239 (pm20) cc_final: 0.6835 (mp0) REVERT: B 16 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6668 (tt0) REVERT: B 27 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7305 (mp0) REVERT: B 65 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7027 (p) REVERT: B 69 GLU cc_start: 0.7250 (pm20) cc_final: 0.6868 (mp0) REVERT: C 16 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6704 (tt0) REVERT: C 27 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7328 (mp0) REVERT: C 65 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7038 (p) REVERT: C 69 GLU cc_start: 0.7216 (pm20) cc_final: 0.6826 (mp0) REVERT: D 27 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7225 (mp0) REVERT: D 65 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.7076 (p) REVERT: D 69 GLU cc_start: 0.7232 (pm20) cc_final: 0.6834 (mp0) REVERT: E 27 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7290 (mp0) REVERT: E 65 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7156 (p) REVERT: E 69 GLU cc_start: 0.7249 (pm20) cc_final: 0.6872 (mp0) REVERT: F 27 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7218 (mp0) REVERT: F 65 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7163 (p) REVERT: G 27 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7271 (mp0) REVERT: G 65 THR cc_start: 0.7326 (OUTLIER) cc_final: 0.7030 (p) REVERT: G 69 GLU cc_start: 0.7199 (pm20) cc_final: 0.6816 (mp0) REVERT: H 16 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6688 (tt0) REVERT: H 27 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7329 (mp0) REVERT: H 65 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7020 (p) REVERT: H 69 GLU cc_start: 0.7201 (pm20) cc_final: 0.6829 (mp0) REVERT: I 16 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6684 (tt0) REVERT: I 27 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7315 (mp0) REVERT: I 65 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7030 (p) REVERT: I 69 GLU cc_start: 0.7204 (pm20) cc_final: 0.6820 (mp0) REVERT: J 14 ARG cc_start: 0.8195 (ttt90) cc_final: 0.7986 (ttt-90) REVERT: J 16 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6910 (tt0) REVERT: J 27 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7305 (mp0) REVERT: J 65 THR cc_start: 0.7331 (OUTLIER) cc_final: 0.7026 (p) REVERT: J 69 GLU cc_start: 0.7227 (pm20) cc_final: 0.6828 (mp0) REVERT: K 27 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7213 (mp0) REVERT: K 65 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.7026 (p) REVERT: K 69 GLU cc_start: 0.7204 (pm20) cc_final: 0.6814 (mp0) REVERT: L 16 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6709 (tt0) REVERT: L 27 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7327 (mp0) REVERT: L 65 THR cc_start: 0.7343 (OUTLIER) cc_final: 0.7033 (p) REVERT: L 69 GLU cc_start: 0.7205 (pm20) cc_final: 0.6812 (mp0) REVERT: L 162 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7462 (mtt-85) REVERT: M 27 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7227 (mp0) REVERT: M 65 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7040 (p) REVERT: M 69 GLU cc_start: 0.7140 (pm20) cc_final: 0.6763 (mp0) REVERT: N 16 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6655 (tt0) REVERT: N 27 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7317 (mp0) REVERT: N 65 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.7012 (p) REVERT: N 69 GLU cc_start: 0.7244 (pm20) cc_final: 0.6833 (mp0) REVERT: O 16 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6707 (tt0) REVERT: O 27 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7338 (mp0) REVERT: O 65 THR cc_start: 0.7344 (OUTLIER) cc_final: 0.7030 (p) REVERT: O 69 GLU cc_start: 0.7226 (pm20) cc_final: 0.6835 (mp0) REVERT: P 16 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6686 (tt0) REVERT: P 27 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7316 (mp0) REVERT: P 65 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7046 (p) REVERT: P 69 GLU cc_start: 0.7223 (pm20) cc_final: 0.6822 (mp0) REVERT: P 162 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7478 (mtt-85) REVERT: Q 27 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7221 (mp0) REVERT: Q 65 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7043 (p) REVERT: Q 69 GLU cc_start: 0.7228 (pm20) cc_final: 0.6833 (mp0) REVERT: R 27 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7290 (mp0) REVERT: R 65 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7045 (p) REVERT: S 27 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7309 (mp0) REVERT: S 65 THR cc_start: 0.7338 (OUTLIER) cc_final: 0.7044 (p) REVERT: S 69 GLU cc_start: 0.7227 (pm20) cc_final: 0.6850 (mp0) REVERT: T 16 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6663 (tt0) REVERT: T 27 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7311 (mp0) REVERT: T 65 THR cc_start: 0.7340 (OUTLIER) cc_final: 0.7030 (p) REVERT: T 69 GLU cc_start: 0.7227 (pm20) cc_final: 0.6820 (mp0) REVERT: U 27 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7269 (mp0) REVERT: U 65 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7024 (p) REVERT: U 69 GLU cc_start: 0.7214 (pm20) cc_final: 0.6831 (mp0) REVERT: V 27 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7279 (mp0) REVERT: V 65 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.7033 (p) REVERT: V 69 GLU cc_start: 0.7231 (pm20) cc_final: 0.6832 (mp0) REVERT: W 27 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7297 (mp0) REVERT: W 65 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7152 (p) REVERT: W 71 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: X 27 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7228 (mp0) REVERT: X 65 THR cc_start: 0.7340 (OUTLIER) cc_final: 0.7047 (p) REVERT: X 69 GLU cc_start: 0.7219 (pm20) cc_final: 0.6824 (mp0) outliers start: 169 outliers final: 138 residues processed: 583 average time/residue: 0.9835 time to fit residues: 656.3873 Evaluate side-chains 578 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 413 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain B residue 136 THR 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 136 THR 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 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 133 LEU Chi-restraints excluded: chain E residue 136 THR 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 136 THR 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 136 THR 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 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 136 THR 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 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 133 LEU Chi-restraints excluded: chain K residue 136 THR 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 136 THR 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 133 LEU Chi-restraints excluded: chain M residue 136 THR 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 133 LEU Chi-restraints excluded: chain N residue 136 THR 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 136 THR 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 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 133 LEU Chi-restraints excluded: chain Q residue 136 THR 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 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 133 LEU Chi-restraints excluded: chain S residue 136 THR 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 136 THR 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 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 133 LEU 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 133 LEU Chi-restraints excluded: chain W residue 136 THR 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 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 25 optimal weight: 9.9990 chunk 412 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 294 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 184 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 454 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN 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 134 GLN 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 = 0.3392 r_free = 0.3392 target = 0.129855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.097151 restraints weight = 37044.425| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.65 r_work: 0.2834 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36120 Z= 0.143 Angle : 0.545 8.462 49080 Z= 0.282 Chirality : 0.046 0.136 5592 Planarity : 0.005 0.039 6528 Dihedral : 4.995 25.587 5136 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.50 % Allowed : 20.59 % Favored : 74.92 % 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 aren not related in a simple way. whole: 0.53 (0.13), residues: 4512 helix: 1.76 (0.12), residues: 1872 sheet: -0.16 (0.13), residues: 1464 loop : -1.16 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 14 TYR 0.005 0.001 TYR P 145 PHE 0.009 0.002 PHE W 44 HIS 0.006 0.001 HIS W 176 Details of bonding type rmsd covalent geometry : bond 0.00327 (36120) covalent geometry : angle 0.54512 (49080) hydrogen bonds : bond 0.03589 ( 2232) hydrogen bonds : angle 3.86634 ( 6264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13470.55 seconds wall clock time: 229 minutes 50.85 seconds (13790.85 seconds total)