Starting phenix.real_space_refine on Mon Jul 6 11:42:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2p_63588/07_2026/9m2p_63588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2p_63588/07_2026/9m2p_63588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m2p_63588/07_2026/9m2p_63588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2p_63588/07_2026/9m2p_63588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m2p_63588/07_2026/9m2p_63588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2p_63588/07_2026/9m2p_63588.map" } resolution = 3.1 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= 0.011 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 21840 2.51 5 N 6696 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35352 Number of models: 1 Model: "" Number of chains: 72 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 8.01, per 1000 atoms: 0.23 Number of scatterers: 35352 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 6696 8.00 N 6696 7.00 C 21840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8448 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 72 sheets defined 42.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 42 through 57 Processing helix chain 'A' and resid 72 through 92 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 148 through 162 removed outlier: 4.537A pdb=" N HIS A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 195 Processing helix chain 'B' and resid 42 through 57 Processing helix chain 'B' and resid 72 through 92 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 195 Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 72 through 92 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 148 through 162 removed outlier: 4.536A pdb=" N HIS C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 195 Processing helix chain 'D' and resid 42 through 57 Processing helix chain 'D' and resid 72 through 92 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 148 through 162 removed outlier: 4.536A pdb=" N HIS D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 195 Processing helix chain 'E' and resid 42 through 57 Processing helix chain 'E' and resid 72 through 92 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 148 through 162 removed outlier: 4.536A pdb=" N HIS E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 195 Processing helix chain 'F' and resid 42 through 57 Processing helix chain 'F' and resid 72 through 92 Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 195 Processing helix chain 'G' and resid 42 through 57 Processing helix chain 'G' and resid 72 through 92 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 148 through 162 removed outlier: 4.536A pdb=" N HIS G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 195 Processing helix chain 'H' and resid 42 through 57 Processing helix chain 'H' and resid 72 through 92 Processing helix chain 'H' and resid 130 through 135 Processing helix chain 'H' and resid 148 through 162 removed outlier: 4.536A pdb=" N HIS H 152 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 195 Processing helix chain 'I' and resid 42 through 57 Processing helix chain 'I' and resid 72 through 92 Processing helix chain 'I' and resid 130 through 135 Processing helix chain 'I' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS I 152 " --> pdb=" O VAL I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 195 Processing helix chain 'J' and resid 42 through 57 Processing helix chain 'J' and resid 72 through 92 Processing helix chain 'J' and resid 130 through 135 Processing helix chain 'J' and resid 148 through 162 removed outlier: 4.536A pdb=" N HIS J 152 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 195 Processing helix chain 'K' and resid 42 through 57 Processing helix chain 'K' and resid 72 through 92 Processing helix chain 'K' and resid 130 through 135 Processing helix chain 'K' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS K 152 " --> pdb=" O VAL K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 195 Processing helix chain 'L' and resid 42 through 57 Processing helix chain 'L' and resid 72 through 92 Processing helix chain 'L' and resid 130 through 135 Processing helix chain 'L' and resid 148 through 162 removed outlier: 4.536A pdb=" N HIS L 152 " --> pdb=" O VAL L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 195 Processing helix chain 'M' and resid 42 through 57 Processing helix chain 'M' and resid 72 through 92 Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'M' and resid 148 through 162 removed outlier: 4.536A pdb=" N HIS M 152 " --> pdb=" O VAL M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 195 Processing helix chain 'N' and resid 42 through 57 Processing helix chain 'N' and resid 72 through 92 Processing helix chain 'N' and resid 130 through 135 Processing helix chain 'N' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS N 152 " --> pdb=" O VAL N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 195 Processing helix chain 'O' and resid 42 through 57 Processing helix chain 'O' and resid 72 through 92 Processing helix chain 'O' and resid 130 through 135 Processing helix chain 'O' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS O 152 " --> pdb=" O VAL O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 195 Processing helix chain 'P' and resid 42 through 57 Processing helix chain 'P' and resid 72 through 92 Processing helix chain 'P' and resid 130 through 135 Processing helix chain 'P' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS P 152 " --> pdb=" O VAL P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 195 Processing helix chain 'Q' and resid 42 through 57 Processing helix chain 'Q' and resid 72 through 92 Processing helix chain 'Q' and resid 130 through 135 Processing helix chain 'Q' and resid 148 through 162 removed outlier: 4.537A pdb=" N HIS Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 195 Processing helix chain 'R' and resid 42 through 57 Processing helix chain 'R' and resid 72 through 92 Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 195 Processing helix chain 'S' and resid 42 through 57 Processing helix chain 'S' and resid 72 through 92 Processing helix chain 'S' and resid 130 through 135 Processing helix chain 'S' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS S 152 " --> pdb=" O VAL S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 195 Processing helix chain 'T' and resid 42 through 57 Processing helix chain 'T' and resid 72 through 92 Processing helix chain 'T' and resid 130 through 135 Processing helix chain 'T' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS T 152 " --> pdb=" O VAL T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 174 through 195 Processing helix chain 'U' and resid 42 through 57 Processing helix chain 'U' and resid 72 through 92 Processing helix chain 'U' and resid 130 through 135 Processing helix chain 'U' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS U 152 " --> pdb=" O VAL U 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 195 Processing helix chain 'V' and resid 42 through 57 Processing helix chain 'V' and resid 72 through 92 Processing helix chain 'V' and resid 130 through 135 Processing helix chain 'V' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS V 152 " --> pdb=" O VAL V 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 174 through 195 Processing helix chain 'W' and resid 42 through 57 Processing helix chain 'W' and resid 72 through 92 Processing helix chain 'W' and resid 130 through 135 Processing helix chain 'W' and resid 148 through 162 removed outlier: 4.535A pdb=" N HIS W 152 " --> pdb=" O VAL W 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 174 through 195 Processing helix chain 'X' and resid 42 through 57 Processing helix chain 'X' and resid 72 through 92 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'X' and resid 148 through 162 removed outlier: 4.536A pdb=" N HIS X 152 " --> pdb=" O VAL X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 174 through 195 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.388A pdb=" N ALA A 37 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA A 64 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP A 39 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY A 66 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107 removed outlier: 6.670A pdb=" N LEU A 111 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR A 123 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 167 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 125 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL A 169 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 127 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.775A 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 removed outlier: 6.387A pdb=" N ALA B 37 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA B 64 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 39 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY B 66 " --> pdb=" O ASP B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107 removed outlier: 6.670A pdb=" N LEU B 111 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR B 123 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL B 167 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL B 125 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL B 169 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR B 127 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.774A 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 removed outlier: 6.388A pdb=" N ALA C 37 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA C 64 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP C 39 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLY C 66 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU C 111 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR C 123 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL C 167 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 125 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL C 169 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C 127 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.773A 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 removed outlier: 6.387A pdb=" N ALA D 37 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA D 64 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP D 39 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY D 66 " --> pdb=" O ASP D 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 100 through 107 removed outlier: 6.670A pdb=" N LEU D 111 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR D 123 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL D 167 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL D 125 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL D 169 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR D 127 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.774A 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 removed outlier: 6.387A pdb=" N ALA E 37 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA E 64 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP E 39 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY E 66 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU E 111 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR E 123 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL E 167 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL E 125 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL E 169 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR E 127 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.773A 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 removed outlier: 6.387A pdb=" N ALA F 37 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA F 64 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP F 39 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY F 66 " --> pdb=" O ASP F 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU F 111 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR F 123 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL F 167 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL F 125 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL F 169 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR F 127 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.772A 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 removed outlier: 6.388A pdb=" N ALA G 37 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA G 64 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP G 39 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY G 66 " --> pdb=" O ASP G 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU G 111 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR G 123 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL G 167 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL G 125 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL G 169 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR G 127 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.773A 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 removed outlier: 6.388A pdb=" N ALA H 37 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ALA H 64 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP H 39 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY H 66 " --> pdb=" O ASP H 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU H 111 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR H 123 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL H 167 " --> pdb=" O TYR H 123 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL H 125 " --> pdb=" O VAL H 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL H 169 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR H 127 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 7.773A 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 removed outlier: 6.387A pdb=" N ALA I 37 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA I 64 " --> pdb=" O ALA I 37 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP I 39 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY I 66 " --> pdb=" O ASP I 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU I 111 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR I 123 " --> pdb=" O LEU I 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL I 167 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL I 125 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL I 169 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR I 127 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 7.772A 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 removed outlier: 6.388A pdb=" N ALA J 37 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA J 64 " --> pdb=" O ALA J 37 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP J 39 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY J 66 " --> pdb=" O ASP J 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU J 111 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR J 123 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL J 167 " --> pdb=" O TYR J 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL J 125 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL J 169 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR J 127 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 7.773A 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 removed outlier: 6.387A pdb=" N ALA K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA K 64 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP K 39 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY K 66 " --> pdb=" O ASP K 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU K 111 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR K 123 " --> pdb=" O LEU K 165 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL K 167 " --> pdb=" O TYR K 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL K 125 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL K 169 " --> pdb=" O VAL K 125 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR K 127 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 7.773A 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 removed outlier: 6.388A pdb=" N ALA L 37 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA L 64 " --> pdb=" O ALA L 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP L 39 " --> pdb=" O ALA L 64 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLY L 66 " --> pdb=" O ASP L 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 100 through 107 removed outlier: 6.670A pdb=" N LEU L 111 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR L 123 " --> pdb=" O LEU L 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL L 167 " --> pdb=" O TYR L 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL L 125 " --> pdb=" O VAL L 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL L 169 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR L 127 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.772A 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 removed outlier: 6.388A pdb=" N ALA M 37 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA M 64 " --> pdb=" O ALA M 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP M 39 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY M 66 " --> pdb=" O ASP M 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 100 through 107 removed outlier: 6.670A pdb=" N LEU M 111 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR M 123 " --> pdb=" O LEU M 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL M 167 " --> pdb=" O TYR M 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL M 125 " --> pdb=" O VAL M 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL M 169 " --> pdb=" O VAL M 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR M 127 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 7.773A 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 removed outlier: 6.387A pdb=" N ALA N 37 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA N 64 " --> pdb=" O ALA N 37 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP N 39 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY N 66 " --> pdb=" O ASP N 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU N 111 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR N 123 " --> pdb=" O LEU N 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL N 167 " --> pdb=" O TYR N 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL N 125 " --> pdb=" O VAL N 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL N 169 " --> pdb=" O VAL N 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR N 127 " --> pdb=" O VAL N 169 " (cutoff:3.500A) removed outlier: 7.772A 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 removed outlier: 6.388A pdb=" N ALA O 37 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA O 64 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP O 39 " --> pdb=" O ALA O 64 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLY O 66 " --> pdb=" O ASP O 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU O 111 " --> pdb=" O LEU O 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR O 123 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL O 167 " --> pdb=" O TYR O 123 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL O 125 " --> pdb=" O VAL O 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL O 169 " --> pdb=" O VAL O 125 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR O 127 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 7.773A 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 removed outlier: 6.388A pdb=" N ALA P 37 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA P 64 " --> pdb=" O ALA P 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP P 39 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY P 66 " --> pdb=" O ASP P 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU P 111 " --> pdb=" O LEU P 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR P 123 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL P 167 " --> pdb=" O TYR P 123 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL P 125 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL P 169 " --> pdb=" O VAL P 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR P 127 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 7.772A 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 removed outlier: 6.388A pdb=" N ALA Q 37 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA Q 64 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP Q 39 " --> pdb=" O ALA Q 64 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY Q 66 " --> pdb=" O ASP Q 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 100 through 107 removed outlier: 6.670A pdb=" N LEU Q 111 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR Q 123 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL Q 167 " --> pdb=" O TYR Q 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL Q 125 " --> pdb=" O VAL Q 167 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL Q 169 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR Q 127 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 7.774A 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 removed outlier: 6.387A pdb=" N ALA R 37 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA R 64 " --> pdb=" O ALA R 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP R 39 " --> pdb=" O ALA R 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY R 66 " --> pdb=" O ASP R 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 100 through 107 removed outlier: 6.670A pdb=" N LEU R 111 " --> pdb=" O LEU R 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR R 123 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL R 167 " --> pdb=" O TYR R 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL R 125 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL R 169 " --> pdb=" O VAL R 125 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR R 127 " --> pdb=" O VAL R 169 " (cutoff:3.500A) removed outlier: 7.774A 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 removed outlier: 6.387A pdb=" N ALA S 37 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA S 64 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP S 39 " --> pdb=" O ALA S 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY S 66 " --> pdb=" O ASP S 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU S 111 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR S 123 " --> pdb=" O LEU S 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL S 167 " --> pdb=" O TYR S 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL S 125 " --> pdb=" O VAL S 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL S 169 " --> pdb=" O VAL S 125 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR S 127 " --> pdb=" O VAL S 169 " (cutoff:3.500A) removed outlier: 7.774A 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 removed outlier: 6.388A pdb=" N ALA T 37 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ALA T 64 " --> pdb=" O ALA T 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP T 39 " --> pdb=" O ALA T 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY T 66 " --> pdb=" O ASP T 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU T 111 " --> pdb=" O LEU T 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR T 123 " --> pdb=" O LEU T 165 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL T 167 " --> pdb=" O TYR T 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL T 125 " --> pdb=" O VAL T 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL T 169 " --> pdb=" O VAL T 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR T 127 " --> pdb=" O VAL T 169 " (cutoff:3.500A) removed outlier: 7.774A 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 removed outlier: 6.387A pdb=" N ALA U 37 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA U 64 " --> pdb=" O ALA U 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP U 39 " --> pdb=" O ALA U 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY U 66 " --> pdb=" O ASP U 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU U 111 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR U 123 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL U 167 " --> pdb=" O TYR U 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL U 125 " --> pdb=" O VAL U 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL U 169 " --> pdb=" O VAL U 125 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR U 127 " --> pdb=" O VAL U 169 " (cutoff:3.500A) removed outlier: 7.775A 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 removed outlier: 6.388A pdb=" N ALA V 37 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA V 64 " --> pdb=" O ALA V 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP V 39 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY V 66 " --> pdb=" O ASP V 39 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU V 111 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR V 123 " --> pdb=" O LEU V 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL V 167 " --> pdb=" O TYR V 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL V 125 " --> pdb=" O VAL V 167 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL V 169 " --> pdb=" O VAL V 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR V 127 " --> pdb=" O VAL V 169 " (cutoff:3.500A) removed outlier: 7.773A 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 removed outlier: 6.388A pdb=" N ALA W 37 " --> pdb=" O VAL W 62 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ALA W 64 " --> pdb=" O ALA W 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP W 39 " --> pdb=" O ALA W 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY W 66 " --> pdb=" O ASP W 39 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 100 through 107 removed outlier: 6.671A pdb=" N LEU W 111 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR W 123 " --> pdb=" O LEU W 165 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL W 167 " --> pdb=" O TYR W 123 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL W 125 " --> pdb=" O VAL W 167 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL W 169 " --> pdb=" O VAL W 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR W 127 " --> pdb=" O VAL W 169 " (cutoff:3.500A) removed outlier: 7.774A 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 removed outlier: 6.388A pdb=" N ALA X 37 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA X 64 " --> pdb=" O ALA X 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP X 39 " --> pdb=" O ALA X 64 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY X 66 " --> pdb=" O ASP X 39 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 100 through 107 removed outlier: 6.669A pdb=" N LEU X 111 " --> pdb=" O LEU X 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR X 123 " --> pdb=" O LEU X 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL X 167 " --> pdb=" O TYR X 123 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL X 125 " --> pdb=" O VAL X 167 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL X 169 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR X 127 " --> pdb=" O VAL X 169 " (cutoff:3.500A) removed outlier: 7.775A 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 2184 hydrogen bonds defined for protein. 6048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.73 Time building geometry restraints manager: 4.16 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: 12667 1.34 - 1.46: 7437 1.46 - 1.58: 15752 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 35976 Sorted by residual: bond pdb=" C VAL C 143 " pdb=" N PRO C 144 " ideal model delta sigma weight residual 1.328 1.354 -0.026 1.26e-02 6.30e+03 4.12e+00 bond pdb=" C ARG M 121 " pdb=" N PRO M 122 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.19e-02 7.06e+03 4.10e+00 bond pdb=" C ARG L 121 " pdb=" N PRO L 122 " ideal model delta sigma weight residual 1.330 1.354 -0.023 1.19e-02 7.06e+03 3.88e+00 bond pdb=" C ARG J 121 " pdb=" N PRO J 122 " ideal model delta sigma weight residual 1.330 1.354 -0.023 1.19e-02 7.06e+03 3.88e+00 bond pdb=" C VAL F 143 " pdb=" N PRO F 144 " ideal model delta sigma weight residual 1.328 1.353 -0.025 1.26e-02 6.30e+03 3.87e+00 ... (remaining 35971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 37486 1.26 - 2.52: 9524 2.52 - 3.79: 1687 3.79 - 5.05: 191 5.05 - 6.31: 24 Bond angle restraints: 48912 Sorted by residual: angle pdb=" CA ASP M 93 " pdb=" CB ASP M 93 " pdb=" CG ASP M 93 " ideal model delta sigma weight residual 112.60 116.24 -3.64 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA ASP V 117 " pdb=" CB ASP V 117 " pdb=" CG ASP V 117 " ideal model delta sigma weight residual 112.60 116.20 -3.60 1.00e+00 1.00e+00 1.30e+01 angle pdb=" CA ASP W 117 " pdb=" CB ASP W 117 " pdb=" CG ASP W 117 " ideal model delta sigma weight residual 112.60 116.20 -3.60 1.00e+00 1.00e+00 1.30e+01 angle pdb=" CA ASP B 117 " pdb=" CB ASP B 117 " pdb=" CG ASP B 117 " ideal model delta sigma weight residual 112.60 116.20 -3.60 1.00e+00 1.00e+00 1.30e+01 angle pdb=" CA ASP J 93 " pdb=" CB ASP J 93 " pdb=" CG ASP J 93 " ideal model delta sigma weight residual 112.60 116.20 -3.60 1.00e+00 1.00e+00 1.29e+01 ... (remaining 48907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 19760 16.41 - 32.82: 1312 32.82 - 49.22: 240 49.22 - 65.63: 96 65.63 - 82.04: 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 180.00 156.63 23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE V 58 " pdb=" C PHE V 58 " pdb=" N ASP V 59 " pdb=" CA ASP V 59 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE B 58 " pdb=" C PHE B 58 " pdb=" N ASP B 59 " pdb=" CA ASP B 59 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 21477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3065 0.044 - 0.088: 1382 0.088 - 0.131: 965 0.131 - 0.175: 127 0.175 - 0.219: 53 Chirality restraints: 5592 Sorted by residual: chirality pdb=" CA ASP G 108 " pdb=" N ASP G 108 " pdb=" C ASP G 108 " pdb=" CB ASP G 108 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP E 108 " pdb=" N ASP E 108 " pdb=" C ASP E 108 " pdb=" CB ASP E 108 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP S 108 " pdb=" N ASP S 108 " pdb=" C ASP S 108 " pdb=" CB ASP S 108 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 5589 not shown) Planarity restraints: 6504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 188 " -0.126 9.50e-02 1.11e+02 5.63e-02 2.02e+00 pdb=" NE ARG A 188 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 188 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 188 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 188 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 188 " 0.125 9.50e-02 1.11e+02 5.59e-02 2.00e+00 pdb=" NE ARG Q 188 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG Q 188 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 188 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 188 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 188 " -0.124 9.50e-02 1.11e+02 5.56e-02 1.98e+00 pdb=" NE ARG H 188 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG H 188 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG H 188 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 188 " -0.003 2.00e-02 2.50e+03 ... (remaining 6501 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1776 2.74 - 3.28: 34953 3.28 - 3.82: 61312 3.82 - 4.36: 76891 4.36 - 4.90: 131068 Nonbonded interactions: 306000 Sorted by model distance: nonbonded pdb=" OE1 GLU Q 77 " pdb="MN MN Q 301 " model vdw 2.198 3.060 nonbonded pdb="MN MN D 302 " pdb=" O HOH D 402 " model vdw 2.200 3.060 nonbonded pdb="MN MN Q 302 " pdb=" O HOH Q 402 " model vdw 2.200 3.060 nonbonded pdb="MN MN W 302 " pdb=" O HOH W 402 " model vdw 2.200 3.060 nonbonded pdb="MN MN E 302 " pdb=" O HOH E 402 " model vdw 2.200 3.060 ... (remaining 305995 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: 0.16 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: 1.990 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.680 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.120 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 0.030 35976 Z= 0.480 Angle : 1.145 6.310 48912 Z= 0.810 Chirality : 0.066 0.219 5592 Planarity : 0.008 0.056 6504 Dihedral : 13.561 82.039 13032 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.12), residues: 4512 helix: -0.13 (0.11), residues: 1872 sheet: -0.25 (0.14), residues: 1488 loop : -2.00 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG U 151 TYR 0.008 0.002 TYR F 123 PHE 0.009 0.002 PHE A 58 HIS 0.006 0.002 HIS P 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.48 (35976) covalent geometry : angle 1.14462 / 0.81 (48912) hydrogen bonds : bond 0.16389 / 11.73 ( 2184) hydrogen bonds : angle 6.28104 / 4.55 ( 6048) *********************** 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 960 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 960 time to evaluate : 1.353 Fit side-chains REVERT: A 29 ASP cc_start: 0.7818 (t0) cc_final: 0.7466 (t70) REVERT: A 39 ASP cc_start: 0.7800 (t0) cc_final: 0.7463 (t70) REVERT: A 63 ARG cc_start: 0.7941 (ttt180) cc_final: 0.7502 (mtm-85) REVERT: A 89 GLN cc_start: 0.8096 (tt0) cc_final: 0.7877 (tt0) REVERT: A 95 ARG cc_start: 0.8668 (ttt180) cc_final: 0.8054 (ttm-80) REVERT: A 107 MET cc_start: 0.8367 (ttt) cc_final: 0.8048 (ttt) REVERT: A 162 ARG cc_start: 0.7754 (mtt180) cc_final: 0.7406 (mtp85) REVERT: B 29 ASP cc_start: 0.7818 (t0) cc_final: 0.7469 (t70) REVERT: B 39 ASP cc_start: 0.7800 (t0) cc_final: 0.7464 (t70) REVERT: B 63 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7500 (mtm-85) REVERT: B 89 GLN cc_start: 0.8063 (tt0) cc_final: 0.7849 (tt0) REVERT: B 93 ASP cc_start: 0.7906 (p0) cc_final: 0.7570 (p0) REVERT: B 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8008 (ttm-80) REVERT: B 107 MET cc_start: 0.8366 (ttt) cc_final: 0.8051 (ttt) REVERT: B 162 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7451 (mtp85) REVERT: C 29 ASP cc_start: 0.7824 (t0) cc_final: 0.7476 (t70) REVERT: C 39 ASP cc_start: 0.7935 (t0) cc_final: 0.7589 (t70) REVERT: C 63 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7499 (mtm-85) REVERT: C 89 GLN cc_start: 0.8065 (tt0) cc_final: 0.7851 (tt0) REVERT: C 93 ASP cc_start: 0.7906 (p0) cc_final: 0.7571 (p0) REVERT: C 95 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: C 107 MET cc_start: 0.8366 (ttt) cc_final: 0.8051 (ttt) REVERT: C 162 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7452 (mtp85) REVERT: D 29 ASP cc_start: 0.7818 (t0) cc_final: 0.7468 (t70) REVERT: D 39 ASP cc_start: 0.7798 (t0) cc_final: 0.7464 (t70) REVERT: D 63 ARG cc_start: 0.7924 (ttt180) cc_final: 0.7500 (mtm-85) REVERT: D 89 GLN cc_start: 0.8065 (tt0) cc_final: 0.7851 (tt0) REVERT: D 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7568 (p0) REVERT: D 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: D 107 MET cc_start: 0.8366 (ttt) cc_final: 0.8053 (ttt) REVERT: D 162 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7450 (mtp85) REVERT: E 29 ASP cc_start: 0.7818 (t0) cc_final: 0.7469 (t70) REVERT: E 39 ASP cc_start: 0.7935 (t0) cc_final: 0.7590 (t70) REVERT: E 63 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7500 (mtm-85) REVERT: E 89 GLN cc_start: 0.8065 (tt0) cc_final: 0.7850 (tt0) REVERT: E 93 ASP cc_start: 0.7906 (p0) cc_final: 0.7570 (p0) REVERT: E 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: E 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8050 (ttt) REVERT: E 162 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7451 (mtp85) REVERT: F 29 ASP cc_start: 0.7816 (t0) cc_final: 0.7470 (t70) REVERT: F 39 ASP cc_start: 0.7937 (t0) cc_final: 0.7591 (t70) REVERT: F 63 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7501 (mtm-85) REVERT: F 89 GLN cc_start: 0.8065 (tt0) cc_final: 0.7851 (tt0) REVERT: F 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7568 (p0) REVERT: F 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: F 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8052 (ttt) REVERT: F 162 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7451 (mtp85) REVERT: G 29 ASP cc_start: 0.7814 (t0) cc_final: 0.7465 (t70) REVERT: G 39 ASP cc_start: 0.7937 (t0) cc_final: 0.7589 (t70) REVERT: G 63 ARG cc_start: 0.7926 (ttt180) cc_final: 0.7502 (mtm-85) REVERT: G 89 GLN cc_start: 0.8065 (tt0) cc_final: 0.7851 (tt0) REVERT: G 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7569 (p0) REVERT: G 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: G 107 MET cc_start: 0.8364 (ttt) cc_final: 0.8049 (ttt) REVERT: G 162 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7449 (mtp85) REVERT: H 29 ASP cc_start: 0.7823 (t0) cc_final: 0.7476 (t70) REVERT: H 39 ASP cc_start: 0.7935 (t0) cc_final: 0.7589 (t70) REVERT: H 63 ARG cc_start: 0.7937 (ttt180) cc_final: 0.7499 (mtm-85) REVERT: H 89 GLN cc_start: 0.8065 (tt0) cc_final: 0.7850 (tt0) REVERT: H 93 ASP cc_start: 0.7906 (p0) cc_final: 0.7570 (p0) REVERT: H 95 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8008 (ttm-80) REVERT: H 107 MET cc_start: 0.8366 (ttt) cc_final: 0.8053 (ttt) REVERT: H 162 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7452 (mtp85) REVERT: I 29 ASP cc_start: 0.7815 (t0) cc_final: 0.7469 (t70) REVERT: I 39 ASP cc_start: 0.7937 (t0) cc_final: 0.7591 (t70) REVERT: I 63 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7501 (mtm-85) REVERT: I 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7850 (tt0) REVERT: I 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7568 (p0) REVERT: I 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: I 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8052 (ttt) REVERT: I 162 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7451 (mtp85) REVERT: J 29 ASP cc_start: 0.7817 (t0) cc_final: 0.7467 (t70) REVERT: J 39 ASP cc_start: 0.7936 (t0) cc_final: 0.7590 (t70) REVERT: J 63 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7500 (mtm-85) REVERT: J 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7850 (tt0) REVERT: J 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7569 (p0) REVERT: J 95 ARG cc_start: 0.8615 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: J 107 MET cc_start: 0.8364 (ttt) cc_final: 0.8049 (ttt) REVERT: J 162 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7450 (mtp85) REVERT: K 29 ASP cc_start: 0.7816 (t0) cc_final: 0.7467 (t70) REVERT: K 39 ASP cc_start: 0.7800 (t0) cc_final: 0.7465 (t70) REVERT: K 63 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7500 (mtm-85) REVERT: K 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7850 (tt0) REVERT: K 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7569 (p0) REVERT: K 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: K 107 MET cc_start: 0.8364 (ttt) cc_final: 0.8051 (ttt) REVERT: K 162 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7450 (mtp85) REVERT: L 29 ASP cc_start: 0.7820 (t0) cc_final: 0.7471 (t70) REVERT: L 39 ASP cc_start: 0.7937 (t0) cc_final: 0.7589 (t70) REVERT: L 63 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7501 (mtm-85) REVERT: L 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7851 (tt0) REVERT: L 93 ASP cc_start: 0.7906 (p0) cc_final: 0.7568 (p0) REVERT: L 95 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8008 (ttm-80) REVERT: L 107 MET cc_start: 0.8363 (ttt) cc_final: 0.8051 (ttt) REVERT: L 162 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7451 (mtp85) REVERT: M 29 ASP cc_start: 0.7815 (t0) cc_final: 0.7466 (t70) REVERT: M 39 ASP cc_start: 0.7801 (t0) cc_final: 0.7464 (t70) REVERT: M 63 ARG cc_start: 0.7940 (ttt180) cc_final: 0.7501 (mtm-85) REVERT: M 89 GLN cc_start: 0.8065 (tt0) cc_final: 0.7851 (tt0) REVERT: M 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7569 (p0) REVERT: M 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8006 (ttm-80) REVERT: M 107 MET cc_start: 0.8363 (ttt) cc_final: 0.8047 (ttt) REVERT: M 162 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7450 (mtp85) REVERT: N 29 ASP cc_start: 0.7816 (t0) cc_final: 0.7467 (t70) REVERT: N 39 ASP cc_start: 0.7938 (t0) cc_final: 0.7590 (t70) REVERT: N 63 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7501 (mtm-85) REVERT: N 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7850 (tt0) REVERT: N 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7567 (p0) REVERT: N 95 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8008 (ttm-80) REVERT: N 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8050 (ttt) REVERT: N 162 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7451 (mtp85) REVERT: O 29 ASP cc_start: 0.7823 (t0) cc_final: 0.7476 (t70) REVERT: O 39 ASP cc_start: 0.7935 (t0) cc_final: 0.7590 (t70) REVERT: O 63 ARG cc_start: 0.7923 (ttt180) cc_final: 0.7500 (mtm-85) REVERT: O 89 GLN cc_start: 0.8065 (tt0) cc_final: 0.7850 (tt0) REVERT: O 93 ASP cc_start: 0.7907 (p0) cc_final: 0.7571 (p0) REVERT: O 95 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8008 (ttm-80) REVERT: O 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8052 (ttt) REVERT: O 162 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7451 (mtp85) REVERT: P 29 ASP cc_start: 0.7816 (t0) cc_final: 0.7467 (t70) REVERT: P 39 ASP cc_start: 0.7938 (t0) cc_final: 0.7590 (t70) REVERT: P 63 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7500 (mtm-85) REVERT: P 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7850 (tt0) REVERT: P 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7568 (p0) REVERT: P 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: P 107 MET cc_start: 0.8364 (ttt) cc_final: 0.8050 (ttt) REVERT: P 162 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7452 (mtp85) REVERT: Q 29 ASP cc_start: 0.7821 (t0) cc_final: 0.7472 (t70) REVERT: Q 39 ASP cc_start: 0.7803 (t0) cc_final: 0.7467 (t70) REVERT: Q 63 ARG cc_start: 0.7928 (ttt180) cc_final: 0.7502 (mtm-85) REVERT: Q 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7848 (tt0) REVERT: Q 95 ARG cc_start: 0.8669 (ttt180) cc_final: 0.8054 (ttm-80) REVERT: Q 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8051 (ttt) REVERT: Q 162 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7451 (mtp85) REVERT: R 29 ASP cc_start: 0.7820 (t0) cc_final: 0.7471 (t70) REVERT: R 39 ASP cc_start: 0.7801 (t0) cc_final: 0.7465 (t70) REVERT: R 63 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7501 (mtm-85) REVERT: R 89 GLN cc_start: 0.8063 (tt0) cc_final: 0.7850 (tt0) REVERT: R 93 ASP cc_start: 0.7906 (p0) cc_final: 0.7571 (p0) REVERT: R 95 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8008 (ttm-80) REVERT: R 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8051 (ttt) REVERT: R 162 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7452 (mtp85) REVERT: S 29 ASP cc_start: 0.7820 (t0) cc_final: 0.7470 (t70) REVERT: S 39 ASP cc_start: 0.7801 (t0) cc_final: 0.7465 (t70) REVERT: S 63 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7500 (mtm-85) REVERT: S 89 GLN cc_start: 0.8063 (tt0) cc_final: 0.7849 (tt0) REVERT: S 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7570 (p0) REVERT: S 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: S 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8051 (ttt) REVERT: S 162 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7451 (mtp85) REVERT: T 29 ASP cc_start: 0.7817 (t0) cc_final: 0.7466 (t70) REVERT: T 39 ASP cc_start: 0.7937 (t0) cc_final: 0.7589 (t70) REVERT: T 63 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7501 (mtm-85) REVERT: T 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7850 (tt0) REVERT: T 93 ASP cc_start: 0.7903 (p0) cc_final: 0.7568 (p0) REVERT: T 95 ARG cc_start: 0.8668 (ttt180) cc_final: 0.8058 (ttm-80) REVERT: T 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8052 (ttt) REVERT: T 162 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7452 (mtp85) REVERT: U 29 ASP cc_start: 0.7818 (t0) cc_final: 0.7468 (t70) REVERT: U 39 ASP cc_start: 0.7798 (t0) cc_final: 0.7464 (t70) REVERT: U 63 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7500 (mtm-85) REVERT: U 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7849 (tt0) REVERT: U 93 ASP cc_start: 0.7906 (p0) cc_final: 0.7569 (p0) REVERT: U 95 ARG cc_start: 0.8663 (ttt180) cc_final: 0.8055 (ttm-80) REVERT: U 107 MET cc_start: 0.8366 (ttt) cc_final: 0.8051 (ttt) REVERT: U 162 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7450 (mtp85) REVERT: V 29 ASP cc_start: 0.7814 (t0) cc_final: 0.7465 (t70) REVERT: V 39 ASP cc_start: 0.7939 (t0) cc_final: 0.7590 (t70) REVERT: V 63 ARG cc_start: 0.7940 (ttt180) cc_final: 0.7501 (mtm-85) REVERT: V 89 GLN cc_start: 0.8064 (tt0) cc_final: 0.7850 (tt0) REVERT: V 93 ASP cc_start: 0.7904 (p0) cc_final: 0.7568 (p0) REVERT: V 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8007 (ttm-80) REVERT: V 107 MET cc_start: 0.8364 (ttt) cc_final: 0.8048 (ttt) REVERT: V 162 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7450 (mtp85) REVERT: W 29 ASP cc_start: 0.7818 (t0) cc_final: 0.7469 (t70) REVERT: W 39 ASP cc_start: 0.7800 (t0) cc_final: 0.7464 (t70) REVERT: W 63 ARG cc_start: 0.7937 (ttt180) cc_final: 0.7499 (mtm-85) REVERT: W 89 GLN cc_start: 0.8063 (tt0) cc_final: 0.7849 (tt0) REVERT: W 93 ASP cc_start: 0.7905 (p0) cc_final: 0.7570 (p0) REVERT: W 95 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8008 (ttm-80) REVERT: W 107 MET cc_start: 0.8365 (ttt) cc_final: 0.8050 (ttt) REVERT: W 162 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7450 (mtp85) REVERT: X 29 ASP cc_start: 0.7819 (t0) cc_final: 0.7470 (t70) REVERT: X 39 ASP cc_start: 0.7802 (t0) cc_final: 0.7464 (t70) REVERT: X 63 ARG cc_start: 0.7926 (ttt180) cc_final: 0.7502 (mtm-85) REVERT: X 89 GLN cc_start: 0.8065 (tt0) cc_final: 0.7852 (tt0) REVERT: X 93 ASP cc_start: 0.7904 (p0) cc_final: 0.7568 (p0) REVERT: X 95 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8008 (ttm-80) REVERT: X 107 MET cc_start: 0.8367 (ttt) cc_final: 0.8056 (ttt) REVERT: X 162 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7451 (mtp85) outliers start: 0 outliers final: 0 residues processed: 960 average time/residue: 0.2548 time to fit residues: 368.5313 Evaluate side-chains 864 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 864 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.112864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.087429 restraints weight = 41053.812| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.90 r_work: 0.2662 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 35976 Z= 0.147 Angle : 0.527 3.936 48912 Z= 0.289 Chirality : 0.045 0.127 5592 Planarity : 0.004 0.025 6504 Dihedral : 4.892 17.315 5088 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.66 % Allowed : 7.29 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4512 helix: 1.82 (0.12), residues: 1872 sheet: 0.09 (0.14), residues: 1488 loop : -1.07 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 99 TYR 0.007 0.001 TYR F 145 PHE 0.011 0.002 PHE H 104 HIS 0.006 0.001 HIS X 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (35976) covalent geometry : angle 0.52734 / 0.29 (48912) hydrogen bonds : bond 0.03636 / 2.58 ( 2184) hydrogen bonds : angle 3.98837 / 2.87 ( 6048) *********************** 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 982 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 958 time to evaluate : 1.320 Fit side-chains REVERT: A 39 ASP cc_start: 0.8305 (t0) cc_final: 0.7894 (t70) REVERT: A 63 ARG cc_start: 0.8425 (ttt180) cc_final: 0.8151 (mtm-85) REVERT: A 89 GLN cc_start: 0.8640 (tt0) cc_final: 0.8420 (tt0) REVERT: A 93 ASP cc_start: 0.8152 (p0) cc_final: 0.7879 (p0) REVERT: A 117 ASP cc_start: 0.8500 (t0) cc_final: 0.8189 (t0) REVERT: A 192 GLN cc_start: 0.9144 (tt0) cc_final: 0.8762 (tt0) REVERT: B 39 ASP cc_start: 0.8306 (t0) cc_final: 0.7916 (t70) REVERT: B 63 ARG cc_start: 0.8417 (ttt180) cc_final: 0.8147 (mtm-85) REVERT: B 89 GLN cc_start: 0.8637 (tt0) cc_final: 0.8414 (tt0) REVERT: B 93 ASP cc_start: 0.8242 (p0) cc_final: 0.8001 (p0) REVERT: B 117 ASP cc_start: 0.8471 (t0) cc_final: 0.8150 (t0) REVERT: B 192 GLN cc_start: 0.9138 (tt0) cc_final: 0.8767 (tt0) REVERT: C 39 ASP cc_start: 0.8310 (t0) cc_final: 0.7918 (t70) REVERT: C 63 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8150 (mtm-85) REVERT: C 89 GLN cc_start: 0.8637 (tt0) cc_final: 0.8414 (tt0) REVERT: C 93 ASP cc_start: 0.8227 (p0) cc_final: 0.7990 (p0) REVERT: C 117 ASP cc_start: 0.8476 (t0) cc_final: 0.8152 (t0) REVERT: C 192 GLN cc_start: 0.9136 (tt0) cc_final: 0.8761 (tt0) REVERT: D 39 ASP cc_start: 0.8284 (t0) cc_final: 0.7907 (t70) REVERT: D 63 ARG cc_start: 0.8410 (ttt180) cc_final: 0.8145 (mtm-85) REVERT: D 89 GLN cc_start: 0.8634 (tt0) cc_final: 0.8411 (tt0) REVERT: D 93 ASP cc_start: 0.8225 (p0) cc_final: 0.7986 (p0) REVERT: D 117 ASP cc_start: 0.8477 (t0) cc_final: 0.8154 (t0) REVERT: D 192 GLN cc_start: 0.9137 (tt0) cc_final: 0.8761 (tt0) REVERT: E 39 ASP cc_start: 0.8299 (t0) cc_final: 0.7905 (t70) REVERT: E 63 ARG cc_start: 0.8414 (ttt180) cc_final: 0.8145 (mtm-85) REVERT: E 89 GLN cc_start: 0.8643 (tt0) cc_final: 0.8420 (tt0) REVERT: E 93 ASP cc_start: 0.8226 (p0) cc_final: 0.7987 (p0) REVERT: E 117 ASP cc_start: 0.8478 (t0) cc_final: 0.8176 (t0) REVERT: E 192 GLN cc_start: 0.9139 (tt0) cc_final: 0.8753 (tt0) REVERT: F 39 ASP cc_start: 0.8306 (t0) cc_final: 0.7918 (t70) REVERT: F 63 ARG cc_start: 0.8417 (ttt180) cc_final: 0.8144 (mtm-85) REVERT: F 89 GLN cc_start: 0.8633 (tt0) cc_final: 0.8410 (tt0) REVERT: F 93 ASP cc_start: 0.8246 (p0) cc_final: 0.8007 (p0) REVERT: F 117 ASP cc_start: 0.8475 (t0) cc_final: 0.8172 (t0) REVERT: F 192 GLN cc_start: 0.9137 (tt0) cc_final: 0.8751 (tt0) REVERT: G 39 ASP cc_start: 0.8312 (t0) cc_final: 0.7921 (t70) REVERT: G 63 ARG cc_start: 0.8390 (ttt180) cc_final: 0.8142 (mtm-85) REVERT: G 89 GLN cc_start: 0.8633 (tt0) cc_final: 0.8411 (tt0) REVERT: G 93 ASP cc_start: 0.8237 (p0) cc_final: 0.7995 (p0) REVERT: G 117 ASP cc_start: 0.8463 (t0) cc_final: 0.8139 (t0) REVERT: G 192 GLN cc_start: 0.9138 (tt0) cc_final: 0.8764 (tt0) REVERT: H 39 ASP cc_start: 0.8309 (t0) cc_final: 0.7917 (t70) REVERT: H 63 ARG cc_start: 0.8429 (ttt180) cc_final: 0.8148 (mtm-85) REVERT: H 89 GLN cc_start: 0.8637 (tt0) cc_final: 0.8413 (tt0) REVERT: H 93 ASP cc_start: 0.8230 (p0) cc_final: 0.7994 (p0) REVERT: H 117 ASP cc_start: 0.8477 (t0) cc_final: 0.8155 (t0) REVERT: H 192 GLN cc_start: 0.9137 (tt0) cc_final: 0.8763 (tt0) REVERT: I 39 ASP cc_start: 0.8306 (t0) cc_final: 0.7919 (t70) REVERT: I 63 ARG cc_start: 0.8417 (ttt180) cc_final: 0.8144 (mtm-85) REVERT: I 89 GLN cc_start: 0.8632 (tt0) cc_final: 0.8410 (tt0) REVERT: I 93 ASP cc_start: 0.8242 (p0) cc_final: 0.8002 (p0) REVERT: I 117 ASP cc_start: 0.8474 (t0) cc_final: 0.8169 (t0) REVERT: I 192 GLN cc_start: 0.9136 (tt0) cc_final: 0.8759 (tt0) REVERT: J 39 ASP cc_start: 0.8314 (t0) cc_final: 0.7923 (t70) REVERT: J 63 ARG cc_start: 0.8421 (ttt180) cc_final: 0.8151 (mtm-85) REVERT: J 89 GLN cc_start: 0.8633 (tt0) cc_final: 0.8413 (tt0) REVERT: J 93 ASP cc_start: 0.8239 (p0) cc_final: 0.7995 (p0) REVERT: J 117 ASP cc_start: 0.8486 (t0) cc_final: 0.8167 (t0) REVERT: J 192 GLN cc_start: 0.9146 (tt0) cc_final: 0.8764 (tt0) REVERT: K 39 ASP cc_start: 0.8315 (t0) cc_final: 0.7922 (t70) REVERT: K 63 ARG cc_start: 0.8429 (ttt180) cc_final: 0.8152 (mtm-85) REVERT: K 89 GLN cc_start: 0.8631 (tt0) cc_final: 0.8410 (tt0) REVERT: K 93 ASP cc_start: 0.8240 (p0) cc_final: 0.7995 (p0) REVERT: K 117 ASP cc_start: 0.8485 (t0) cc_final: 0.8168 (t0) REVERT: K 192 GLN cc_start: 0.9145 (tt0) cc_final: 0.8771 (tt0) REVERT: L 39 ASP cc_start: 0.8287 (t0) cc_final: 0.7899 (t70) REVERT: L 63 ARG cc_start: 0.8423 (ttt180) cc_final: 0.8144 (mtm-85) REVERT: L 89 GLN cc_start: 0.8637 (tt0) cc_final: 0.8412 (tt0) REVERT: L 93 ASP cc_start: 0.8238 (p0) cc_final: 0.7995 (p0) REVERT: L 117 ASP cc_start: 0.8468 (t0) cc_final: 0.8163 (t0) REVERT: L 192 GLN cc_start: 0.9134 (tt0) cc_final: 0.8754 (tt0) REVERT: M 39 ASP cc_start: 0.8311 (t0) cc_final: 0.7926 (t70) REVERT: M 63 ARG cc_start: 0.8387 (ttt180) cc_final: 0.8141 (mtm-85) REVERT: M 89 GLN cc_start: 0.8634 (tt0) cc_final: 0.8411 (tt0) REVERT: M 93 ASP cc_start: 0.8238 (p0) cc_final: 0.7997 (p0) REVERT: M 117 ASP cc_start: 0.8468 (t0) cc_final: 0.8144 (t0) REVERT: M 192 GLN cc_start: 0.9138 (tt0) cc_final: 0.8764 (tt0) REVERT: N 39 ASP cc_start: 0.8309 (t0) cc_final: 0.7918 (t70) REVERT: N 63 ARG cc_start: 0.8406 (ttt180) cc_final: 0.8141 (mtm-85) REVERT: N 89 GLN cc_start: 0.8637 (tt0) cc_final: 0.8415 (tt0) REVERT: N 93 ASP cc_start: 0.8238 (p0) cc_final: 0.7995 (p0) REVERT: N 117 ASP cc_start: 0.8466 (t0) cc_final: 0.8142 (t0) REVERT: N 192 GLN cc_start: 0.9131 (tt0) cc_final: 0.8755 (tt0) REVERT: O 39 ASP cc_start: 0.8303 (t0) cc_final: 0.7915 (t70) REVERT: O 63 ARG cc_start: 0.8426 (ttt180) cc_final: 0.8150 (mtm-85) REVERT: O 89 GLN cc_start: 0.8635 (tt0) cc_final: 0.8411 (tt0) REVERT: O 93 ASP cc_start: 0.8233 (p0) cc_final: 0.7995 (p0) REVERT: O 117 ASP cc_start: 0.8475 (t0) cc_final: 0.8173 (t0) REVERT: O 192 GLN cc_start: 0.9138 (tt0) cc_final: 0.8764 (tt0) REVERT: P 39 ASP cc_start: 0.8308 (t0) cc_final: 0.7917 (t70) REVERT: P 63 ARG cc_start: 0.8408 (ttt180) cc_final: 0.8141 (mtm-85) REVERT: P 89 GLN cc_start: 0.8634 (tt0) cc_final: 0.8410 (tt0) REVERT: P 93 ASP cc_start: 0.8238 (p0) cc_final: 0.7994 (p0) REVERT: P 117 ASP cc_start: 0.8470 (t0) cc_final: 0.8144 (t0) REVERT: P 192 GLN cc_start: 0.9135 (tt0) cc_final: 0.8760 (tt0) REVERT: Q 39 ASP cc_start: 0.8294 (t0) cc_final: 0.7891 (t70) REVERT: Q 63 ARG cc_start: 0.8418 (ttt180) cc_final: 0.8144 (mtm-85) REVERT: Q 89 GLN cc_start: 0.8640 (tt0) cc_final: 0.8416 (tt0) REVERT: Q 93 ASP cc_start: 0.8151 (p0) cc_final: 0.7883 (p0) REVERT: Q 117 ASP cc_start: 0.8478 (t0) cc_final: 0.8152 (t0) REVERT: Q 192 GLN cc_start: 0.9135 (tt0) cc_final: 0.8758 (tt0) REVERT: R 39 ASP cc_start: 0.8288 (t0) cc_final: 0.7899 (t70) REVERT: R 63 ARG cc_start: 0.8425 (ttt180) cc_final: 0.8146 (mtm-85) REVERT: R 89 GLN cc_start: 0.8644 (tt0) cc_final: 0.8423 (tt0) REVERT: R 93 ASP cc_start: 0.8241 (p0) cc_final: 0.7997 (p0) REVERT: R 117 ASP cc_start: 0.8466 (t0) cc_final: 0.8139 (t0) REVERT: R 192 GLN cc_start: 0.9134 (tt0) cc_final: 0.8756 (tt0) REVERT: S 39 ASP cc_start: 0.8293 (t0) cc_final: 0.7919 (t70) REVERT: S 63 ARG cc_start: 0.8412 (ttt180) cc_final: 0.8150 (mtm-85) REVERT: S 89 GLN cc_start: 0.8638 (tt0) cc_final: 0.8417 (tt0) REVERT: S 93 ASP cc_start: 0.8242 (p0) cc_final: 0.8002 (p0) REVERT: S 117 ASP cc_start: 0.8472 (t0) cc_final: 0.8151 (t0) REVERT: S 192 GLN cc_start: 0.9139 (tt0) cc_final: 0.8768 (tt0) REVERT: T 39 ASP cc_start: 0.8292 (t0) cc_final: 0.7918 (t70) REVERT: T 63 ARG cc_start: 0.8411 (ttt180) cc_final: 0.8141 (mtm-85) REVERT: T 89 GLN cc_start: 0.8633 (tt0) cc_final: 0.8409 (tt0) REVERT: T 93 ASP cc_start: 0.8238 (p0) cc_final: 0.7994 (p0) REVERT: T 117 ASP cc_start: 0.8471 (t0) cc_final: 0.8147 (t0) REVERT: T 192 GLN cc_start: 0.9133 (tt0) cc_final: 0.8748 (tt0) REVERT: U 39 ASP cc_start: 0.8302 (t0) cc_final: 0.7908 (t70) REVERT: U 63 ARG cc_start: 0.8415 (ttt180) cc_final: 0.8146 (mtm-85) REVERT: U 89 GLN cc_start: 0.8635 (tt0) cc_final: 0.8414 (tt0) REVERT: U 93 ASP cc_start: 0.8222 (p0) cc_final: 0.7983 (p0) REVERT: U 117 ASP cc_start: 0.8478 (t0) cc_final: 0.8156 (t0) REVERT: U 192 GLN cc_start: 0.9138 (tt0) cc_final: 0.8753 (tt0) REVERT: V 39 ASP cc_start: 0.8315 (t0) cc_final: 0.7923 (t70) REVERT: V 63 ARG cc_start: 0.8392 (ttt180) cc_final: 0.8140 (mtm-85) REVERT: V 89 GLN cc_start: 0.8633 (tt0) cc_final: 0.8413 (tt0) REVERT: V 93 ASP cc_start: 0.8241 (p0) cc_final: 0.7997 (p0) REVERT: V 117 ASP cc_start: 0.8465 (t0) cc_final: 0.8141 (t0) REVERT: V 192 GLN cc_start: 0.9138 (tt0) cc_final: 0.8765 (tt0) REVERT: W 39 ASP cc_start: 0.8302 (t0) cc_final: 0.7917 (t70) REVERT: W 63 ARG cc_start: 0.8415 (ttt180) cc_final: 0.8148 (mtm-85) REVERT: W 89 GLN cc_start: 0.8628 (tt0) cc_final: 0.8405 (tt0) REVERT: W 93 ASP cc_start: 0.8238 (p0) cc_final: 0.7997 (p0) REVERT: W 117 ASP cc_start: 0.8468 (t0) cc_final: 0.8169 (t0) REVERT: W 192 GLN cc_start: 0.9138 (tt0) cc_final: 0.8768 (tt0) REVERT: X 39 ASP cc_start: 0.8285 (t0) cc_final: 0.7899 (t70) REVERT: X 63 ARG cc_start: 0.8425 (ttt180) cc_final: 0.8147 (mtm-85) REVERT: X 89 GLN cc_start: 0.8617 (tt0) cc_final: 0.8393 (tt0) REVERT: X 93 ASP cc_start: 0.8239 (p0) cc_final: 0.7994 (p0) REVERT: X 117 ASP cc_start: 0.8465 (t0) cc_final: 0.8161 (t0) REVERT: X 192 GLN cc_start: 0.9133 (tt0) cc_final: 0.8753 (tt0) outliers start: 24 outliers final: 24 residues processed: 958 average time/residue: 0.2854 time to fit residues: 401.7523 Evaluate side-chains 910 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 886 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain X residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 265 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 438 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 426 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 364 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 369 optimal weight: 0.0670 chunk 273 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.083584 restraints weight = 41055.362| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.99 r_work: 0.2614 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35976 Z= 0.178 Angle : 0.522 3.755 48912 Z= 0.284 Chirality : 0.045 0.131 5592 Planarity : 0.004 0.033 6504 Dihedral : 4.805 16.874 5088 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.66 % Allowed : 9.21 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.13), residues: 4512 helix: 2.18 (0.12), residues: 1872 sheet: 0.23 (0.14), residues: 1488 loop : -0.64 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 162 TYR 0.007 0.001 TYR S 45 PHE 0.010 0.002 PHE C 104 HIS 0.006 0.002 HIS R 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (35976) covalent geometry : angle 0.52226 / 0.28 (48912) hydrogen bonds : bond 0.04007 / 2.84 ( 2184) hydrogen bonds : angle 3.88713 / 2.80 ( 6048) *********************** 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 845 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 821 time to evaluate : 1.266 Fit side-chains REVERT: A 39 ASP cc_start: 0.8363 (t0) cc_final: 0.7937 (t70) REVERT: A 63 ARG cc_start: 0.8389 (ttt180) cc_final: 0.8073 (mtm-85) REVERT: A 89 GLN cc_start: 0.8637 (tt0) cc_final: 0.8372 (tt0) REVERT: A 117 ASP cc_start: 0.8517 (t0) cc_final: 0.8187 (t70) REVERT: A 119 SER cc_start: 0.8838 (m) cc_final: 0.8544 (t) REVERT: B 39 ASP cc_start: 0.8360 (t0) cc_final: 0.7939 (t70) REVERT: B 63 ARG cc_start: 0.8413 (ttt180) cc_final: 0.8095 (mtm-85) REVERT: B 89 GLN cc_start: 0.8638 (tt0) cc_final: 0.8379 (tt0) REVERT: B 117 ASP cc_start: 0.8503 (t0) cc_final: 0.8170 (t70) REVERT: B 119 SER cc_start: 0.8829 (m) cc_final: 0.8527 (t) REVERT: C 39 ASP cc_start: 0.8350 (t0) cc_final: 0.7929 (t70) REVERT: C 63 ARG cc_start: 0.8404 (ttt180) cc_final: 0.8082 (mtm-85) REVERT: C 89 GLN cc_start: 0.8649 (tt0) cc_final: 0.8389 (tt0) REVERT: C 117 ASP cc_start: 0.8515 (t0) cc_final: 0.8184 (t70) REVERT: C 119 SER cc_start: 0.8822 (m) cc_final: 0.8525 (t) REVERT: D 39 ASP cc_start: 0.8363 (t0) cc_final: 0.7933 (t70) REVERT: D 63 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8085 (mtm-85) REVERT: D 89 GLN cc_start: 0.8644 (tt0) cc_final: 0.8382 (tt0) REVERT: D 117 ASP cc_start: 0.8519 (t0) cc_final: 0.8189 (t70) REVERT: D 119 SER cc_start: 0.8839 (m) cc_final: 0.8541 (t) REVERT: E 39 ASP cc_start: 0.8363 (t0) cc_final: 0.7936 (t70) REVERT: E 63 ARG cc_start: 0.8401 (ttt180) cc_final: 0.8082 (mtm-85) REVERT: E 89 GLN cc_start: 0.8648 (tt0) cc_final: 0.8390 (tt0) REVERT: E 117 ASP cc_start: 0.8516 (t0) cc_final: 0.8188 (t70) REVERT: E 119 SER cc_start: 0.8842 (m) cc_final: 0.8547 (t) REVERT: F 39 ASP cc_start: 0.8364 (t0) cc_final: 0.7942 (t70) REVERT: F 63 ARG cc_start: 0.8414 (ttt180) cc_final: 0.8083 (mtm-85) REVERT: F 89 GLN cc_start: 0.8643 (tt0) cc_final: 0.8380 (tt0) REVERT: F 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8177 (t70) REVERT: F 119 SER cc_start: 0.8826 (m) cc_final: 0.8532 (t) REVERT: G 39 ASP cc_start: 0.8367 (t0) cc_final: 0.7942 (t70) REVERT: G 63 ARG cc_start: 0.8407 (ttt180) cc_final: 0.8088 (mtm-85) REVERT: G 89 GLN cc_start: 0.8641 (tt0) cc_final: 0.8380 (tt0) REVERT: G 117 ASP cc_start: 0.8508 (t0) cc_final: 0.8175 (t70) REVERT: G 119 SER cc_start: 0.8821 (m) cc_final: 0.8525 (t) REVERT: H 39 ASP cc_start: 0.8364 (t0) cc_final: 0.7943 (t70) REVERT: H 63 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8081 (mtm-85) REVERT: H 89 GLN cc_start: 0.8647 (tt0) cc_final: 0.8385 (tt0) REVERT: H 117 ASP cc_start: 0.8513 (t0) cc_final: 0.8179 (t70) REVERT: H 119 SER cc_start: 0.8819 (m) cc_final: 0.8524 (t) REVERT: I 39 ASP cc_start: 0.8359 (t0) cc_final: 0.7936 (t70) REVERT: I 63 ARG cc_start: 0.8412 (ttt180) cc_final: 0.8081 (mtm-85) REVERT: I 89 GLN cc_start: 0.8641 (tt0) cc_final: 0.8378 (tt0) REVERT: I 117 ASP cc_start: 0.8517 (t0) cc_final: 0.8186 (t70) REVERT: I 119 SER cc_start: 0.8833 (m) cc_final: 0.8540 (t) REVERT: J 39 ASP cc_start: 0.8369 (t0) cc_final: 0.7944 (t70) REVERT: J 63 ARG cc_start: 0.8391 (ttt180) cc_final: 0.8075 (mtm-85) REVERT: J 89 GLN cc_start: 0.8640 (tt0) cc_final: 0.8378 (tt0) REVERT: J 117 ASP cc_start: 0.8525 (t0) cc_final: 0.8192 (t70) REVERT: J 119 SER cc_start: 0.8835 (m) cc_final: 0.8535 (t) REVERT: K 39 ASP cc_start: 0.8372 (t0) cc_final: 0.7947 (t70) REVERT: K 63 ARG cc_start: 0.8396 (ttt180) cc_final: 0.8080 (mtm-85) REVERT: K 89 GLN cc_start: 0.8647 (tt0) cc_final: 0.8387 (tt0) REVERT: K 117 ASP cc_start: 0.8519 (t0) cc_final: 0.8184 (t70) REVERT: K 119 SER cc_start: 0.8839 (m) cc_final: 0.8538 (t) REVERT: K 192 GLN cc_start: 0.9200 (tt0) cc_final: 0.8920 (tt0) REVERT: L 39 ASP cc_start: 0.8347 (t0) cc_final: 0.7922 (t70) REVERT: L 63 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8091 (mtm-85) REVERT: L 89 GLN cc_start: 0.8641 (tt0) cc_final: 0.8378 (tt0) REVERT: L 117 ASP cc_start: 0.8530 (t0) cc_final: 0.8193 (t70) REVERT: L 119 SER cc_start: 0.8823 (m) cc_final: 0.8528 (t) REVERT: L 192 GLN cc_start: 0.9192 (tt0) cc_final: 0.8912 (tt0) REVERT: M 39 ASP cc_start: 0.8365 (t0) cc_final: 0.7942 (t70) REVERT: M 63 ARG cc_start: 0.8395 (ttt180) cc_final: 0.8083 (mtm-85) REVERT: M 89 GLN cc_start: 0.8648 (tt0) cc_final: 0.8387 (tt0) REVERT: M 117 ASP cc_start: 0.8518 (t0) cc_final: 0.8185 (t70) REVERT: M 119 SER cc_start: 0.8824 (m) cc_final: 0.8528 (t) REVERT: N 39 ASP cc_start: 0.8354 (t0) cc_final: 0.7930 (t70) REVERT: N 63 ARG cc_start: 0.8395 (ttt180) cc_final: 0.8081 (mtm-85) REVERT: N 89 GLN cc_start: 0.8630 (tt0) cc_final: 0.8371 (tt0) REVERT: N 117 ASP cc_start: 0.8525 (t0) cc_final: 0.8195 (t70) REVERT: N 119 SER cc_start: 0.8830 (m) cc_final: 0.8533 (t) REVERT: O 39 ASP cc_start: 0.8362 (t0) cc_final: 0.7939 (t70) REVERT: O 63 ARG cc_start: 0.8401 (ttt180) cc_final: 0.8083 (mtm-85) REVERT: O 89 GLN cc_start: 0.8646 (tt0) cc_final: 0.8385 (tt0) REVERT: O 117 ASP cc_start: 0.8515 (t0) cc_final: 0.8184 (t70) REVERT: O 119 SER cc_start: 0.8824 (m) cc_final: 0.8527 (t) REVERT: P 39 ASP cc_start: 0.8356 (t0) cc_final: 0.7934 (t70) REVERT: P 63 ARG cc_start: 0.8400 (ttt180) cc_final: 0.8080 (mtm-85) REVERT: P 89 GLN cc_start: 0.8632 (tt0) cc_final: 0.8371 (tt0) REVERT: P 117 ASP cc_start: 0.8520 (t0) cc_final: 0.8189 (t70) REVERT: P 119 SER cc_start: 0.8826 (m) cc_final: 0.8530 (t) REVERT: Q 39 ASP cc_start: 0.8360 (t0) cc_final: 0.7936 (t70) REVERT: Q 63 ARG cc_start: 0.8415 (ttt180) cc_final: 0.8081 (mtm-85) REVERT: Q 89 GLN cc_start: 0.8637 (tt0) cc_final: 0.8374 (tt0) REVERT: Q 117 ASP cc_start: 0.8516 (t0) cc_final: 0.8179 (t70) REVERT: Q 119 SER cc_start: 0.8833 (m) cc_final: 0.8543 (t) REVERT: R 39 ASP cc_start: 0.8357 (t0) cc_final: 0.7933 (t70) REVERT: R 63 ARG cc_start: 0.8400 (ttt180) cc_final: 0.8090 (mtm-85) REVERT: R 89 GLN cc_start: 0.8637 (tt0) cc_final: 0.8376 (tt0) REVERT: R 117 ASP cc_start: 0.8520 (t0) cc_final: 0.8186 (t70) REVERT: R 119 SER cc_start: 0.8826 (m) cc_final: 0.8531 (t) REVERT: R 192 GLN cc_start: 0.9193 (tt0) cc_final: 0.8912 (tt0) REVERT: S 39 ASP cc_start: 0.8355 (t0) cc_final: 0.7930 (t70) REVERT: S 63 ARG cc_start: 0.8411 (ttt180) cc_final: 0.8092 (mtm-85) REVERT: S 89 GLN cc_start: 0.8642 (tt0) cc_final: 0.8382 (tt0) REVERT: S 117 ASP cc_start: 0.8524 (t0) cc_final: 0.8191 (t70) REVERT: S 119 SER cc_start: 0.8828 (m) cc_final: 0.8525 (t) REVERT: T 39 ASP cc_start: 0.8359 (t0) cc_final: 0.7937 (t70) REVERT: T 63 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8080 (mtm-85) REVERT: T 89 GLN cc_start: 0.8632 (tt0) cc_final: 0.8372 (tt0) REVERT: T 117 ASP cc_start: 0.8520 (t0) cc_final: 0.8189 (t70) REVERT: T 119 SER cc_start: 0.8829 (m) cc_final: 0.8532 (t) REVERT: U 39 ASP cc_start: 0.8366 (t0) cc_final: 0.7940 (t70) REVERT: U 63 ARG cc_start: 0.8397 (ttt180) cc_final: 0.8086 (mtm-85) REVERT: U 89 GLN cc_start: 0.8646 (tt0) cc_final: 0.8384 (tt0) REVERT: U 117 ASP cc_start: 0.8524 (t0) cc_final: 0.8192 (t70) REVERT: U 119 SER cc_start: 0.8839 (m) cc_final: 0.8542 (t) REVERT: V 39 ASP cc_start: 0.8363 (t0) cc_final: 0.7939 (t70) REVERT: V 63 ARG cc_start: 0.8407 (ttt180) cc_final: 0.8086 (mtm-85) REVERT: V 89 GLN cc_start: 0.8643 (tt0) cc_final: 0.8381 (tt0) REVERT: V 117 ASP cc_start: 0.8515 (t0) cc_final: 0.8183 (t70) REVERT: V 119 SER cc_start: 0.8822 (m) cc_final: 0.8524 (t) REVERT: W 39 ASP cc_start: 0.8360 (t0) cc_final: 0.7936 (t70) REVERT: W 63 ARG cc_start: 0.8403 (ttt180) cc_final: 0.8093 (mtm-85) REVERT: W 89 GLN cc_start: 0.8642 (tt0) cc_final: 0.8385 (tt0) REVERT: W 117 ASP cc_start: 0.8512 (t0) cc_final: 0.8182 (t70) REVERT: W 119 SER cc_start: 0.8834 (m) cc_final: 0.8535 (t) REVERT: X 39 ASP cc_start: 0.8354 (t0) cc_final: 0.7930 (t70) REVERT: X 63 ARG cc_start: 0.8409 (ttt180) cc_final: 0.8087 (mtm-85) REVERT: X 89 GLN cc_start: 0.8640 (tt0) cc_final: 0.8378 (tt0) REVERT: X 117 ASP cc_start: 0.8525 (t0) cc_final: 0.8193 (t70) REVERT: X 119 SER cc_start: 0.8825 (m) cc_final: 0.8531 (t) outliers start: 24 outliers final: 24 residues processed: 845 average time/residue: 0.2644 time to fit residues: 337.6721 Evaluate side-chains 754 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 730 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain W residue 152 HIS 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 199 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 422 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 192 GLN O 192 GLN X 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.107766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.081946 restraints weight = 42149.922| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 1.98 r_work: 0.2577 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2422 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 35976 Z= 0.292 Angle : 0.595 4.468 48912 Z= 0.321 Chirality : 0.049 0.148 5592 Planarity : 0.004 0.032 6504 Dihedral : 5.109 17.639 5088 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.32 % Allowed : 11.13 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.13), residues: 4512 helix: 2.03 (0.12), residues: 1872 sheet: 0.36 (0.13), residues: 1488 loop : -0.81 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 162 TYR 0.009 0.002 TYR U 45 PHE 0.012 0.002 PHE B 104 HIS 0.007 0.002 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.29 (35976) covalent geometry : angle 0.59487 / 0.32 (48912) hydrogen bonds : bond 0.04725 / 3.35 ( 2184) hydrogen bonds : angle 4.04076 / 2.91 ( 6048) *********************** 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 711 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 663 time to evaluate : 1.423 Fit side-chains REVERT: A 39 ASP cc_start: 0.8514 (t0) cc_final: 0.8094 (t70) REVERT: A 63 ARG cc_start: 0.8426 (ttt180) cc_final: 0.8107 (mtm-85) REVERT: A 117 ASP cc_start: 0.8498 (t0) cc_final: 0.8161 (t70) REVERT: B 39 ASP cc_start: 0.8483 (t0) cc_final: 0.8067 (t70) REVERT: B 63 ARG cc_start: 0.8418 (ttt180) cc_final: 0.8102 (mtm-85) REVERT: B 117 ASP cc_start: 0.8504 (t0) cc_final: 0.8171 (t70) REVERT: C 39 ASP cc_start: 0.8494 (t0) cc_final: 0.8075 (t70) REVERT: C 63 ARG cc_start: 0.8422 (ttt180) cc_final: 0.8098 (mtm-85) REVERT: C 117 ASP cc_start: 0.8514 (t0) cc_final: 0.8177 (t70) REVERT: D 39 ASP cc_start: 0.8493 (t0) cc_final: 0.8076 (t70) REVERT: D 63 ARG cc_start: 0.8405 (ttt180) cc_final: 0.8109 (mtm-85) REVERT: D 117 ASP cc_start: 0.8513 (t0) cc_final: 0.8178 (t70) REVERT: E 39 ASP cc_start: 0.8487 (t0) cc_final: 0.8070 (t70) REVERT: E 63 ARG cc_start: 0.8410 (ttt180) cc_final: 0.8110 (mtm-85) REVERT: E 117 ASP cc_start: 0.8512 (t0) cc_final: 0.8178 (t70) REVERT: F 39 ASP cc_start: 0.8500 (t0) cc_final: 0.8082 (t70) REVERT: F 63 ARG cc_start: 0.8412 (ttt180) cc_final: 0.8110 (mtm-85) REVERT: F 117 ASP cc_start: 0.8514 (t0) cc_final: 0.8179 (t70) REVERT: G 39 ASP cc_start: 0.8511 (t0) cc_final: 0.8099 (t70) REVERT: G 63 ARG cc_start: 0.8413 (ttt180) cc_final: 0.8106 (mtm-85) REVERT: G 117 ASP cc_start: 0.8521 (t0) cc_final: 0.8188 (t70) REVERT: H 39 ASP cc_start: 0.8503 (t0) cc_final: 0.8086 (t70) REVERT: H 63 ARG cc_start: 0.8423 (ttt180) cc_final: 0.8096 (mtm-85) REVERT: H 117 ASP cc_start: 0.8517 (t0) cc_final: 0.8183 (t70) REVERT: I 39 ASP cc_start: 0.8494 (t0) cc_final: 0.8074 (t70) REVERT: I 63 ARG cc_start: 0.8406 (ttt180) cc_final: 0.8107 (mtm-85) REVERT: I 117 ASP cc_start: 0.8517 (t0) cc_final: 0.8181 (t70) REVERT: J 39 ASP cc_start: 0.8508 (t0) cc_final: 0.8091 (t70) REVERT: J 63 ARG cc_start: 0.8420 (ttt180) cc_final: 0.8110 (mtm-85) REVERT: J 117 ASP cc_start: 0.8505 (t0) cc_final: 0.8168 (t70) REVERT: K 39 ASP cc_start: 0.8512 (t0) cc_final: 0.8093 (t70) REVERT: K 63 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8110 (mtm-85) REVERT: K 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8162 (t70) REVERT: L 39 ASP cc_start: 0.8490 (t0) cc_final: 0.8074 (t70) REVERT: L 63 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8096 (mtm-85) REVERT: L 117 ASP cc_start: 0.8522 (t0) cc_final: 0.8192 (t70) REVERT: M 39 ASP cc_start: 0.8506 (t0) cc_final: 0.8091 (t70) REVERT: M 63 ARG cc_start: 0.8396 (ttt180) cc_final: 0.8096 (mtm-85) REVERT: M 117 ASP cc_start: 0.8521 (t0) cc_final: 0.8189 (t70) REVERT: N 39 ASP cc_start: 0.8488 (t0) cc_final: 0.8071 (t70) REVERT: N 63 ARG cc_start: 0.8404 (ttt180) cc_final: 0.8098 (mtm-85) REVERT: N 117 ASP cc_start: 0.8511 (t0) cc_final: 0.8178 (t70) REVERT: O 39 ASP cc_start: 0.8492 (t0) cc_final: 0.8074 (t70) REVERT: O 63 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8097 (mtm-85) REVERT: O 117 ASP cc_start: 0.8512 (t0) cc_final: 0.8178 (t70) REVERT: P 39 ASP cc_start: 0.8490 (t0) cc_final: 0.8074 (t70) REVERT: P 63 ARG cc_start: 0.8390 (ttt180) cc_final: 0.8096 (mtm-85) REVERT: P 117 ASP cc_start: 0.8516 (t0) cc_final: 0.8182 (t70) REVERT: Q 39 ASP cc_start: 0.8498 (t0) cc_final: 0.8081 (t70) REVERT: Q 63 ARG cc_start: 0.8405 (ttt180) cc_final: 0.8105 (mtm-85) REVERT: Q 117 ASP cc_start: 0.8505 (t0) cc_final: 0.8172 (t70) REVERT: R 39 ASP cc_start: 0.8484 (t0) cc_final: 0.8066 (t70) REVERT: R 63 ARG cc_start: 0.8401 (ttt180) cc_final: 0.8096 (mtm-85) REVERT: R 117 ASP cc_start: 0.8515 (t0) cc_final: 0.8183 (t70) REVERT: S 39 ASP cc_start: 0.8480 (t0) cc_final: 0.8062 (t70) REVERT: S 63 ARG cc_start: 0.8424 (ttt180) cc_final: 0.8108 (mtm-85) REVERT: S 117 ASP cc_start: 0.8500 (t0) cc_final: 0.8167 (t70) REVERT: T 39 ASP cc_start: 0.8491 (t0) cc_final: 0.8077 (t70) REVERT: T 63 ARG cc_start: 0.8396 (ttt180) cc_final: 0.8102 (mtm-85) REVERT: T 117 ASP cc_start: 0.8514 (t0) cc_final: 0.8182 (t70) REVERT: U 39 ASP cc_start: 0.8494 (t0) cc_final: 0.8077 (t70) REVERT: U 63 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8106 (mtm-85) REVERT: U 117 ASP cc_start: 0.8515 (t0) cc_final: 0.8183 (t70) REVERT: V 39 ASP cc_start: 0.8518 (t0) cc_final: 0.8104 (t70) REVERT: V 63 ARG cc_start: 0.8416 (ttt180) cc_final: 0.8110 (mtm-85) REVERT: V 117 ASP cc_start: 0.8514 (t0) cc_final: 0.8181 (t70) REVERT: W 39 ASP cc_start: 0.8487 (t0) cc_final: 0.8073 (t70) REVERT: W 63 ARG cc_start: 0.8416 (ttt180) cc_final: 0.8109 (mtm-85) REVERT: W 117 ASP cc_start: 0.8500 (t0) cc_final: 0.8166 (t70) REVERT: X 39 ASP cc_start: 0.8491 (t0) cc_final: 0.8074 (t70) REVERT: X 63 ARG cc_start: 0.8414 (ttt180) cc_final: 0.8100 (mtm-85) REVERT: X 117 ASP cc_start: 0.8516 (t0) cc_final: 0.8185 (t70) outliers start: 48 outliers final: 48 residues processed: 711 average time/residue: 0.3013 time to fit residues: 315.9257 Evaluate side-chains 654 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 606 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 133 LEU 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 133 LEU 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 133 LEU 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 133 LEU 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 133 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 289 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 365 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 415 optimal weight: 2.9990 chunk 323 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 367 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN B 192 GLN C 192 GLN D 192 GLN E 192 GLN F 192 GLN G 192 GLN H 192 GLN I 192 GLN J 192 GLN M 192 GLN N 192 GLN O 192 GLN P 192 GLN Q 192 GLN S 192 GLN T 192 GLN U 192 GLN V 192 GLN W 192 GLN X 192 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.110742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.085651 restraints weight = 41120.346| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.85 r_work: 0.2638 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 35976 Z= 0.239 Angle : 0.549 4.202 48912 Z= 0.297 Chirality : 0.047 0.139 5592 Planarity : 0.004 0.031 6504 Dihedral : 4.981 17.217 5088 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.32 % Allowed : 11.60 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.13), residues: 4512 helix: 2.10 (0.12), residues: 1872 sheet: 0.44 (0.14), residues: 1488 loop : -0.81 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 162 TYR 0.008 0.002 TYR A 45 PHE 0.011 0.002 PHE W 104 HIS 0.006 0.002 HIS D 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (35976) covalent geometry : angle 0.54906 / 0.30 (48912) hydrogen bonds : bond 0.04301 / 3.05 ( 2184) hydrogen bonds : angle 3.95293 / 2.85 ( 6048) *********************** 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 694 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 646 time to evaluate : 1.437 Fit side-chains REVERT: A 39 ASP cc_start: 0.8469 (t0) cc_final: 0.8062 (t70) REVERT: A 63 ARG cc_start: 0.8457 (ttt180) cc_final: 0.8177 (mtm-85) REVERT: A 117 ASP cc_start: 0.8414 (t0) cc_final: 0.8111 (t70) REVERT: A 119 SER cc_start: 0.8893 (m) cc_final: 0.8633 (t) REVERT: B 39 ASP cc_start: 0.8466 (t0) cc_final: 0.8057 (t70) REVERT: B 63 ARG cc_start: 0.8421 (ttt180) cc_final: 0.8165 (mtm-85) REVERT: B 117 ASP cc_start: 0.8420 (t0) cc_final: 0.8118 (t70) REVERT: B 119 SER cc_start: 0.8897 (m) cc_final: 0.8636 (t) REVERT: C 39 ASP cc_start: 0.8463 (t0) cc_final: 0.8046 (t70) REVERT: C 63 ARG cc_start: 0.8442 (ttt180) cc_final: 0.8172 (mtm-85) REVERT: C 117 ASP cc_start: 0.8424 (t0) cc_final: 0.8121 (t70) REVERT: C 119 SER cc_start: 0.8888 (m) cc_final: 0.8628 (t) REVERT: D 39 ASP cc_start: 0.8481 (t0) cc_final: 0.8074 (t70) REVERT: D 63 ARG cc_start: 0.8444 (ttt180) cc_final: 0.8179 (mtm-85) REVERT: D 117 ASP cc_start: 0.8413 (t0) cc_final: 0.8111 (t70) REVERT: D 119 SER cc_start: 0.8894 (m) cc_final: 0.8635 (t) REVERT: E 39 ASP cc_start: 0.8481 (t0) cc_final: 0.8074 (t70) REVERT: E 63 ARG cc_start: 0.8446 (ttt180) cc_final: 0.8188 (mtm-85) REVERT: E 117 ASP cc_start: 0.8414 (t0) cc_final: 0.8111 (t70) REVERT: E 119 SER cc_start: 0.8890 (m) cc_final: 0.8632 (t) REVERT: F 39 ASP cc_start: 0.8475 (t0) cc_final: 0.8065 (t70) REVERT: F 63 ARG cc_start: 0.8428 (ttt180) cc_final: 0.8179 (mtm-85) REVERT: F 117 ASP cc_start: 0.8421 (t0) cc_final: 0.8118 (t70) REVERT: F 119 SER cc_start: 0.8894 (m) cc_final: 0.8636 (t) REVERT: G 39 ASP cc_start: 0.8480 (t0) cc_final: 0.8069 (t70) REVERT: G 63 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8183 (mtm-85) REVERT: G 117 ASP cc_start: 0.8416 (t0) cc_final: 0.8114 (t70) REVERT: G 119 SER cc_start: 0.8880 (m) cc_final: 0.8618 (t) REVERT: H 39 ASP cc_start: 0.8465 (t0) cc_final: 0.8063 (t70) REVERT: H 63 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8175 (mtm-85) REVERT: H 117 ASP cc_start: 0.8427 (t0) cc_final: 0.8123 (t70) REVERT: H 119 SER cc_start: 0.8890 (m) cc_final: 0.8630 (t) REVERT: I 39 ASP cc_start: 0.8469 (t0) cc_final: 0.8060 (t70) REVERT: I 63 ARG cc_start: 0.8428 (ttt180) cc_final: 0.8176 (mtm-85) REVERT: I 117 ASP cc_start: 0.8420 (t0) cc_final: 0.8117 (t70) REVERT: I 119 SER cc_start: 0.8893 (m) cc_final: 0.8636 (t) REVERT: J 39 ASP cc_start: 0.8480 (t0) cc_final: 0.8071 (t70) REVERT: J 63 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8167 (mtm-85) REVERT: J 117 ASP cc_start: 0.8420 (t0) cc_final: 0.8119 (t70) REVERT: J 119 SER cc_start: 0.8905 (m) cc_final: 0.8644 (t) REVERT: K 39 ASP cc_start: 0.8483 (t0) cc_final: 0.8073 (t70) REVERT: K 63 ARG cc_start: 0.8459 (ttt180) cc_final: 0.8178 (mtm-85) REVERT: K 117 ASP cc_start: 0.8415 (t0) cc_final: 0.8111 (t70) REVERT: K 119 SER cc_start: 0.8893 (m) cc_final: 0.8629 (t) REVERT: L 39 ASP cc_start: 0.8456 (t0) cc_final: 0.8047 (t70) REVERT: L 63 ARG cc_start: 0.8406 (ttt180) cc_final: 0.8168 (mtm-85) REVERT: L 117 ASP cc_start: 0.8422 (t0) cc_final: 0.8118 (t70) REVERT: L 119 SER cc_start: 0.8883 (m) cc_final: 0.8626 (t) REVERT: M 39 ASP cc_start: 0.8481 (t0) cc_final: 0.8072 (t70) REVERT: M 63 ARG cc_start: 0.8441 (ttt180) cc_final: 0.8181 (mtm-85) REVERT: M 117 ASP cc_start: 0.8411 (t0) cc_final: 0.8111 (t70) REVERT: M 119 SER cc_start: 0.8880 (m) cc_final: 0.8620 (t) REVERT: N 39 ASP cc_start: 0.8459 (t0) cc_final: 0.8050 (t70) REVERT: N 63 ARG cc_start: 0.8407 (ttt180) cc_final: 0.8158 (mtm-85) REVERT: N 117 ASP cc_start: 0.8406 (t0) cc_final: 0.8109 (t70) REVERT: N 119 SER cc_start: 0.8877 (m) cc_final: 0.8618 (t) REVERT: O 39 ASP cc_start: 0.8462 (t0) cc_final: 0.8053 (t70) REVERT: O 63 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8179 (mtm-85) REVERT: O 117 ASP cc_start: 0.8432 (t0) cc_final: 0.8129 (t70) REVERT: O 119 SER cc_start: 0.8887 (m) cc_final: 0.8626 (t) REVERT: P 39 ASP cc_start: 0.8457 (t0) cc_final: 0.8049 (t70) REVERT: P 63 ARG cc_start: 0.8416 (ttt180) cc_final: 0.8164 (mtm-85) REVERT: P 117 ASP cc_start: 0.8414 (t0) cc_final: 0.8116 (t70) REVERT: P 119 SER cc_start: 0.8876 (m) cc_final: 0.8618 (t) REVERT: Q 39 ASP cc_start: 0.8464 (t0) cc_final: 0.8056 (t70) REVERT: Q 63 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8175 (mtm-85) REVERT: Q 117 ASP cc_start: 0.8422 (t0) cc_final: 0.8121 (t70) REVERT: Q 119 SER cc_start: 0.8886 (m) cc_final: 0.8632 (t) REVERT: R 39 ASP cc_start: 0.8455 (t0) cc_final: 0.8046 (t70) REVERT: R 63 ARG cc_start: 0.8420 (ttt180) cc_final: 0.8168 (mtm-85) REVERT: R 117 ASP cc_start: 0.8413 (t0) cc_final: 0.8109 (t70) REVERT: R 119 SER cc_start: 0.8890 (m) cc_final: 0.8632 (t) REVERT: S 39 ASP cc_start: 0.8474 (t0) cc_final: 0.8065 (t70) REVERT: S 63 ARG cc_start: 0.8440 (ttt180) cc_final: 0.8175 (mtm-85) REVERT: S 117 ASP cc_start: 0.8408 (t0) cc_final: 0.8107 (t70) REVERT: S 119 SER cc_start: 0.8894 (m) cc_final: 0.8634 (t) REVERT: T 39 ASP cc_start: 0.8461 (t0) cc_final: 0.8048 (t70) REVERT: T 63 ARG cc_start: 0.8413 (ttt180) cc_final: 0.8166 (mtm-85) REVERT: T 117 ASP cc_start: 0.8424 (t0) cc_final: 0.8127 (t70) REVERT: T 119 SER cc_start: 0.8875 (m) cc_final: 0.8616 (t) REVERT: U 39 ASP cc_start: 0.8469 (t0) cc_final: 0.8061 (t70) REVERT: U 63 ARG cc_start: 0.8440 (ttt180) cc_final: 0.8189 (mtm-85) REVERT: U 117 ASP cc_start: 0.8415 (t0) cc_final: 0.8112 (t70) REVERT: U 119 SER cc_start: 0.8892 (m) cc_final: 0.8636 (t) REVERT: V 39 ASP cc_start: 0.8494 (t0) cc_final: 0.8085 (t70) REVERT: V 63 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8184 (mtm-85) REVERT: V 117 ASP cc_start: 0.8407 (t0) cc_final: 0.8104 (t70) REVERT: V 119 SER cc_start: 0.8880 (m) cc_final: 0.8619 (t) REVERT: W 39 ASP cc_start: 0.8466 (t0) cc_final: 0.8056 (t70) REVERT: W 63 ARG cc_start: 0.8437 (ttt180) cc_final: 0.8179 (mtm-85) REVERT: W 117 ASP cc_start: 0.8414 (t0) cc_final: 0.8113 (t70) REVERT: W 119 SER cc_start: 0.8899 (m) cc_final: 0.8638 (t) REVERT: X 39 ASP cc_start: 0.8460 (t0) cc_final: 0.8042 (t70) REVERT: X 63 ARG cc_start: 0.8418 (ttt180) cc_final: 0.8162 (mtm-85) REVERT: X 117 ASP cc_start: 0.8419 (t0) cc_final: 0.8115 (t70) REVERT: X 119 SER cc_start: 0.8889 (m) cc_final: 0.8630 (t) outliers start: 48 outliers final: 48 residues processed: 694 average time/residue: 0.3098 time to fit residues: 315.5481 Evaluate side-chains 690 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 642 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 133 LEU 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 133 LEU 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 133 LEU 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 133 LEU 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 133 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 60 optimal weight: 7.9990 chunk 319 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 374 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 424 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN B 192 GLN C 192 GLN D 192 GLN E 192 GLN F 192 GLN G 192 GLN H 192 GLN I 192 GLN J 192 GLN K 192 GLN L 192 GLN M 192 GLN N 192 GLN O 192 GLN P 192 GLN Q 192 GLN R 192 GLN S 192 GLN T 192 GLN U 192 GLN V 192 GLN W 192 GLN X 192 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.106806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.081022 restraints weight = 42949.389| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 1.98 r_work: 0.2577 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 35976 Z= 0.368 Angle : 0.634 4.621 48912 Z= 0.343 Chirality : 0.050 0.157 5592 Planarity : 0.005 0.032 6504 Dihedral : 5.295 17.740 5088 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.63 % Allowed : 10.47 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.13), residues: 4512 helix: 1.87 (0.12), residues: 1872 sheet: 0.32 (0.13), residues: 1488 loop : -1.14 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG V 162 TYR 0.009 0.002 TYR X 45 PHE 0.012 0.003 PHE Q 154 HIS 0.009 0.002 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00876 / 0.37 (35976) covalent geometry : angle 0.63438 / 0.34 (48912) hydrogen bonds : bond 0.05231 / 3.72 ( 2184) hydrogen bonds : angle 4.13604 / 2.98 ( 6048) *********************** 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 721 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 625 time to evaluate : 1.402 Fit side-chains REVERT: A 39 ASP cc_start: 0.8597 (t0) cc_final: 0.8192 (t70) REVERT: A 63 ARG cc_start: 0.8441 (ttt180) cc_final: 0.8138 (mtm-85) REVERT: A 117 ASP cc_start: 0.8489 (t0) cc_final: 0.8161 (t70) REVERT: A 119 SER cc_start: 0.8972 (m) cc_final: 0.8686 (t) REVERT: B 39 ASP cc_start: 0.8575 (t0) cc_final: 0.8171 (t70) REVERT: B 63 ARG cc_start: 0.8443 (ttt180) cc_final: 0.8143 (mtm-85) REVERT: B 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8166 (t70) REVERT: B 119 SER cc_start: 0.8972 (m) cc_final: 0.8678 (t) REVERT: C 39 ASP cc_start: 0.8569 (t0) cc_final: 0.8164 (t70) REVERT: C 63 ARG cc_start: 0.8469 (ttt180) cc_final: 0.8151 (mtm-85) REVERT: C 117 ASP cc_start: 0.8494 (t0) cc_final: 0.8165 (t70) REVERT: C 119 SER cc_start: 0.8972 (m) cc_final: 0.8687 (t) REVERT: D 39 ASP cc_start: 0.8588 (t0) cc_final: 0.8184 (t70) REVERT: D 63 ARG cc_start: 0.8473 (ttt180) cc_final: 0.8163 (mtm-85) REVERT: D 117 ASP cc_start: 0.8502 (t0) cc_final: 0.8174 (t70) REVERT: D 119 SER cc_start: 0.8970 (m) cc_final: 0.8681 (t) REVERT: E 39 ASP cc_start: 0.8591 (t0) cc_final: 0.8185 (t70) REVERT: E 63 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8167 (mtm-85) REVERT: E 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8170 (t70) REVERT: E 119 SER cc_start: 0.8968 (m) cc_final: 0.8680 (t) REVERT: F 39 ASP cc_start: 0.8578 (t0) cc_final: 0.8172 (t70) REVERT: F 63 ARG cc_start: 0.8452 (ttt180) cc_final: 0.8156 (mtm-85) REVERT: F 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8167 (t70) REVERT: F 119 SER cc_start: 0.8974 (m) cc_final: 0.8684 (t) REVERT: G 39 ASP cc_start: 0.8591 (t0) cc_final: 0.8184 (t70) REVERT: G 63 ARG cc_start: 0.8449 (ttt180) cc_final: 0.8150 (mtm-85) REVERT: G 117 ASP cc_start: 0.8501 (t0) cc_final: 0.8173 (t70) REVERT: G 119 SER cc_start: 0.8962 (m) cc_final: 0.8674 (t) REVERT: H 39 ASP cc_start: 0.8579 (t0) cc_final: 0.8174 (t70) REVERT: H 63 ARG cc_start: 0.8459 (ttt180) cc_final: 0.8146 (mtm-85) REVERT: H 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8168 (t70) REVERT: H 119 SER cc_start: 0.8973 (m) cc_final: 0.8685 (t) REVERT: I 39 ASP cc_start: 0.8570 (t0) cc_final: 0.8162 (t70) REVERT: I 63 ARG cc_start: 0.8455 (ttt180) cc_final: 0.8155 (mtm-85) REVERT: I 117 ASP cc_start: 0.8493 (t0) cc_final: 0.8163 (t70) REVERT: I 119 SER cc_start: 0.8972 (m) cc_final: 0.8684 (t) REVERT: J 39 ASP cc_start: 0.8601 (t0) cc_final: 0.8198 (t70) REVERT: J 63 ARG cc_start: 0.8442 (ttt180) cc_final: 0.8141 (mtm-85) REVERT: J 117 ASP cc_start: 0.8501 (t0) cc_final: 0.8172 (t70) REVERT: J 119 SER cc_start: 0.8982 (m) cc_final: 0.8693 (t) REVERT: K 39 ASP cc_start: 0.8602 (t0) cc_final: 0.8199 (t70) REVERT: K 63 ARG cc_start: 0.8449 (ttt180) cc_final: 0.8145 (mtm-85) REVERT: K 117 ASP cc_start: 0.8495 (t0) cc_final: 0.8166 (t70) REVERT: K 119 SER cc_start: 0.8977 (m) cc_final: 0.8688 (t) REVERT: L 39 ASP cc_start: 0.8563 (t0) cc_final: 0.8153 (t70) REVERT: L 63 ARG cc_start: 0.8444 (ttt180) cc_final: 0.8148 (mtm-85) REVERT: L 117 ASP cc_start: 0.8491 (t0) cc_final: 0.8157 (t70) REVERT: L 119 SER cc_start: 0.8969 (m) cc_final: 0.8686 (t) REVERT: M 39 ASP cc_start: 0.8592 (t0) cc_final: 0.8185 (t70) REVERT: M 63 ARG cc_start: 0.8443 (ttt180) cc_final: 0.8147 (mtm-85) REVERT: M 117 ASP cc_start: 0.8492 (t0) cc_final: 0.8162 (t70) REVERT: M 119 SER cc_start: 0.8963 (m) cc_final: 0.8677 (t) REVERT: N 39 ASP cc_start: 0.8570 (t0) cc_final: 0.8163 (t70) REVERT: N 63 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8139 (mtm-85) REVERT: N 117 ASP cc_start: 0.8491 (t0) cc_final: 0.8165 (t70) REVERT: N 119 SER cc_start: 0.8966 (m) cc_final: 0.8674 (t) REVERT: O 39 ASP cc_start: 0.8576 (t0) cc_final: 0.8170 (t70) REVERT: O 63 ARG cc_start: 0.8464 (ttt180) cc_final: 0.8150 (mtm-85) REVERT: O 117 ASP cc_start: 0.8498 (t0) cc_final: 0.8168 (t70) REVERT: O 119 SER cc_start: 0.8971 (m) cc_final: 0.8684 (t) REVERT: P 39 ASP cc_start: 0.8577 (t0) cc_final: 0.8173 (t70) REVERT: P 63 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8139 (mtm-85) REVERT: P 117 ASP cc_start: 0.8490 (t0) cc_final: 0.8162 (t70) REVERT: P 119 SER cc_start: 0.8964 (m) cc_final: 0.8672 (t) REVERT: Q 39 ASP cc_start: 0.8582 (t0) cc_final: 0.8176 (t70) REVERT: Q 63 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8154 (mtm-85) REVERT: Q 117 ASP cc_start: 0.8493 (t0) cc_final: 0.8165 (t70) REVERT: Q 119 SER cc_start: 0.8967 (m) cc_final: 0.8683 (t) REVERT: R 39 ASP cc_start: 0.8567 (t0) cc_final: 0.8157 (t70) REVERT: R 63 ARG cc_start: 0.8454 (ttt180) cc_final: 0.8147 (mtm-85) REVERT: R 117 ASP cc_start: 0.8488 (t0) cc_final: 0.8158 (t70) REVERT: R 119 SER cc_start: 0.8969 (m) cc_final: 0.8682 (t) REVERT: S 39 ASP cc_start: 0.8577 (t0) cc_final: 0.8171 (t70) REVERT: S 63 ARG cc_start: 0.8449 (ttt180) cc_final: 0.8147 (mtm-85) REVERT: S 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8166 (t70) REVERT: S 119 SER cc_start: 0.8976 (m) cc_final: 0.8684 (t) REVERT: T 39 ASP cc_start: 0.8580 (t0) cc_final: 0.8176 (t70) REVERT: T 63 ARG cc_start: 0.8422 (ttt180) cc_final: 0.8133 (mtm-85) REVERT: T 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8172 (t70) REVERT: T 119 SER cc_start: 0.8963 (m) cc_final: 0.8672 (t) REVERT: U 39 ASP cc_start: 0.8586 (t0) cc_final: 0.8181 (t70) REVERT: U 63 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8166 (mtm-85) REVERT: U 117 ASP cc_start: 0.8502 (t0) cc_final: 0.8174 (t70) REVERT: U 119 SER cc_start: 0.8969 (m) cc_final: 0.8680 (t) REVERT: V 39 ASP cc_start: 0.8598 (t0) cc_final: 0.8191 (t70) REVERT: V 63 ARG cc_start: 0.8446 (ttt180) cc_final: 0.8145 (mtm-85) REVERT: V 117 ASP cc_start: 0.8494 (t0) cc_final: 0.8165 (t70) REVERT: V 119 SER cc_start: 0.8964 (m) cc_final: 0.8676 (t) REVERT: W 39 ASP cc_start: 0.8577 (t0) cc_final: 0.8174 (t70) REVERT: W 63 ARG cc_start: 0.8453 (ttt180) cc_final: 0.8149 (mtm-85) REVERT: W 117 ASP cc_start: 0.8498 (t0) cc_final: 0.8167 (t70) REVERT: W 119 SER cc_start: 0.8975 (m) cc_final: 0.8681 (t) REVERT: X 39 ASP cc_start: 0.8569 (t0) cc_final: 0.8161 (t70) REVERT: X 63 ARG cc_start: 0.8453 (ttt180) cc_final: 0.8146 (mtm-85) REVERT: X 117 ASP cc_start: 0.8499 (t0) cc_final: 0.8165 (t70) REVERT: X 119 SER cc_start: 0.8969 (m) cc_final: 0.8685 (t) outliers start: 96 outliers final: 72 residues processed: 721 average time/residue: 0.3068 time to fit residues: 326.1830 Evaluate side-chains 713 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 641 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 157 LEU Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 133 LEU Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 133 LEU Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain V residue 157 LEU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain W residue 157 LEU Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 152 HIS Chi-restraints excluded: chain X residue 157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 413 optimal weight: 0.9990 chunk 365 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 321 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN B 192 GLN C 192 GLN D 192 GLN E 192 GLN F 192 GLN G 192 GLN H 192 GLN I 192 GLN J 192 GLN K 192 GLN L 192 GLN M 192 GLN N 192 GLN O 192 GLN P 192 GLN Q 192 GLN R 192 GLN S 192 GLN T 192 GLN U 192 GLN V 192 GLN W 192 GLN X 192 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.090720 restraints weight = 40948.024| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.88 r_work: 0.2663 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 35976 Z= 0.120 Angle : 0.471 3.416 48912 Z= 0.255 Chirality : 0.044 0.170 5592 Planarity : 0.004 0.031 6504 Dihedral : 4.670 16.316 5088 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.18 % Allowed : 11.76 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.13), residues: 4512 helix: 2.40 (0.12), residues: 1872 sheet: 0.42 (0.13), residues: 1488 loop : -0.82 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 95 TYR 0.006 0.001 TYR M 145 PHE 0.006 0.001 PHE D 104 HIS 0.005 0.001 HIS P 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (35976) covalent geometry : angle 0.47125 / 0.26 (48912) hydrogen bonds : bond 0.03269 / 2.31 ( 2184) hydrogen bonds : angle 3.77422 / 2.72 ( 6048) *********************** 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 839 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 796 time to evaluate : 1.420 Fit side-chains REVERT: A 39 ASP cc_start: 0.8454 (t0) cc_final: 0.8037 (t70) REVERT: A 63 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8141 (mtm-85) REVERT: A 95 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7949 (tpp80) REVERT: A 117 ASP cc_start: 0.8425 (t0) cc_final: 0.8090 (t70) REVERT: A 119 SER cc_start: 0.8840 (m) cc_final: 0.8564 (t) REVERT: B 39 ASP cc_start: 0.8441 (t0) cc_final: 0.8030 (t70) REVERT: B 63 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8132 (mtm-85) REVERT: B 117 ASP cc_start: 0.8436 (t0) cc_final: 0.8102 (t70) REVERT: B 119 SER cc_start: 0.8854 (m) cc_final: 0.8572 (t) REVERT: C 29 ASP cc_start: 0.7977 (t70) cc_final: 0.7752 (t70) REVERT: C 39 ASP cc_start: 0.8347 (t0) cc_final: 0.7941 (t70) REVERT: C 63 ARG cc_start: 0.8442 (ttt180) cc_final: 0.8139 (mtm-85) REVERT: C 117 ASP cc_start: 0.8437 (t0) cc_final: 0.8102 (t70) REVERT: C 119 SER cc_start: 0.8860 (m) cc_final: 0.8573 (t) REVERT: D 29 ASP cc_start: 0.8039 (t70) cc_final: 0.7813 (t70) REVERT: D 39 ASP cc_start: 0.8464 (t0) cc_final: 0.8064 (t70) REVERT: D 63 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8155 (mtm-85) REVERT: D 117 ASP cc_start: 0.8426 (t0) cc_final: 0.8089 (t70) REVERT: D 119 SER cc_start: 0.8856 (m) cc_final: 0.8571 (t) REVERT: E 29 ASP cc_start: 0.8001 (t70) cc_final: 0.7775 (t70) REVERT: E 39 ASP cc_start: 0.8468 (t0) cc_final: 0.8067 (t70) REVERT: E 63 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8158 (mtm-85) REVERT: E 117 ASP cc_start: 0.8424 (t0) cc_final: 0.8086 (t70) REVERT: E 119 SER cc_start: 0.8856 (m) cc_final: 0.8571 (t) REVERT: F 29 ASP cc_start: 0.8005 (t70) cc_final: 0.7774 (t70) REVERT: F 39 ASP cc_start: 0.8454 (t0) cc_final: 0.8058 (t70) REVERT: F 63 ARG cc_start: 0.8446 (ttt180) cc_final: 0.8150 (mtm-85) REVERT: F 117 ASP cc_start: 0.8424 (t0) cc_final: 0.8089 (t70) REVERT: F 119 SER cc_start: 0.8854 (m) cc_final: 0.8573 (t) REVERT: G 29 ASP cc_start: 0.8041 (t70) cc_final: 0.7813 (t70) REVERT: G 39 ASP cc_start: 0.8445 (t0) cc_final: 0.8045 (t70) REVERT: G 63 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8143 (mtm-85) REVERT: G 117 ASP cc_start: 0.8434 (t0) cc_final: 0.8100 (t70) REVERT: G 119 SER cc_start: 0.8859 (m) cc_final: 0.8576 (t) REVERT: H 29 ASP cc_start: 0.8032 (t70) cc_final: 0.7810 (t70) REVERT: H 39 ASP cc_start: 0.8461 (t0) cc_final: 0.8058 (t70) REVERT: H 63 ARG cc_start: 0.8440 (ttt180) cc_final: 0.8138 (mtm-85) REVERT: H 117 ASP cc_start: 0.8444 (t0) cc_final: 0.8110 (t70) REVERT: H 119 SER cc_start: 0.8855 (m) cc_final: 0.8570 (t) REVERT: I 29 ASP cc_start: 0.8044 (t70) cc_final: 0.7816 (t70) REVERT: I 39 ASP cc_start: 0.8459 (t0) cc_final: 0.8062 (t70) REVERT: I 63 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8153 (mtm-85) REVERT: I 117 ASP cc_start: 0.8429 (t0) cc_final: 0.8096 (t70) REVERT: I 119 SER cc_start: 0.8855 (m) cc_final: 0.8574 (t) REVERT: J 29 ASP cc_start: 0.7995 (t70) cc_final: 0.7765 (t70) REVERT: J 39 ASP cc_start: 0.8449 (t0) cc_final: 0.8048 (t70) REVERT: J 63 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8148 (mtm-85) REVERT: J 117 ASP cc_start: 0.8430 (t0) cc_final: 0.8094 (t70) REVERT: J 119 SER cc_start: 0.8865 (m) cc_final: 0.8581 (t) REVERT: K 29 ASP cc_start: 0.8047 (t70) cc_final: 0.7820 (t70) REVERT: K 39 ASP cc_start: 0.8448 (t0) cc_final: 0.8045 (t70) REVERT: K 63 ARG cc_start: 0.8452 (ttt180) cc_final: 0.8148 (mtm-85) REVERT: K 117 ASP cc_start: 0.8420 (t0) cc_final: 0.8082 (t70) REVERT: K 119 SER cc_start: 0.8862 (m) cc_final: 0.8577 (t) REVERT: L 29 ASP cc_start: 0.7986 (t70) cc_final: 0.7761 (t70) REVERT: L 39 ASP cc_start: 0.8347 (t0) cc_final: 0.7942 (t70) REVERT: L 63 ARG cc_start: 0.8437 (ttt180) cc_final: 0.8139 (mtm-85) REVERT: L 117 ASP cc_start: 0.8423 (t0) cc_final: 0.8086 (t70) REVERT: L 119 SER cc_start: 0.8857 (m) cc_final: 0.8573 (t) REVERT: M 29 ASP cc_start: 0.7988 (t70) cc_final: 0.7756 (t70) REVERT: M 39 ASP cc_start: 0.8453 (t0) cc_final: 0.8058 (t70) REVERT: M 63 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8150 (mtm-85) REVERT: M 117 ASP cc_start: 0.8427 (t0) cc_final: 0.8092 (t70) REVERT: M 119 SER cc_start: 0.8860 (m) cc_final: 0.8576 (t) REVERT: N 29 ASP cc_start: 0.7975 (t70) cc_final: 0.7746 (t70) REVERT: N 39 ASP cc_start: 0.8448 (t0) cc_final: 0.8047 (t70) REVERT: N 63 ARG cc_start: 0.8391 (ttt180) cc_final: 0.8134 (mtm-85) REVERT: N 117 ASP cc_start: 0.8427 (t0) cc_final: 0.8093 (t70) REVERT: N 119 SER cc_start: 0.8858 (m) cc_final: 0.8569 (t) REVERT: O 29 ASP cc_start: 0.8034 (t70) cc_final: 0.7813 (t70) REVERT: O 39 ASP cc_start: 0.8343 (t0) cc_final: 0.7936 (t70) REVERT: O 63 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8143 (mtm-85) REVERT: O 117 ASP cc_start: 0.8430 (t0) cc_final: 0.8095 (t70) REVERT: O 119 SER cc_start: 0.8861 (m) cc_final: 0.8572 (t) REVERT: P 39 ASP cc_start: 0.8456 (t0) cc_final: 0.8045 (t70) REVERT: P 63 ARG cc_start: 0.8397 (ttt180) cc_final: 0.8131 (mtm-85) REVERT: P 117 ASP cc_start: 0.8430 (t0) cc_final: 0.8098 (t70) REVERT: P 119 SER cc_start: 0.8861 (m) cc_final: 0.8573 (t) REVERT: Q 39 ASP cc_start: 0.8461 (t0) cc_final: 0.8053 (t70) REVERT: Q 63 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8144 (mtm-85) REVERT: Q 95 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.8023 (tpp80) REVERT: Q 117 ASP cc_start: 0.8416 (t0) cc_final: 0.8081 (t70) REVERT: Q 119 SER cc_start: 0.8836 (m) cc_final: 0.8565 (t) REVERT: R 29 ASP cc_start: 0.7982 (t70) cc_final: 0.7754 (t70) REVERT: R 39 ASP cc_start: 0.8450 (t0) cc_final: 0.8050 (t70) REVERT: R 63 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8139 (mtm-85) REVERT: R 117 ASP cc_start: 0.8427 (t0) cc_final: 0.8092 (t70) REVERT: R 119 SER cc_start: 0.8860 (m) cc_final: 0.8574 (t) REVERT: S 29 ASP cc_start: 0.8040 (t70) cc_final: 0.7816 (t70) REVERT: S 39 ASP cc_start: 0.8441 (t0) cc_final: 0.8042 (t70) REVERT: S 63 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8135 (mtm-85) REVERT: S 117 ASP cc_start: 0.8429 (t0) cc_final: 0.8095 (t70) REVERT: S 119 SER cc_start: 0.8857 (m) cc_final: 0.8570 (t) REVERT: T 39 ASP cc_start: 0.8456 (t0) cc_final: 0.8043 (t70) REVERT: T 63 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8129 (mtm-85) REVERT: T 117 ASP cc_start: 0.8434 (t0) cc_final: 0.8103 (t70) REVERT: T 119 SER cc_start: 0.8858 (m) cc_final: 0.8570 (t) REVERT: U 29 ASP cc_start: 0.8053 (t70) cc_final: 0.7831 (t70) REVERT: U 39 ASP cc_start: 0.8357 (t0) cc_final: 0.7951 (t70) REVERT: U 63 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8156 (mtm-85) REVERT: U 117 ASP cc_start: 0.8423 (t0) cc_final: 0.8085 (t70) REVERT: U 119 SER cc_start: 0.8854 (m) cc_final: 0.8570 (t) REVERT: V 29 ASP cc_start: 0.8052 (t70) cc_final: 0.7827 (t70) REVERT: V 39 ASP cc_start: 0.8451 (t0) cc_final: 0.8054 (t70) REVERT: V 63 ARG cc_start: 0.8446 (ttt180) cc_final: 0.8147 (mtm-85) REVERT: V 117 ASP cc_start: 0.8433 (t0) cc_final: 0.8098 (t70) REVERT: V 119 SER cc_start: 0.8858 (m) cc_final: 0.8573 (t) REVERT: W 29 ASP cc_start: 0.8044 (t70) cc_final: 0.7820 (t70) REVERT: W 39 ASP cc_start: 0.8444 (t0) cc_final: 0.8042 (t70) REVERT: W 63 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8139 (mtm-85) REVERT: W 117 ASP cc_start: 0.8437 (t0) cc_final: 0.8105 (t70) REVERT: W 119 SER cc_start: 0.8857 (m) cc_final: 0.8574 (t) REVERT: X 29 ASP cc_start: 0.8030 (t70) cc_final: 0.7807 (t70) REVERT: X 39 ASP cc_start: 0.8442 (t0) cc_final: 0.8041 (t70) REVERT: X 63 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8135 (mtm-85) REVERT: X 117 ASP cc_start: 0.8425 (t0) cc_final: 0.8088 (t70) REVERT: X 119 SER cc_start: 0.8863 (m) cc_final: 0.8575 (t) outliers start: 43 outliers final: 19 residues processed: 820 average time/residue: 0.2890 time to fit residues: 355.8347 Evaluate side-chains 717 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 698 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain X residue 68 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 123 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 385 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN B 89 GLN C 89 GLN D 89 GLN E 89 GLN F 89 GLN G 89 GLN H 89 GLN I 89 GLN J 89 GLN K 89 GLN K 192 GLN L 89 GLN L 192 GLN M 89 GLN M 192 GLN N 89 GLN O 89 GLN O 192 GLN P 89 GLN Q 89 GLN R 89 GLN R 192 GLN S 89 GLN T 89 GLN U 89 GLN V 89 GLN W 89 GLN X 89 GLN X 192 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.107514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.081811 restraints weight = 43005.227| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 1.96 r_work: 0.2574 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 35976 Z= 0.380 Angle : 0.648 4.775 48912 Z= 0.350 Chirality : 0.051 0.161 5592 Planarity : 0.005 0.033 6504 Dihedral : 5.273 17.504 5088 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.58 % Allowed : 11.18 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.13), residues: 4512 helix: 2.00 (0.12), residues: 1872 sheet: 0.38 (0.13), residues: 1488 loop : -1.04 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 95 TYR 0.011 0.002 TYR G 45 PHE 0.013 0.003 PHE S 154 HIS 0.008 0.002 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00904 / 0.38 (35976) covalent geometry : angle 0.64805 / 0.35 (48912) hydrogen bonds : bond 0.05238 / 3.72 ( 2184) hydrogen bonds : angle 4.14618 / 2.99 ( 6048) *********************** 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 739 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 645 time to evaluate : 1.442 Fit side-chains REVERT: A 39 ASP cc_start: 0.8609 (t0) cc_final: 0.8211 (t70) REVERT: A 63 ARG cc_start: 0.8478 (ttt180) cc_final: 0.8134 (mtm-85) REVERT: A 117 ASP cc_start: 0.8506 (t0) cc_final: 0.8189 (t70) REVERT: A 119 SER cc_start: 0.8965 (m) cc_final: 0.8666 (t) REVERT: B 39 ASP cc_start: 0.8602 (t0) cc_final: 0.8206 (t70) REVERT: B 63 ARG cc_start: 0.8476 (ttt180) cc_final: 0.8134 (mtm-85) REVERT: B 117 ASP cc_start: 0.8493 (t0) cc_final: 0.8173 (t70) REVERT: B 119 SER cc_start: 0.8958 (m) cc_final: 0.8656 (t) REVERT: C 39 ASP cc_start: 0.8589 (t0) cc_final: 0.8194 (t70) REVERT: C 63 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8137 (mtm-85) REVERT: C 117 ASP cc_start: 0.8510 (t0) cc_final: 0.8187 (t70) REVERT: C 119 SER cc_start: 0.8972 (m) cc_final: 0.8670 (t) REVERT: D 39 ASP cc_start: 0.8596 (t0) cc_final: 0.8197 (t70) REVERT: D 63 ARG cc_start: 0.8466 (ttt180) cc_final: 0.8142 (mtm-85) REVERT: D 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8176 (t70) REVERT: D 119 SER cc_start: 0.8969 (m) cc_final: 0.8670 (t) REVERT: E 39 ASP cc_start: 0.8595 (t0) cc_final: 0.8197 (t70) REVERT: E 63 ARG cc_start: 0.8437 (ttt180) cc_final: 0.8132 (mtm-85) REVERT: E 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8177 (t70) REVERT: E 119 SER cc_start: 0.8969 (m) cc_final: 0.8671 (t) REVERT: F 39 ASP cc_start: 0.8587 (t0) cc_final: 0.8187 (t70) REVERT: F 63 ARG cc_start: 0.8446 (ttt180) cc_final: 0.8129 (mtm-85) REVERT: F 117 ASP cc_start: 0.8495 (t0) cc_final: 0.8171 (t70) REVERT: F 119 SER cc_start: 0.8965 (m) cc_final: 0.8668 (t) REVERT: G 39 ASP cc_start: 0.8606 (t0) cc_final: 0.8207 (t70) REVERT: G 63 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8130 (mtm-85) REVERT: G 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8177 (t70) REVERT: G 119 SER cc_start: 0.8957 (m) cc_final: 0.8659 (t) REVERT: H 39 ASP cc_start: 0.8594 (t0) cc_final: 0.8195 (t70) REVERT: H 63 ARG cc_start: 0.8472 (ttt180) cc_final: 0.8142 (mtm-85) REVERT: H 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8187 (t70) REVERT: H 119 SER cc_start: 0.8973 (m) cc_final: 0.8672 (t) REVERT: I 39 ASP cc_start: 0.8588 (t0) cc_final: 0.8186 (t70) REVERT: I 63 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8135 (mtm-85) REVERT: I 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8171 (t70) REVERT: I 119 SER cc_start: 0.8969 (m) cc_final: 0.8672 (t) REVERT: J 39 ASP cc_start: 0.8606 (t0) cc_final: 0.8208 (t70) REVERT: J 63 ARG cc_start: 0.8472 (ttt180) cc_final: 0.8131 (mtm-85) REVERT: J 117 ASP cc_start: 0.8500 (t0) cc_final: 0.8183 (t70) REVERT: J 119 SER cc_start: 0.8973 (m) cc_final: 0.8673 (t) REVERT: K 39 ASP cc_start: 0.8608 (t0) cc_final: 0.8211 (t70) REVERT: K 63 ARG cc_start: 0.8473 (ttt180) cc_final: 0.8136 (mtm-85) REVERT: K 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8186 (t70) REVERT: K 119 SER cc_start: 0.8921 (m) cc_final: 0.8672 (t) REVERT: L 39 ASP cc_start: 0.8580 (t0) cc_final: 0.8182 (t70) REVERT: L 63 ARG cc_start: 0.8461 (ttt180) cc_final: 0.8124 (mtm-85) REVERT: L 117 ASP cc_start: 0.8503 (t0) cc_final: 0.8186 (t70) REVERT: L 119 SER cc_start: 0.8913 (m) cc_final: 0.8666 (t) REVERT: M 39 ASP cc_start: 0.8604 (t0) cc_final: 0.8204 (t70) REVERT: M 63 ARG cc_start: 0.8463 (ttt180) cc_final: 0.8132 (mtm-85) REVERT: M 117 ASP cc_start: 0.8495 (t0) cc_final: 0.8174 (t70) REVERT: M 119 SER cc_start: 0.8956 (m) cc_final: 0.8658 (t) REVERT: N 39 ASP cc_start: 0.8589 (t0) cc_final: 0.8189 (t70) REVERT: N 63 ARG cc_start: 0.8453 (ttt180) cc_final: 0.8124 (mtm-85) REVERT: N 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8177 (t70) REVERT: N 119 SER cc_start: 0.8965 (m) cc_final: 0.8664 (t) REVERT: O 39 ASP cc_start: 0.8588 (t0) cc_final: 0.8192 (t70) REVERT: O 63 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8152 (mtm-85) REVERT: O 117 ASP cc_start: 0.8504 (t0) cc_final: 0.8191 (t70) REVERT: O 119 SER cc_start: 0.8925 (m) cc_final: 0.8676 (t) REVERT: P 39 ASP cc_start: 0.8593 (t0) cc_final: 0.8194 (t70) REVERT: P 63 ARG cc_start: 0.8461 (ttt180) cc_final: 0.8135 (mtm-85) REVERT: P 117 ASP cc_start: 0.8494 (t0) cc_final: 0.8173 (t70) REVERT: P 119 SER cc_start: 0.8962 (m) cc_final: 0.8663 (t) REVERT: Q 39 ASP cc_start: 0.8600 (t0) cc_final: 0.8201 (t70) REVERT: Q 63 ARG cc_start: 0.8462 (ttt180) cc_final: 0.8146 (mtm-85) REVERT: Q 117 ASP cc_start: 0.8501 (t0) cc_final: 0.8178 (t70) REVERT: Q 119 SER cc_start: 0.8960 (m) cc_final: 0.8667 (t) REVERT: R 39 ASP cc_start: 0.8583 (t0) cc_final: 0.8183 (t70) REVERT: R 63 ARG cc_start: 0.8457 (ttt180) cc_final: 0.8123 (mtm-85) REVERT: R 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8183 (t70) REVERT: R 119 SER cc_start: 0.8957 (m) cc_final: 0.8659 (t) REVERT: S 39 ASP cc_start: 0.8589 (t0) cc_final: 0.8189 (t70) REVERT: S 63 ARG cc_start: 0.8478 (ttt180) cc_final: 0.8130 (mtm-85) REVERT: S 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8176 (t70) REVERT: S 119 SER cc_start: 0.8959 (m) cc_final: 0.8662 (t) REVERT: T 39 ASP cc_start: 0.8592 (t0) cc_final: 0.8192 (t70) REVERT: T 63 ARG cc_start: 0.8459 (ttt180) cc_final: 0.8131 (mtm-85) REVERT: T 117 ASP cc_start: 0.8493 (t0) cc_final: 0.8172 (t70) REVERT: T 119 SER cc_start: 0.8963 (m) cc_final: 0.8664 (t) REVERT: U 39 ASP cc_start: 0.8591 (t0) cc_final: 0.8195 (t70) REVERT: U 63 ARG cc_start: 0.8472 (ttt180) cc_final: 0.8147 (mtm-85) REVERT: U 117 ASP cc_start: 0.8499 (t0) cc_final: 0.8177 (t70) REVERT: U 119 SER cc_start: 0.8965 (m) cc_final: 0.8667 (t) REVERT: V 39 ASP cc_start: 0.8605 (t0) cc_final: 0.8205 (t70) REVERT: V 63 ARG cc_start: 0.8462 (ttt180) cc_final: 0.8136 (mtm-85) REVERT: V 117 ASP cc_start: 0.8493 (t0) cc_final: 0.8174 (t70) REVERT: V 119 SER cc_start: 0.8955 (m) cc_final: 0.8657 (t) REVERT: W 39 ASP cc_start: 0.8595 (t0) cc_final: 0.8198 (t70) REVERT: W 63 ARG cc_start: 0.8480 (ttt180) cc_final: 0.8138 (mtm-85) REVERT: W 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8176 (t70) REVERT: W 119 SER cc_start: 0.8964 (m) cc_final: 0.8662 (t) REVERT: X 39 ASP cc_start: 0.8585 (t0) cc_final: 0.8184 (t70) REVERT: X 63 ARG cc_start: 0.8463 (ttt180) cc_final: 0.8125 (mtm-85) REVERT: X 117 ASP cc_start: 0.8507 (t0) cc_final: 0.8181 (t70) REVERT: X 119 SER cc_start: 0.8961 (m) cc_final: 0.8666 (t) outliers start: 94 outliers final: 91 residues processed: 716 average time/residue: 0.3076 time to fit residues: 324.8239 Evaluate side-chains 730 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 639 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 157 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 127 THR Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 127 THR Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain V residue 157 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain W residue 157 LEU Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 152 HIS Chi-restraints excluded: chain X residue 157 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 439 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 370 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 318 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN B 192 GLN C 192 GLN D 192 GLN E 192 GLN F 192 GLN G 192 GLN H 192 GLN I 192 GLN J 192 GLN K 192 GLN L 192 GLN M 192 GLN N 192 GLN O 192 GLN P 192 GLN Q 192 GLN R 192 GLN S 192 GLN T 192 GLN U 192 GLN V 192 GLN W 192 GLN X 192 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.088689 restraints weight = 41950.550| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.89 r_work: 0.2645 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 35976 Z= 0.158 Angle : 0.504 3.839 48912 Z= 0.273 Chirality : 0.045 0.152 5592 Planarity : 0.004 0.031 6504 Dihedral : 4.782 16.695 5088 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.52 % Allowed : 13.38 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.13), residues: 4512 helix: 2.30 (0.12), residues: 1872 sheet: 0.32 (0.14), residues: 1488 loop : -0.97 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 95 TYR 0.007 0.001 TYR T 45 PHE 0.008 0.002 PHE P 104 HIS 0.005 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (35976) covalent geometry : angle 0.50435 / 0.27 (48912) hydrogen bonds : bond 0.03699 / 2.62 ( 2184) hydrogen bonds : angle 3.86793 / 2.79 ( 6048) *********************** 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 721 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 702 time to evaluate : 1.499 Fit side-chains REVERT: A 39 ASP cc_start: 0.8463 (t0) cc_final: 0.8059 (t70) REVERT: A 63 ARG cc_start: 0.8486 (ttt180) cc_final: 0.8217 (mtm-85) REVERT: A 95 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7974 (tpp80) REVERT: A 117 ASP cc_start: 0.8418 (t0) cc_final: 0.8112 (t70) REVERT: A 192 GLN cc_start: 0.9178 (tt0) cc_final: 0.8913 (tt0) REVERT: B 39 ASP cc_start: 0.8449 (t0) cc_final: 0.8046 (t70) REVERT: B 63 ARG cc_start: 0.8483 (ttt180) cc_final: 0.8213 (mtm-85) REVERT: B 117 ASP cc_start: 0.8397 (t0) cc_final: 0.8093 (t70) REVERT: C 39 ASP cc_start: 0.8431 (t0) cc_final: 0.8019 (t70) REVERT: C 63 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8185 (mtm-85) REVERT: C 117 ASP cc_start: 0.8408 (t0) cc_final: 0.8101 (t70) REVERT: C 197 ASP cc_start: 0.7729 (t0) cc_final: 0.7522 (t0) REVERT: D 39 ASP cc_start: 0.8450 (t0) cc_final: 0.8052 (t70) REVERT: D 63 ARG cc_start: 0.8468 (ttt180) cc_final: 0.8199 (mtm-85) REVERT: D 117 ASP cc_start: 0.8405 (t0) cc_final: 0.8099 (t70) REVERT: E 39 ASP cc_start: 0.8446 (t0) cc_final: 0.8048 (t70) REVERT: E 63 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8195 (mtm-85) REVERT: E 117 ASP cc_start: 0.8408 (t0) cc_final: 0.8104 (t70) REVERT: F 39 ASP cc_start: 0.8439 (t0) cc_final: 0.8039 (t70) REVERT: F 63 ARG cc_start: 0.8475 (ttt180) cc_final: 0.8202 (mtm-85) REVERT: F 117 ASP cc_start: 0.8405 (t0) cc_final: 0.8099 (t70) REVERT: G 39 ASP cc_start: 0.8433 (t0) cc_final: 0.8036 (t70) REVERT: G 63 ARG cc_start: 0.8475 (ttt180) cc_final: 0.8197 (mtm-85) REVERT: G 117 ASP cc_start: 0.8400 (t0) cc_final: 0.8095 (t70) REVERT: H 39 ASP cc_start: 0.8445 (t0) cc_final: 0.8040 (t70) REVERT: H 63 ARG cc_start: 0.8466 (ttt180) cc_final: 0.8211 (mtm-85) REVERT: H 117 ASP cc_start: 0.8413 (t0) cc_final: 0.8110 (t70) REVERT: I 39 ASP cc_start: 0.8442 (t0) cc_final: 0.8044 (t70) REVERT: I 63 ARG cc_start: 0.8485 (ttt180) cc_final: 0.8209 (mtm-85) REVERT: I 117 ASP cc_start: 0.8404 (t0) cc_final: 0.8095 (t70) REVERT: J 39 ASP cc_start: 0.8451 (t0) cc_final: 0.8050 (t70) REVERT: J 63 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8217 (mtm-85) REVERT: J 117 ASP cc_start: 0.8416 (t0) cc_final: 0.8111 (t70) REVERT: K 39 ASP cc_start: 0.8455 (t0) cc_final: 0.8051 (t70) REVERT: K 63 ARG cc_start: 0.8490 (ttt180) cc_final: 0.8219 (mtm-85) REVERT: K 117 ASP cc_start: 0.8407 (t0) cc_final: 0.8099 (t70) REVERT: L 39 ASP cc_start: 0.8424 (t0) cc_final: 0.8018 (t70) REVERT: L 63 ARG cc_start: 0.8465 (ttt180) cc_final: 0.8187 (mtm-85) REVERT: L 117 ASP cc_start: 0.8403 (t0) cc_final: 0.8095 (t70) REVERT: L 197 ASP cc_start: 0.7734 (t0) cc_final: 0.7533 (t0) REVERT: M 39 ASP cc_start: 0.8429 (t0) cc_final: 0.8031 (t70) REVERT: M 63 ARG cc_start: 0.8461 (ttt180) cc_final: 0.8190 (mtm-85) REVERT: M 117 ASP cc_start: 0.8396 (t0) cc_final: 0.8090 (t70) REVERT: N 39 ASP cc_start: 0.8428 (t0) cc_final: 0.8024 (t70) REVERT: N 63 ARG cc_start: 0.8468 (ttt180) cc_final: 0.8190 (mtm-85) REVERT: N 117 ASP cc_start: 0.8405 (t0) cc_final: 0.8100 (t70) REVERT: O 39 ASP cc_start: 0.8442 (t0) cc_final: 0.8037 (t70) REVERT: O 63 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8203 (mtm-85) REVERT: O 117 ASP cc_start: 0.8415 (t0) cc_final: 0.8107 (t70) REVERT: O 197 ASP cc_start: 0.7730 (t0) cc_final: 0.7524 (t0) REVERT: P 39 ASP cc_start: 0.8457 (t0) cc_final: 0.8052 (t70) REVERT: P 63 ARG cc_start: 0.8459 (ttt180) cc_final: 0.8209 (mtm-85) REVERT: P 117 ASP cc_start: 0.8409 (t0) cc_final: 0.8107 (t70) REVERT: Q 39 ASP cc_start: 0.8465 (t0) cc_final: 0.8064 (t70) REVERT: Q 63 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8228 (mtm-85) REVERT: Q 95 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7992 (tpp80) REVERT: Q 117 ASP cc_start: 0.8402 (t0) cc_final: 0.8095 (t70) REVERT: R 39 ASP cc_start: 0.8432 (t0) cc_final: 0.8033 (t70) REVERT: R 63 ARG cc_start: 0.8467 (ttt180) cc_final: 0.8197 (mtm-85) REVERT: R 117 ASP cc_start: 0.8409 (t0) cc_final: 0.8100 (t70) REVERT: S 39 ASP cc_start: 0.8424 (t0) cc_final: 0.8022 (t70) REVERT: S 63 ARG cc_start: 0.8478 (ttt180) cc_final: 0.8195 (mtm-85) REVERT: S 117 ASP cc_start: 0.8394 (t0) cc_final: 0.8089 (t70) REVERT: T 39 ASP cc_start: 0.8451 (t0) cc_final: 0.8046 (t70) REVERT: T 63 ARG cc_start: 0.8465 (ttt180) cc_final: 0.8213 (mtm-85) REVERT: T 117 ASP cc_start: 0.8406 (t0) cc_final: 0.8104 (t70) REVERT: U 39 ASP cc_start: 0.8439 (t0) cc_final: 0.8032 (t70) REVERT: U 63 ARG cc_start: 0.8476 (ttt180) cc_final: 0.8196 (mtm-85) REVERT: U 117 ASP cc_start: 0.8411 (t0) cc_final: 0.8106 (t70) REVERT: U 197 ASP cc_start: 0.7741 (t0) cc_final: 0.7533 (t0) REVERT: V 39 ASP cc_start: 0.8434 (t0) cc_final: 0.8034 (t70) REVERT: V 63 ARG cc_start: 0.8482 (ttt180) cc_final: 0.8203 (mtm-85) REVERT: V 117 ASP cc_start: 0.8400 (t0) cc_final: 0.8092 (t70) REVERT: W 39 ASP cc_start: 0.8448 (t0) cc_final: 0.8044 (t70) REVERT: W 63 ARG cc_start: 0.8487 (ttt180) cc_final: 0.8216 (mtm-85) REVERT: W 117 ASP cc_start: 0.8398 (t0) cc_final: 0.8092 (t70) REVERT: X 39 ASP cc_start: 0.8426 (t0) cc_final: 0.8027 (t70) REVERT: X 63 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8193 (mtm-85) REVERT: X 117 ASP cc_start: 0.8397 (t0) cc_final: 0.8088 (t70) outliers start: 19 outliers final: 19 residues processed: 710 average time/residue: 0.3071 time to fit residues: 322.5762 Evaluate side-chains 675 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 656 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain S residue 127 THR Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 133 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 86 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 405 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 450 optimal weight: 9.9990 chunk 436 optimal weight: 0.9990 chunk 366 optimal weight: 8.9990 chunk 271 optimal weight: 7.9990 chunk 202 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 362 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 192 GLN C 192 GLN D 192 GLN E 192 GLN F 192 GLN G 192 GLN H 192 GLN I 192 GLN J 192 GLN P 192 GLN S 192 GLN T 192 GLN U 192 GLN V 192 GLN W 192 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.113418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.088176 restraints weight = 41935.866| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 1.90 r_work: 0.2625 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 35976 Z= 0.188 Angle : 0.544 6.304 48912 Z= 0.289 Chirality : 0.046 0.154 5592 Planarity : 0.004 0.033 6504 Dihedral : 4.778 16.814 5088 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.63 % Allowed : 13.98 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.13), residues: 4512 helix: 2.36 (0.12), residues: 1872 sheet: 0.27 (0.13), residues: 1488 loop : -0.91 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 95 TYR 0.008 0.002 TYR C 45 PHE 0.009 0.002 PHE D 104 HIS 0.005 0.001 HIS D 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (35976) covalent geometry : angle 0.54441 / 0.29 (48912) hydrogen bonds : bond 0.03976 / 2.82 ( 2184) hydrogen bonds : angle 3.88318 / 2.80 ( 6048) ********************** 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 743 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 720 time to evaluate : 1.414 Fit side-chains REVERT: A 39 ASP cc_start: 0.8493 (t0) cc_final: 0.8090 (t70) REVERT: A 63 ARG cc_start: 0.8461 (ttt180) cc_final: 0.8197 (mtm-85) REVERT: A 95 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7952 (tpp80) REVERT: A 117 ASP cc_start: 0.8434 (t0) cc_final: 0.8129 (t70) REVERT: A 119 SER cc_start: 0.8875 (m) cc_final: 0.8607 (t) REVERT: B 39 ASP cc_start: 0.8465 (t0) cc_final: 0.8062 (t70) REVERT: B 63 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8208 (mtm-85) REVERT: B 117 ASP cc_start: 0.8419 (t0) cc_final: 0.8112 (t70) REVERT: B 119 SER cc_start: 0.8875 (m) cc_final: 0.8601 (t) REVERT: C 39 ASP cc_start: 0.8469 (t0) cc_final: 0.8060 (t70) REVERT: C 63 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8165 (mtm-85) REVERT: C 117 ASP cc_start: 0.8432 (t0) cc_final: 0.8132 (t70) REVERT: D 39 ASP cc_start: 0.8481 (t0) cc_final: 0.8078 (t70) REVERT: D 63 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8182 (mtm-85) REVERT: D 117 ASP cc_start: 0.8434 (t0) cc_final: 0.8128 (t70) REVERT: D 119 SER cc_start: 0.8889 (m) cc_final: 0.8615 (t) REVERT: E 39 ASP cc_start: 0.8479 (t0) cc_final: 0.8076 (t70) REVERT: E 63 ARG cc_start: 0.8437 (ttt180) cc_final: 0.8179 (mtm-85) REVERT: E 117 ASP cc_start: 0.8432 (t0) cc_final: 0.8126 (t70) REVERT: E 119 SER cc_start: 0.8884 (m) cc_final: 0.8611 (t) REVERT: F 39 ASP cc_start: 0.8471 (t0) cc_final: 0.8067 (t70) REVERT: F 63 ARG cc_start: 0.8440 (ttt180) cc_final: 0.8177 (mtm-85) REVERT: F 117 ASP cc_start: 0.8422 (t0) cc_final: 0.8117 (t70) REVERT: F 119 SER cc_start: 0.8871 (m) cc_final: 0.8597 (t) REVERT: G 39 ASP cc_start: 0.8467 (t0) cc_final: 0.8064 (t70) REVERT: G 63 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8175 (mtm-85) REVERT: G 117 ASP cc_start: 0.8415 (t0) cc_final: 0.8109 (t70) REVERT: G 119 SER cc_start: 0.8874 (m) cc_final: 0.8601 (t) REVERT: H 39 ASP cc_start: 0.8461 (t0) cc_final: 0.8056 (t70) REVERT: H 63 ARG cc_start: 0.8456 (ttt180) cc_final: 0.8197 (mtm-85) REVERT: H 117 ASP cc_start: 0.8432 (t0) cc_final: 0.8128 (t70) REVERT: H 119 SER cc_start: 0.8882 (m) cc_final: 0.8609 (t) REVERT: I 39 ASP cc_start: 0.8470 (t0) cc_final: 0.8067 (t70) REVERT: I 63 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8180 (mtm-85) REVERT: I 117 ASP cc_start: 0.8417 (t0) cc_final: 0.8109 (t70) REVERT: I 119 SER cc_start: 0.8875 (m) cc_final: 0.8602 (t) REVERT: J 39 ASP cc_start: 0.8491 (t0) cc_final: 0.8088 (t70) REVERT: J 63 ARG cc_start: 0.8464 (ttt180) cc_final: 0.8198 (mtm-85) REVERT: J 117 ASP cc_start: 0.8427 (t0) cc_final: 0.8123 (t70) REVERT: J 119 SER cc_start: 0.8892 (m) cc_final: 0.8616 (t) REVERT: K 39 ASP cc_start: 0.8487 (t0) cc_final: 0.8084 (t70) REVERT: K 63 ARG cc_start: 0.8477 (ttt180) cc_final: 0.8200 (mtm-85) REVERT: K 117 ASP cc_start: 0.8427 (t0) cc_final: 0.8122 (t70) REVERT: K 119 SER cc_start: 0.8890 (m) cc_final: 0.8614 (t) REVERT: L 39 ASP cc_start: 0.8449 (t0) cc_final: 0.8036 (t70) REVERT: L 63 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8155 (mtm-85) REVERT: L 117 ASP cc_start: 0.8426 (t0) cc_final: 0.8116 (t70) REVERT: L 119 SER cc_start: 0.8869 (m) cc_final: 0.8597 (t) REVERT: M 39 ASP cc_start: 0.8476 (t0) cc_final: 0.8073 (t70) REVERT: M 63 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8171 (mtm-85) REVERT: M 117 ASP cc_start: 0.8416 (t0) cc_final: 0.8109 (t70) REVERT: M 119 SER cc_start: 0.8877 (m) cc_final: 0.8604 (t) REVERT: N 39 ASP cc_start: 0.8469 (t0) cc_final: 0.8068 (t70) REVERT: N 63 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8165 (mtm-85) REVERT: N 117 ASP cc_start: 0.8415 (t0) cc_final: 0.8108 (t70) REVERT: N 119 SER cc_start: 0.8880 (m) cc_final: 0.8604 (t) REVERT: O 39 ASP cc_start: 0.8467 (t0) cc_final: 0.8055 (t70) REVERT: O 63 ARG cc_start: 0.8450 (ttt180) cc_final: 0.8191 (mtm-85) REVERT: O 117 ASP cc_start: 0.8430 (t0) cc_final: 0.8126 (t70) REVERT: O 119 SER cc_start: 0.8881 (m) cc_final: 0.8608 (t) REVERT: P 39 ASP cc_start: 0.8472 (t0) cc_final: 0.8073 (t70) REVERT: P 63 ARG cc_start: 0.8437 (ttt180) cc_final: 0.8191 (mtm-85) REVERT: P 117 ASP cc_start: 0.8425 (t0) cc_final: 0.8120 (t70) REVERT: P 119 SER cc_start: 0.8877 (m) cc_final: 0.8599 (t) REVERT: Q 39 ASP cc_start: 0.8481 (t0) cc_final: 0.8079 (t70) REVERT: Q 63 ARG cc_start: 0.8459 (ttt180) cc_final: 0.8207 (mtm-85) REVERT: Q 95 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7973 (tpp80) REVERT: Q 117 ASP cc_start: 0.8427 (t0) cc_final: 0.8120 (t70) REVERT: Q 119 SER cc_start: 0.8860 (m) cc_final: 0.8594 (t) REVERT: R 39 ASP cc_start: 0.8455 (t0) cc_final: 0.8053 (t70) REVERT: R 63 ARG cc_start: 0.8450 (ttt180) cc_final: 0.8170 (mtm-85) REVERT: R 117 ASP cc_start: 0.8422 (t0) cc_final: 0.8114 (t70) REVERT: R 119 SER cc_start: 0.8874 (m) cc_final: 0.8600 (t) REVERT: S 39 ASP cc_start: 0.8456 (t0) cc_final: 0.8053 (t70) REVERT: S 63 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8175 (mtm-85) REVERT: S 117 ASP cc_start: 0.8419 (t0) cc_final: 0.8114 (t70) REVERT: S 119 SER cc_start: 0.8878 (m) cc_final: 0.8604 (t) REVERT: T 39 ASP cc_start: 0.8466 (t0) cc_final: 0.8069 (t70) REVERT: T 63 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8203 (mtm-85) REVERT: T 117 ASP cc_start: 0.8423 (t0) cc_final: 0.8121 (t70) REVERT: T 119 SER cc_start: 0.8878 (m) cc_final: 0.8602 (t) REVERT: U 39 ASP cc_start: 0.8480 (t0) cc_final: 0.8064 (t70) REVERT: U 63 ARG cc_start: 0.8440 (ttt180) cc_final: 0.8174 (mtm-85) REVERT: U 117 ASP cc_start: 0.8438 (t0) cc_final: 0.8141 (t70) REVERT: V 39 ASP cc_start: 0.8477 (t0) cc_final: 0.8075 (t70) REVERT: V 63 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8178 (mtm-85) REVERT: V 117 ASP cc_start: 0.8421 (t0) cc_final: 0.8115 (t70) REVERT: V 119 SER cc_start: 0.8881 (m) cc_final: 0.8606 (t) REVERT: W 39 ASP cc_start: 0.8461 (t0) cc_final: 0.8057 (t70) REVERT: W 63 ARG cc_start: 0.8480 (ttt180) cc_final: 0.8196 (mtm-85) REVERT: W 117 ASP cc_start: 0.8419 (t0) cc_final: 0.8114 (t70) REVERT: W 119 SER cc_start: 0.8881 (m) cc_final: 0.8607 (t) REVERT: X 39 ASP cc_start: 0.8453 (t0) cc_final: 0.8051 (t70) REVERT: X 63 ARG cc_start: 0.8440 (ttt180) cc_final: 0.8163 (mtm-85) REVERT: X 117 ASP cc_start: 0.8422 (t0) cc_final: 0.8112 (t70) REVERT: X 119 SER cc_start: 0.8874 (m) cc_final: 0.8600 (t) outliers start: 23 outliers final: 23 residues processed: 731 average time/residue: 0.3030 time to fit residues: 328.0185 Evaluate side-chains 695 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 672 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain S residue 127 THR Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 133 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 257 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 302 optimal weight: 0.9980 chunk 446 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 369 optimal weight: 4.9990 chunk 260 optimal weight: 0.0050 chunk 281 optimal weight: 1.9990 chunk 341 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN B 192 GLN C 73 HIS C 192 GLN D 192 GLN E 192 GLN F 73 HIS F 192 GLN G 192 GLN H 192 GLN I 192 GLN J 73 HIS J 192 GLN K 73 HIS P 192 GLN Q 73 HIS S 192 GLN T 192 GLN U 192 GLN V 192 GLN W 192 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.117729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.092912 restraints weight = 41294.290| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.84 r_work: 0.2766 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 35976 Z= 0.092 Angle : 0.474 6.549 48912 Z= 0.249 Chirality : 0.043 0.148 5592 Planarity : 0.004 0.033 6504 Dihedral : 4.319 15.157 5088 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.66 % Allowed : 14.28 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.13), residues: 4512 helix: 2.70 (0.12), residues: 1872 sheet: 0.25 (0.14), residues: 1488 loop : -0.89 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.005 0.001 TYR Q 145 PHE 0.008 0.001 PHE W 104 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (35976) covalent geometry : angle 0.47351 / 0.25 (48912) hydrogen bonds : bond 0.02782 / 1.96 ( 2184) hydrogen bonds : angle 3.64820 / 2.63 ( 6048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9179.48 seconds wall clock time: 158 minutes 13.55 seconds (9493.55 seconds total)