Starting phenix.real_space_refine on Tue Aug 26 08:38:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2p_63588/08_2025/9m2p_63588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2p_63588/08_2025/9m2p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9m2p_63588/08_2025/9m2p_63588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2p_63588/08_2025/9m2p_63588.map" model { file = "/net/cci-nas-00/data/ceres_data/9m2p_63588/08_2025/9m2p_63588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2p_63588/08_2025/9m2p_63588.cif" } 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-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 8.10, 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: 3.25 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.4 microseconds 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: 1.44 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: 8.35 Time building geometry restraints manager: 4.36 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 2.320 nonbonded pdb="MN MN D 302 " pdb=" O HOH D 402 " model vdw 2.200 2.320 nonbonded pdb="MN MN Q 302 " pdb=" O HOH Q 402 " model vdw 2.200 2.320 nonbonded pdb="MN MN W 302 " pdb=" O HOH W 402 " model vdw 2.200 2.320 nonbonded pdb="MN MN E 302 " pdb=" O HOH E 402 " model vdw 2.200 2.320 ... (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: 0.13 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.060 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.150 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 aren 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 covalent geometry : bond 0.00712 (35976) covalent geometry : angle 1.14462 (48912) hydrogen bonds : bond 0.16389 ( 2184) hydrogen bonds : angle 6.28104 ( 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 : 1.406 Fit side-chains REVERT: A 29 ASP cc_start: 0.7818 (t0) cc_final: 0.7467 (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: 0.8097 (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: 0.7819 (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: 0.7817 (t0) cc_final: 0.7467 (t70) REVERT: D 39 ASP cc_start: 0.7799 (t0) cc_final: 0.7464 (t70) REVERT: D 63 ARG cc_start: 0.7925 (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: 0.8064 (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: 0.8364 (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: 0.7797 (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: 0.7938 (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: 0.8064 (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: 0.8363 (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: 0.7590 (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: 0.7907 (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: 0.7451 (mtp85) REVERT: I 29 ASP cc_start: 0.7815 (t0) cc_final: 0.7469 (t70) REVERT: I 39 ASP cc_start: 0.7936 (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: 0.7569 (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: 0.7797 (mtt180) cc_final: 0.7451 (mtp85) REVERT: J 29 ASP cc_start: 0.7816 (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: 0.7799 (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: 0.8065 (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: 0.8363 (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: 0.7590 (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: 0.8364 (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: 0.7814 (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: 0.8007 (ttm-80) REVERT: M 107 MET cc_start: 0.8364 (ttt) cc_final: 0.8047 (ttt) REVERT: M 162 ARG cc_start: 0.7796 (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: 0.7501 (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: 0.8051 (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: 0.8364 (ttt) cc_final: 0.8051 (ttt) REVERT: Q 162 ARG cc_start: 0.7797 (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: 0.7849 (tt0) REVERT: R 93 ASP cc_start: 0.7905 (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: 0.7799 (mtt180) cc_final: 0.7453 (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: 0.8366 (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: 0.7816 (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: 0.8063 (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: 0.8669 (ttt180) cc_final: 0.8058 (ttm-80) REVERT: T 107 MET cc_start: 0.8364 (ttt) cc_final: 0.8051 (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: 0.7939 (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: 0.7813 (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: 0.7569 (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: 0.7819 (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: 0.7569 (p0) REVERT: W 95 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8008 (ttm-80) REVERT: W 107 MET cc_start: 0.8366 (ttt) cc_final: 0.8050 (ttt) REVERT: W 162 ARG cc_start: 0.7796 (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: 0.8055 (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: 0.2681 time to fit residues: 386.2641 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 : 0.996 ------------------------------------------------------------------------------- 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: 0.9980 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: 4.9990 chunk 401 optimal weight: 3.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.110410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.084485 restraints weight = 42567.196| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.02 r_work: 0.2618 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 35976 Z= 0.155 Angle : 0.533 3.955 48912 Z= 0.292 Chirality : 0.045 0.129 5592 Planarity : 0.004 0.025 6504 Dihedral : 4.943 17.606 5088 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.32 % Allowed : 6.80 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.13), residues: 4512 helix: 1.89 (0.12), residues: 1872 sheet: 0.08 (0.14), residues: 1488 loop : -1.11 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 99 TYR 0.007 0.001 TYR X 145 PHE 0.012 0.002 PHE I 104 HIS 0.006 0.001 HIS Q 176 Details of bonding type rmsd covalent geometry : bond 0.00353 (35976) covalent geometry : angle 0.53336 (48912) hydrogen bonds : bond 0.03828 ( 2184) hydrogen bonds : angle 4.01015 ( 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 960 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 912 time to evaluate : 1.341 Fit side-chains REVERT: A 39 ASP cc_start: 0.8375 (t0) cc_final: 0.7954 (t70) REVERT: A 63 ARG cc_start: 0.8446 (ttt180) cc_final: 0.8185 (mtm-85) REVERT: A 93 ASP cc_start: 0.8104 (p0) cc_final: 0.7796 (p0) REVERT: A 95 ARG cc_start: 0.8494 (ttt180) cc_final: 0.8275 (ttm-80) REVERT: A 117 ASP cc_start: 0.8516 (t0) cc_final: 0.8212 (t70) REVERT: A 192 GLN cc_start: 0.9200 (tt0) cc_final: 0.8832 (tt0) REVERT: B 39 ASP cc_start: 0.8359 (t0) cc_final: 0.7944 (t70) REVERT: B 63 ARG cc_start: 0.8464 (ttt180) cc_final: 0.8185 (mtm-85) REVERT: B 95 ARG cc_start: 0.8435 (ttt180) cc_final: 0.8222 (ttm-80) REVERT: B 117 ASP cc_start: 0.8516 (t0) cc_final: 0.8215 (t70) REVERT: B 192 GLN cc_start: 0.9190 (tt0) cc_final: 0.8825 (tt0) REVERT: C 39 ASP cc_start: 0.8377 (t0) cc_final: 0.7962 (t70) REVERT: C 63 ARG cc_start: 0.8450 (ttt180) cc_final: 0.8182 (mtm-85) REVERT: C 95 ARG cc_start: 0.8434 (ttt180) cc_final: 0.8215 (ttm-80) REVERT: C 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8202 (t70) REVERT: C 192 GLN cc_start: 0.9191 (tt0) cc_final: 0.8824 (tt0) REVERT: D 39 ASP cc_start: 0.8365 (t0) cc_final: 0.7945 (t70) REVERT: D 63 ARG cc_start: 0.8408 (ttt180) cc_final: 0.8171 (mtm-85) REVERT: D 95 ARG cc_start: 0.8434 (ttt180) cc_final: 0.8222 (ttm-80) REVERT: D 117 ASP cc_start: 0.8508 (t0) cc_final: 0.8204 (t70) REVERT: D 192 GLN cc_start: 0.9179 (tt0) cc_final: 0.8804 (tt0) REVERT: E 39 ASP cc_start: 0.8366 (t0) cc_final: 0.7949 (t70) REVERT: E 63 ARG cc_start: 0.8421 (ttt180) cc_final: 0.8170 (mtm-85) REVERT: E 95 ARG cc_start: 0.8443 (ttt180) cc_final: 0.8229 (ttm-80) REVERT: E 117 ASP cc_start: 0.8507 (t0) cc_final: 0.8203 (t70) REVERT: E 192 GLN cc_start: 0.9182 (tt0) cc_final: 0.8809 (tt0) REVERT: F 39 ASP cc_start: 0.8350 (t0) cc_final: 0.7931 (t70) REVERT: F 63 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8177 (mtm-85) REVERT: F 95 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8225 (ttm-80) REVERT: F 117 ASP cc_start: 0.8518 (t0) cc_final: 0.8211 (t70) REVERT: F 192 GLN cc_start: 0.9178 (tt0) cc_final: 0.8808 (tt0) REVERT: G 39 ASP cc_start: 0.8360 (t0) cc_final: 0.7945 (t70) REVERT: G 63 ARG cc_start: 0.8436 (ttt180) cc_final: 0.8178 (mtm-85) REVERT: G 95 ARG cc_start: 0.8477 (ttt180) cc_final: 0.8225 (ttm-80) REVERT: G 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8205 (t70) REVERT: G 192 GLN cc_start: 0.9190 (tt0) cc_final: 0.8824 (tt0) REVERT: H 39 ASP cc_start: 0.8384 (t0) cc_final: 0.7970 (t70) REVERT: H 63 ARG cc_start: 0.8454 (ttt180) cc_final: 0.8182 (mtm-85) REVERT: H 95 ARG cc_start: 0.8424 (ttt180) cc_final: 0.8215 (ttm-80) REVERT: H 117 ASP cc_start: 0.8510 (t0) cc_final: 0.8204 (t70) REVERT: H 192 GLN cc_start: 0.9190 (tt0) cc_final: 0.8824 (tt0) REVERT: I 39 ASP cc_start: 0.8357 (t0) cc_final: 0.7939 (t70) REVERT: I 63 ARG cc_start: 0.8425 (ttt180) cc_final: 0.8177 (mtm-85) REVERT: I 95 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8226 (ttm-80) REVERT: I 117 ASP cc_start: 0.8518 (t0) cc_final: 0.8211 (t70) REVERT: I 192 GLN cc_start: 0.9176 (tt0) cc_final: 0.8804 (tt0) REVERT: J 39 ASP cc_start: 0.8374 (t0) cc_final: 0.7956 (t70) REVERT: J 63 ARG cc_start: 0.8453 (ttt180) cc_final: 0.8184 (mtm-85) REVERT: J 95 ARG cc_start: 0.8486 (ttt180) cc_final: 0.8235 (ttm-80) REVERT: J 117 ASP cc_start: 0.8516 (t0) cc_final: 0.8208 (t70) REVERT: J 192 GLN cc_start: 0.9195 (tt0) cc_final: 0.8827 (tt0) REVERT: K 39 ASP cc_start: 0.8373 (t0) cc_final: 0.7954 (t70) REVERT: K 63 ARG cc_start: 0.8444 (ttt180) cc_final: 0.8181 (mtm-85) REVERT: K 95 ARG cc_start: 0.8489 (ttt180) cc_final: 0.8237 (ttm-80) REVERT: K 117 ASP cc_start: 0.8517 (t0) cc_final: 0.8212 (t70) REVERT: K 192 GLN cc_start: 0.9195 (tt0) cc_final: 0.8828 (tt0) REVERT: L 39 ASP cc_start: 0.8357 (t0) cc_final: 0.7942 (t70) REVERT: L 63 ARG cc_start: 0.8425 (ttt180) cc_final: 0.8175 (mtm-85) REVERT: L 95 ARG cc_start: 0.8462 (ttt180) cc_final: 0.8230 (ttm-80) REVERT: L 117 ASP cc_start: 0.8517 (t0) cc_final: 0.8212 (t70) REVERT: L 192 GLN cc_start: 0.9180 (tt0) cc_final: 0.8810 (tt0) REVERT: M 39 ASP cc_start: 0.8360 (t0) cc_final: 0.7944 (t70) REVERT: M 63 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8173 (mtm-85) REVERT: M 95 ARG cc_start: 0.8464 (ttt180) cc_final: 0.8220 (ttm-80) REVERT: M 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8204 (t70) REVERT: M 192 GLN cc_start: 0.9191 (tt0) cc_final: 0.8825 (tt0) REVERT: N 39 ASP cc_start: 0.8367 (t0) cc_final: 0.7950 (t70) REVERT: N 63 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8168 (mtm-85) REVERT: N 95 ARG cc_start: 0.8461 (ttt180) cc_final: 0.8234 (ttm-80) REVERT: N 117 ASP cc_start: 0.8526 (t0) cc_final: 0.8224 (t70) REVERT: N 192 GLN cc_start: 0.9186 (tt0) cc_final: 0.8816 (tt0) REVERT: O 39 ASP cc_start: 0.8383 (t0) cc_final: 0.7968 (t70) REVERT: O 63 ARG cc_start: 0.8453 (ttt180) cc_final: 0.8183 (mtm-85) REVERT: O 95 ARG cc_start: 0.8427 (ttt180) cc_final: 0.8212 (ttm-80) REVERT: O 117 ASP cc_start: 0.8511 (t0) cc_final: 0.8205 (t70) REVERT: O 192 GLN cc_start: 0.9192 (tt0) cc_final: 0.8826 (tt0) REVERT: P 39 ASP cc_start: 0.8370 (t0) cc_final: 0.7956 (t70) REVERT: P 63 ARG cc_start: 0.8443 (ttt180) cc_final: 0.8168 (mtm-85) REVERT: P 95 ARG cc_start: 0.8450 (ttt180) cc_final: 0.8231 (ttm-80) REVERT: P 117 ASP cc_start: 0.8523 (t0) cc_final: 0.8221 (t70) REVERT: P 192 GLN cc_start: 0.9187 (tt0) cc_final: 0.8818 (tt0) REVERT: Q 39 ASP cc_start: 0.8358 (t0) cc_final: 0.7937 (t70) REVERT: Q 63 ARG cc_start: 0.8424 (ttt180) cc_final: 0.8176 (mtm-85) REVERT: Q 93 ASP cc_start: 0.8086 (p0) cc_final: 0.7781 (p0) REVERT: Q 95 ARG cc_start: 0.8482 (ttt180) cc_final: 0.8268 (ttm-80) REVERT: Q 117 ASP cc_start: 0.8517 (t0) cc_final: 0.8210 (t70) REVERT: Q 192 GLN cc_start: 0.9179 (tt0) cc_final: 0.8810 (tt0) REVERT: R 39 ASP cc_start: 0.8356 (t0) cc_final: 0.7937 (t70) REVERT: R 63 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8176 (mtm-85) REVERT: R 95 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8237 (ttm-80) REVERT: R 117 ASP cc_start: 0.8521 (t0) cc_final: 0.8215 (t70) REVERT: R 192 GLN cc_start: 0.9181 (tt0) cc_final: 0.8814 (tt0) REVERT: S 39 ASP cc_start: 0.8364 (t0) cc_final: 0.7946 (t70) REVERT: S 63 ARG cc_start: 0.8461 (ttt180) cc_final: 0.8187 (mtm-85) REVERT: S 95 ARG cc_start: 0.8421 (ttt180) cc_final: 0.8217 (ttm-80) REVERT: S 117 ASP cc_start: 0.8513 (t0) cc_final: 0.8212 (t70) REVERT: S 192 GLN cc_start: 0.9189 (tt0) cc_final: 0.8822 (tt0) REVERT: T 39 ASP cc_start: 0.8367 (t0) cc_final: 0.7950 (t70) REVERT: T 63 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8169 (mtm-85) REVERT: T 95 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8235 (ttm-80) REVERT: T 117 ASP cc_start: 0.8521 (t0) cc_final: 0.8218 (t70) REVERT: T 192 GLN cc_start: 0.9190 (tt0) cc_final: 0.8818 (tt0) REVERT: U 39 ASP cc_start: 0.8371 (t0) cc_final: 0.7954 (t70) REVERT: U 63 ARG cc_start: 0.8416 (ttt180) cc_final: 0.8173 (mtm-85) REVERT: U 95 ARG cc_start: 0.8446 (ttt180) cc_final: 0.8226 (ttm-80) REVERT: U 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8206 (t70) REVERT: U 192 GLN cc_start: 0.9177 (tt0) cc_final: 0.8804 (tt0) REVERT: V 39 ASP cc_start: 0.8361 (t0) cc_final: 0.7947 (t70) REVERT: V 63 ARG cc_start: 0.8435 (ttt180) cc_final: 0.8177 (mtm-85) REVERT: V 95 ARG cc_start: 0.8483 (ttt180) cc_final: 0.8227 (ttm-80) REVERT: V 117 ASP cc_start: 0.8510 (t0) cc_final: 0.8205 (t70) REVERT: V 192 GLN cc_start: 0.9192 (tt0) cc_final: 0.8827 (tt0) REVERT: W 39 ASP cc_start: 0.8361 (t0) cc_final: 0.7945 (t70) REVERT: W 63 ARG cc_start: 0.8468 (ttt180) cc_final: 0.8186 (mtm-85) REVERT: W 95 ARG cc_start: 0.8424 (ttt180) cc_final: 0.8218 (ttm-80) REVERT: W 117 ASP cc_start: 0.8518 (t0) cc_final: 0.8217 (t70) REVERT: W 192 GLN cc_start: 0.9193 (tt0) cc_final: 0.8828 (tt0) REVERT: X 39 ASP cc_start: 0.8359 (t0) cc_final: 0.7939 (t70) REVERT: X 63 ARG cc_start: 0.8422 (ttt180) cc_final: 0.8174 (mtm-85) REVERT: X 95 ARG cc_start: 0.8465 (ttt180) cc_final: 0.8234 (ttm-80) REVERT: X 117 ASP cc_start: 0.8525 (t0) cc_final: 0.8219 (t70) REVERT: X 192 GLN cc_start: 0.9177 (tt0) cc_final: 0.8805 (tt0) outliers start: 48 outliers final: 48 residues processed: 936 average time/residue: 0.2769 time to fit residues: 386.5105 Evaluate side-chains 960 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 912 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 152 HIS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 265 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 438 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 426 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 364 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 369 optimal weight: 0.0980 chunk 273 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 89 GLN M 89 GLN N 89 GLN O 89 GLN P 89 GLN Q 89 GLN R 89 GLN S 89 GLN T 89 GLN U 89 GLN V 89 GLN W 89 GLN X 89 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.110257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.084398 restraints weight = 42536.019| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.01 r_work: 0.2620 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35976 Z= 0.145 Angle : 0.500 3.503 48912 Z= 0.271 Chirality : 0.045 0.132 5592 Planarity : 0.004 0.033 6504 Dihedral : 4.669 16.515 5088 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.13), residues: 4512 helix: 2.23 (0.12), residues: 1872 sheet: 0.21 (0.14), residues: 1488 loop : -0.59 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 99 TYR 0.006 0.001 TYR J 145 PHE 0.009 0.001 PHE N 104 HIS 0.005 0.001 HIS V 176 Details of bonding type rmsd covalent geometry : bond 0.00338 (35976) covalent geometry : angle 0.50037 (48912) hydrogen bonds : bond 0.03651 ( 2184) hydrogen bonds : angle 3.78021 ( 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 851 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 851 time to evaluate : 1.356 Fit side-chains REVERT: A 39 ASP cc_start: 0.8392 (t0) cc_final: 0.7973 (t70) REVERT: A 63 ARG cc_start: 0.8478 (ttt180) cc_final: 0.8231 (mtm-85) REVERT: A 93 ASP cc_start: 0.8142 (p0) cc_final: 0.7913 (p0) REVERT: A 117 ASP cc_start: 0.8439 (t0) cc_final: 0.8182 (t70) REVERT: A 192 GLN cc_start: 0.9252 (tt0) cc_final: 0.8929 (tt0) REVERT: B 39 ASP cc_start: 0.8390 (t0) cc_final: 0.7977 (t70) REVERT: B 63 ARG cc_start: 0.8506 (ttt180) cc_final: 0.8240 (mtm-85) REVERT: B 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8177 (t70) REVERT: B 192 GLN cc_start: 0.9256 (tt0) cc_final: 0.8936 (tt0) REVERT: C 39 ASP cc_start: 0.8397 (t0) cc_final: 0.7982 (t70) REVERT: C 63 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8240 (mtm-85) REVERT: C 117 ASP cc_start: 0.8457 (t0) cc_final: 0.8177 (t70) REVERT: C 192 GLN cc_start: 0.9261 (tt0) cc_final: 0.8940 (tt0) REVERT: D 39 ASP cc_start: 0.8392 (t0) cc_final: 0.7972 (t70) REVERT: D 63 ARG cc_start: 0.8504 (ttt180) cc_final: 0.8237 (mtm-85) REVERT: D 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8188 (t70) REVERT: D 192 GLN cc_start: 0.9254 (tt0) cc_final: 0.8938 (tt0) REVERT: E 39 ASP cc_start: 0.8400 (t0) cc_final: 0.7983 (t70) REVERT: E 63 ARG cc_start: 0.8510 (ttt180) cc_final: 0.8234 (mtm-85) REVERT: E 117 ASP cc_start: 0.8446 (t0) cc_final: 0.8187 (t70) REVERT: E 192 GLN cc_start: 0.9255 (tt0) cc_final: 0.8932 (tt0) REVERT: F 39 ASP cc_start: 0.8389 (t0) cc_final: 0.7976 (t70) REVERT: F 63 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8241 (mtm-85) REVERT: F 117 ASP cc_start: 0.8446 (t0) cc_final: 0.8176 (t70) REVERT: F 192 GLN cc_start: 0.9257 (tt0) cc_final: 0.8942 (tt0) REVERT: G 39 ASP cc_start: 0.8380 (t0) cc_final: 0.7966 (t70) REVERT: G 63 ARG cc_start: 0.8495 (ttt180) cc_final: 0.8238 (mtm-85) REVERT: G 117 ASP cc_start: 0.8432 (t0) cc_final: 0.8154 (t70) REVERT: G 192 GLN cc_start: 0.9251 (tt0) cc_final: 0.8925 (tt0) REVERT: H 39 ASP cc_start: 0.8396 (t0) cc_final: 0.7982 (t70) REVERT: H 63 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8247 (mtm-85) REVERT: H 117 ASP cc_start: 0.8453 (t0) cc_final: 0.8193 (t70) REVERT: H 192 GLN cc_start: 0.9261 (tt0) cc_final: 0.8940 (tt0) REVERT: I 39 ASP cc_start: 0.8389 (t0) cc_final: 0.7974 (t70) REVERT: I 63 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8240 (mtm-85) REVERT: I 117 ASP cc_start: 0.8441 (t0) cc_final: 0.8170 (t70) REVERT: I 192 GLN cc_start: 0.9256 (tt0) cc_final: 0.8933 (tt0) REVERT: J 39 ASP cc_start: 0.8390 (t0) cc_final: 0.7976 (t70) REVERT: J 63 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8231 (mtm-85) REVERT: J 117 ASP cc_start: 0.8442 (t0) cc_final: 0.8183 (t70) REVERT: J 192 GLN cc_start: 0.9254 (tt0) cc_final: 0.8929 (tt0) REVERT: K 39 ASP cc_start: 0.8392 (t0) cc_final: 0.7977 (t70) REVERT: K 63 ARG cc_start: 0.8475 (ttt180) cc_final: 0.8232 (mtm-85) REVERT: K 117 ASP cc_start: 0.8450 (t0) cc_final: 0.8182 (t70) REVERT: K 192 GLN cc_start: 0.9254 (tt0) cc_final: 0.8930 (tt0) REVERT: L 39 ASP cc_start: 0.8370 (t0) cc_final: 0.7958 (t70) REVERT: L 63 ARG cc_start: 0.8541 (ttt180) cc_final: 0.8246 (mtm-85) REVERT: L 117 ASP cc_start: 0.8444 (t0) cc_final: 0.8184 (t70) REVERT: L 192 GLN cc_start: 0.9254 (tt0) cc_final: 0.8931 (tt0) REVERT: M 39 ASP cc_start: 0.8383 (t0) cc_final: 0.7969 (t70) REVERT: M 63 ARG cc_start: 0.8503 (ttt180) cc_final: 0.8236 (mtm-85) REVERT: M 117 ASP cc_start: 0.8434 (t0) cc_final: 0.8175 (t70) REVERT: M 192 GLN cc_start: 0.9252 (tt0) cc_final: 0.8929 (tt0) REVERT: N 39 ASP cc_start: 0.8382 (t0) cc_final: 0.7969 (t70) REVERT: N 63 ARG cc_start: 0.8511 (ttt180) cc_final: 0.8239 (mtm-85) REVERT: N 117 ASP cc_start: 0.8446 (t0) cc_final: 0.8187 (t70) REVERT: N 192 GLN cc_start: 0.9262 (tt0) cc_final: 0.8943 (tt0) REVERT: O 39 ASP cc_start: 0.8396 (t0) cc_final: 0.7979 (t70) REVERT: O 63 ARG cc_start: 0.8505 (ttt180) cc_final: 0.8242 (mtm-85) REVERT: O 117 ASP cc_start: 0.8457 (t0) cc_final: 0.8185 (t70) REVERT: O 192 GLN cc_start: 0.9260 (tt0) cc_final: 0.8939 (tt0) REVERT: P 39 ASP cc_start: 0.8392 (t0) cc_final: 0.7979 (t70) REVERT: P 63 ARG cc_start: 0.8513 (ttt180) cc_final: 0.8238 (mtm-85) REVERT: P 117 ASP cc_start: 0.8448 (t0) cc_final: 0.8186 (t70) REVERT: P 192 GLN cc_start: 0.9263 (tt0) cc_final: 0.8943 (tt0) REVERT: Q 39 ASP cc_start: 0.8394 (t0) cc_final: 0.7978 (t70) REVERT: Q 63 ARG cc_start: 0.8513 (ttt180) cc_final: 0.8241 (mtm-85) REVERT: Q 93 ASP cc_start: 0.8132 (p0) cc_final: 0.7900 (p0) REVERT: Q 117 ASP cc_start: 0.8439 (t0) cc_final: 0.8179 (t70) REVERT: Q 192 GLN cc_start: 0.9256 (tt0) cc_final: 0.8936 (tt0) REVERT: R 39 ASP cc_start: 0.8366 (t0) cc_final: 0.7957 (t70) REVERT: R 63 ARG cc_start: 0.8537 (ttt180) cc_final: 0.8245 (mtm-85) REVERT: R 117 ASP cc_start: 0.8443 (t0) cc_final: 0.8183 (t70) REVERT: R 192 GLN cc_start: 0.9252 (tt0) cc_final: 0.8928 (tt0) REVERT: S 39 ASP cc_start: 0.8392 (t0) cc_final: 0.7979 (t70) REVERT: S 63 ARG cc_start: 0.8503 (ttt180) cc_final: 0.8241 (mtm-85) REVERT: S 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8184 (t70) REVERT: S 192 GLN cc_start: 0.9256 (tt0) cc_final: 0.8937 (tt0) REVERT: T 39 ASP cc_start: 0.8385 (t0) cc_final: 0.7971 (t70) REVERT: T 63 ARG cc_start: 0.8506 (ttt180) cc_final: 0.8238 (mtm-85) REVERT: T 117 ASP cc_start: 0.8447 (t0) cc_final: 0.8187 (t70) REVERT: T 192 GLN cc_start: 0.9261 (tt0) cc_final: 0.8938 (tt0) REVERT: U 39 ASP cc_start: 0.8392 (t0) cc_final: 0.7971 (t70) REVERT: U 63 ARG cc_start: 0.8499 (ttt180) cc_final: 0.8231 (mtm-85) REVERT: U 117 ASP cc_start: 0.8443 (t0) cc_final: 0.8185 (t70) REVERT: U 192 GLN cc_start: 0.9255 (tt0) cc_final: 0.8933 (tt0) REVERT: V 39 ASP cc_start: 0.8384 (t0) cc_final: 0.7970 (t70) REVERT: V 63 ARG cc_start: 0.8504 (ttt180) cc_final: 0.8240 (mtm-85) REVERT: V 117 ASP cc_start: 0.8435 (t0) cc_final: 0.8173 (t70) REVERT: V 192 GLN cc_start: 0.9248 (tt0) cc_final: 0.8922 (tt0) REVERT: W 39 ASP cc_start: 0.8388 (t0) cc_final: 0.7974 (t70) REVERT: W 63 ARG cc_start: 0.8500 (ttt180) cc_final: 0.8240 (mtm-85) REVERT: W 117 ASP cc_start: 0.8447 (t0) cc_final: 0.8189 (t70) REVERT: W 192 GLN cc_start: 0.9256 (tt0) cc_final: 0.8935 (tt0) REVERT: X 39 ASP cc_start: 0.8371 (t0) cc_final: 0.7964 (t70) REVERT: X 63 ARG cc_start: 0.8544 (ttt180) cc_final: 0.8246 (mtm-85) REVERT: X 117 ASP cc_start: 0.8444 (t0) cc_final: 0.8181 (t70) REVERT: X 192 GLN cc_start: 0.9254 (tt0) cc_final: 0.8931 (tt0) outliers start: 0 outliers final: 0 residues processed: 851 average time/residue: 0.2892 time to fit residues: 363.0169 Evaluate side-chains 821 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 821 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 422 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 324 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 229 optimal weight: 0.0010 chunk 92 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 89 GLN M 89 GLN N 89 GLN O 89 GLN P 89 GLN Q 89 GLN R 89 GLN S 89 GLN T 89 GLN U 89 GLN V 89 GLN W 89 GLN X 89 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.114797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.089595 restraints weight = 41320.740| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.78 r_work: 0.2709 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 35976 Z= 0.104 Angle : 0.454 3.263 48912 Z= 0.244 Chirality : 0.043 0.134 5592 Planarity : 0.004 0.031 6504 Dihedral : 4.384 15.473 5088 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.32 % Allowed : 7.89 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.13), residues: 4512 helix: 2.55 (0.12), residues: 1872 sheet: 0.27 (0.13), residues: 1488 loop : -0.36 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 95 TYR 0.005 0.001 TYR D 145 PHE 0.008 0.001 PHE E 104 HIS 0.004 0.001 HIS M 176 Details of bonding type rmsd covalent geometry : bond 0.00235 (35976) covalent geometry : angle 0.45421 (48912) hydrogen bonds : bond 0.03004 ( 2184) hydrogen bonds : angle 3.58958 ( 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 931 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 883 time to evaluate : 1.258 Fit side-chains REVERT: A 39 ASP cc_start: 0.8167 (t0) cc_final: 0.7761 (t70) REVERT: A 117 ASP cc_start: 0.8357 (t0) cc_final: 0.8085 (t70) REVERT: A 119 SER cc_start: 0.8697 (m) cc_final: 0.8417 (t) REVERT: B 39 ASP cc_start: 0.8149 (t0) cc_final: 0.7740 (t70) REVERT: B 117 ASP cc_start: 0.8353 (t0) cc_final: 0.8087 (t70) REVERT: C 39 ASP cc_start: 0.8163 (t0) cc_final: 0.7751 (t70) REVERT: C 117 ASP cc_start: 0.8375 (t0) cc_final: 0.8101 (t70) REVERT: C 119 SER cc_start: 0.8676 (m) cc_final: 0.8395 (t) REVERT: D 39 ASP cc_start: 0.8175 (t0) cc_final: 0.7767 (t70) REVERT: D 117 ASP cc_start: 0.8380 (t0) cc_final: 0.8106 (t70) REVERT: D 119 SER cc_start: 0.8698 (m) cc_final: 0.8411 (t) REVERT: E 39 ASP cc_start: 0.8174 (t0) cc_final: 0.7767 (t70) REVERT: E 117 ASP cc_start: 0.8376 (t0) cc_final: 0.8099 (t70) REVERT: E 119 SER cc_start: 0.8696 (m) cc_final: 0.8411 (t) REVERT: F 39 ASP cc_start: 0.8177 (t0) cc_final: 0.7767 (t70) REVERT: F 117 ASP cc_start: 0.8365 (t0) cc_final: 0.8095 (t70) REVERT: G 39 ASP cc_start: 0.8178 (t0) cc_final: 0.7770 (t70) REVERT: G 117 ASP cc_start: 0.8368 (t0) cc_final: 0.8093 (t70) REVERT: G 119 SER cc_start: 0.8687 (m) cc_final: 0.8412 (t) REVERT: H 39 ASP cc_start: 0.8167 (t0) cc_final: 0.7756 (t70) REVERT: H 117 ASP cc_start: 0.8376 (t0) cc_final: 0.8104 (t70) REVERT: H 119 SER cc_start: 0.8678 (m) cc_final: 0.8395 (t) REVERT: I 39 ASP cc_start: 0.8174 (t0) cc_final: 0.7765 (t70) REVERT: I 117 ASP cc_start: 0.8363 (t0) cc_final: 0.8094 (t70) REVERT: J 39 ASP cc_start: 0.8171 (t0) cc_final: 0.7764 (t70) REVERT: J 117 ASP cc_start: 0.8358 (t0) cc_final: 0.8086 (t70) REVERT: J 119 SER cc_start: 0.8698 (m) cc_final: 0.8419 (t) REVERT: K 39 ASP cc_start: 0.8163 (t0) cc_final: 0.7757 (t70) REVERT: K 117 ASP cc_start: 0.8348 (t0) cc_final: 0.8083 (t70) REVERT: L 39 ASP cc_start: 0.8168 (t0) cc_final: 0.7759 (t70) REVERT: L 117 ASP cc_start: 0.8371 (t0) cc_final: 0.8097 (t70) REVERT: L 119 SER cc_start: 0.8691 (m) cc_final: 0.8410 (t) REVERT: M 39 ASP cc_start: 0.8181 (t0) cc_final: 0.7773 (t70) REVERT: M 117 ASP cc_start: 0.8362 (t0) cc_final: 0.8086 (t70) REVERT: M 119 SER cc_start: 0.8694 (m) cc_final: 0.8418 (t) REVERT: N 39 ASP cc_start: 0.8189 (t0) cc_final: 0.7780 (t70) REVERT: N 117 ASP cc_start: 0.8366 (t0) cc_final: 0.8096 (t70) REVERT: N 119 SER cc_start: 0.8698 (m) cc_final: 0.8423 (t) REVERT: O 39 ASP cc_start: 0.8169 (t0) cc_final: 0.7759 (t70) REVERT: O 117 ASP cc_start: 0.8373 (t0) cc_final: 0.8104 (t70) REVERT: P 39 ASP cc_start: 0.8188 (t0) cc_final: 0.7778 (t70) REVERT: P 117 ASP cc_start: 0.8361 (t0) cc_final: 0.8091 (t70) REVERT: P 119 SER cc_start: 0.8693 (m) cc_final: 0.8414 (t) REVERT: Q 39 ASP cc_start: 0.8174 (t0) cc_final: 0.7770 (t70) REVERT: Q 117 ASP cc_start: 0.8376 (t0) cc_final: 0.8097 (t70) REVERT: Q 119 SER cc_start: 0.8693 (m) cc_final: 0.8417 (t) REVERT: R 39 ASP cc_start: 0.8165 (t0) cc_final: 0.7753 (t70) REVERT: R 117 ASP cc_start: 0.8362 (t0) cc_final: 0.8088 (t70) REVERT: R 119 SER cc_start: 0.8687 (m) cc_final: 0.8406 (t) REVERT: S 39 ASP cc_start: 0.8151 (t0) cc_final: 0.7747 (t70) REVERT: S 117 ASP cc_start: 0.8367 (t0) cc_final: 0.8094 (t70) REVERT: S 119 SER cc_start: 0.8690 (m) cc_final: 0.8408 (t) REVERT: T 39 ASP cc_start: 0.8185 (t0) cc_final: 0.7773 (t70) REVERT: T 117 ASP cc_start: 0.8360 (t0) cc_final: 0.8090 (t70) REVERT: T 119 SER cc_start: 0.8695 (m) cc_final: 0.8420 (t) REVERT: U 39 ASP cc_start: 0.8173 (t0) cc_final: 0.7768 (t70) REVERT: U 117 ASP cc_start: 0.8378 (t0) cc_final: 0.8102 (t70) REVERT: U 119 SER cc_start: 0.8688 (m) cc_final: 0.8403 (t) REVERT: V 39 ASP cc_start: 0.8180 (t0) cc_final: 0.7770 (t70) REVERT: V 117 ASP cc_start: 0.8363 (t0) cc_final: 0.8090 (t70) REVERT: V 119 SER cc_start: 0.8690 (m) cc_final: 0.8416 (t) REVERT: W 39 ASP cc_start: 0.8152 (t0) cc_final: 0.7743 (t70) REVERT: W 117 ASP cc_start: 0.8369 (t0) cc_final: 0.8098 (t70) REVERT: W 119 SER cc_start: 0.8695 (m) cc_final: 0.8415 (t) REVERT: X 39 ASP cc_start: 0.8167 (t0) cc_final: 0.7755 (t70) REVERT: X 117 ASP cc_start: 0.8374 (t0) cc_final: 0.8098 (t70) REVERT: X 119 SER cc_start: 0.8690 (m) cc_final: 0.8411 (t) outliers start: 48 outliers final: 0 residues processed: 907 average time/residue: 0.2606 time to fit residues: 358.0849 Evaluate side-chains 807 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 807 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 289 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 415 optimal weight: 8.9990 chunk 323 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 367 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 89 GLN M 89 GLN N 89 GLN O 89 GLN P 89 GLN Q 89 GLN R 89 GLN S 89 GLN T 89 GLN U 89 GLN V 89 GLN W 89 GLN X 89 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.081136 restraints weight = 42369.069| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.09 r_work: 0.2560 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.060 35976 Z= 0.398 Angle : 0.669 4.852 48912 Z= 0.358 Chirality : 0.052 0.159 5592 Planarity : 0.005 0.033 6504 Dihedral : 5.230 17.851 5088 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.54 % Allowed : 11.62 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.13), residues: 4512 helix: 2.01 (0.12), residues: 1872 sheet: 0.42 (0.14), residues: 1488 loop : -0.93 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 99 TYR 0.010 0.003 TYR J 45 PHE 0.014 0.003 PHE X 104 HIS 0.008 0.002 HIS L 152 Details of bonding type rmsd covalent geometry : bond 0.00952 (35976) covalent geometry : angle 0.66885 (48912) hydrogen bonds : bond 0.05288 ( 2184) hydrogen bonds : angle 4.06873 ( 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 700 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 644 time to evaluate : 1.439 Fit side-chains REVERT: A 39 ASP cc_start: 0.8557 (t0) cc_final: 0.8129 (t70) REVERT: A 117 ASP cc_start: 0.8594 (t0) cc_final: 0.8252 (t70) REVERT: B 39 ASP cc_start: 0.8549 (t0) cc_final: 0.8123 (t70) REVERT: B 117 ASP cc_start: 0.8601 (t0) cc_final: 0.8261 (t70) REVERT: C 39 ASP cc_start: 0.8560 (t0) cc_final: 0.8139 (t70) REVERT: C 117 ASP cc_start: 0.8613 (t0) cc_final: 0.8276 (t70) REVERT: D 39 ASP cc_start: 0.8553 (t0) cc_final: 0.8128 (t70) REVERT: D 117 ASP cc_start: 0.8606 (t0) cc_final: 0.8268 (t70) REVERT: E 39 ASP cc_start: 0.8563 (t0) cc_final: 0.8139 (t70) REVERT: E 117 ASP cc_start: 0.8597 (t0) cc_final: 0.8258 (t70) REVERT: F 39 ASP cc_start: 0.8546 (t0) cc_final: 0.8115 (t70) REVERT: F 117 ASP cc_start: 0.8590 (t0) cc_final: 0.8251 (t70) REVERT: G 39 ASP cc_start: 0.8556 (t0) cc_final: 0.8130 (t70) REVERT: G 117 ASP cc_start: 0.8600 (t0) cc_final: 0.8259 (t70) REVERT: H 39 ASP cc_start: 0.8563 (t0) cc_final: 0.8138 (t70) REVERT: H 117 ASP cc_start: 0.8618 (t0) cc_final: 0.8278 (t70) REVERT: I 39 ASP cc_start: 0.8553 (t0) cc_final: 0.8122 (t70) REVERT: I 117 ASP cc_start: 0.8589 (t0) cc_final: 0.8249 (t70) REVERT: J 39 ASP cc_start: 0.8559 (t0) cc_final: 0.8133 (t70) REVERT: J 117 ASP cc_start: 0.8592 (t0) cc_final: 0.8254 (t70) REVERT: K 39 ASP cc_start: 0.8559 (t0) cc_final: 0.8131 (t70) REVERT: K 117 ASP cc_start: 0.8587 (t0) cc_final: 0.8249 (t70) REVERT: L 39 ASP cc_start: 0.8558 (t0) cc_final: 0.8128 (t70) REVERT: L 117 ASP cc_start: 0.8609 (t0) cc_final: 0.8270 (t70) REVERT: M 39 ASP cc_start: 0.8557 (t0) cc_final: 0.8130 (t70) REVERT: M 117 ASP cc_start: 0.8595 (t0) cc_final: 0.8255 (t70) REVERT: N 39 ASP cc_start: 0.8569 (t0) cc_final: 0.8142 (t70) REVERT: N 117 ASP cc_start: 0.8601 (t0) cc_final: 0.8257 (t70) REVERT: O 39 ASP cc_start: 0.8552 (t0) cc_final: 0.8127 (t70) REVERT: O 117 ASP cc_start: 0.8611 (t0) cc_final: 0.8267 (t70) REVERT: P 39 ASP cc_start: 0.8567 (t0) cc_final: 0.8139 (t70) REVERT: P 117 ASP cc_start: 0.8600 (t0) cc_final: 0.8259 (t70) REVERT: Q 39 ASP cc_start: 0.8547 (t0) cc_final: 0.8118 (t70) REVERT: Q 117 ASP cc_start: 0.8591 (t0) cc_final: 0.8249 (t70) REVERT: R 39 ASP cc_start: 0.8555 (t0) cc_final: 0.8124 (t70) REVERT: R 117 ASP cc_start: 0.8607 (t0) cc_final: 0.8272 (t70) REVERT: S 39 ASP cc_start: 0.8557 (t0) cc_final: 0.8134 (t70) REVERT: S 117 ASP cc_start: 0.8608 (t0) cc_final: 0.8270 (t70) REVERT: T 39 ASP cc_start: 0.8570 (t0) cc_final: 0.8146 (t70) REVERT: T 117 ASP cc_start: 0.8598 (t0) cc_final: 0.8256 (t70) REVERT: U 39 ASP cc_start: 0.8514 (t0) cc_final: 0.8076 (t70) REVERT: U 117 ASP cc_start: 0.8608 (t0) cc_final: 0.8270 (t70) REVERT: V 39 ASP cc_start: 0.8551 (t0) cc_final: 0.8122 (t70) REVERT: V 117 ASP cc_start: 0.8595 (t0) cc_final: 0.8252 (t70) REVERT: W 39 ASP cc_start: 0.8506 (t0) cc_final: 0.8068 (t70) REVERT: W 117 ASP cc_start: 0.8607 (t0) cc_final: 0.8271 (t70) REVERT: X 39 ASP cc_start: 0.8564 (t0) cc_final: 0.8137 (t70) REVERT: X 117 ASP cc_start: 0.8609 (t0) cc_final: 0.8271 (t70) outliers start: 56 outliers final: 24 residues processed: 700 average time/residue: 0.3078 time to fit residues: 314.9755 Evaluate side-chains 764 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 740 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 60 optimal weight: 0.8980 chunk 319 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 374 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 221 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 89 GLN M 89 GLN N 89 GLN O 89 GLN P 89 GLN Q 89 GLN R 89 GLN S 89 GLN T 89 GLN U 89 GLN V 89 GLN W 89 GLN X 89 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.086879 restraints weight = 42488.662| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.98 r_work: 0.2644 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 35976 Z= 0.126 Angle : 0.481 3.384 48912 Z= 0.260 Chirality : 0.044 0.134 5592 Planarity : 0.004 0.030 6504 Dihedral : 4.606 16.406 5088 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.75 % Allowed : 11.43 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.13), residues: 4512 helix: 2.44 (0.12), residues: 1872 sheet: 0.34 (0.13), residues: 1488 loop : -0.75 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 95 TYR 0.006 0.001 TYR X 145 PHE 0.007 0.001 PHE A 104 HIS 0.005 0.001 HIS W 176 Details of bonding type rmsd covalent geometry : bond 0.00289 (35976) covalent geometry : angle 0.48132 (48912) hydrogen bonds : bond 0.03344 ( 2184) hydrogen bonds : angle 3.66222 ( 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 866 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 802 time to evaluate : 1.486 Fit side-chains REVERT: A 39 ASP cc_start: 0.8410 (t0) cc_final: 0.7978 (t70) REVERT: A 117 ASP cc_start: 0.8450 (t0) cc_final: 0.8140 (t70) REVERT: A 119 SER cc_start: 0.8870 (m) cc_final: 0.8561 (t) REVERT: A 192 GLN cc_start: 0.9063 (tt0) cc_final: 0.8746 (tt0) REVERT: B 39 ASP cc_start: 0.8407 (t0) cc_final: 0.7971 (t70) REVERT: B 117 ASP cc_start: 0.8444 (t0) cc_final: 0.8135 (t70) REVERT: B 192 GLN cc_start: 0.9044 (tt0) cc_final: 0.8715 (tt0) REVERT: C 39 ASP cc_start: 0.8399 (t0) cc_final: 0.7964 (t70) REVERT: C 117 ASP cc_start: 0.8446 (t0) cc_final: 0.8132 (t70) REVERT: C 192 GLN cc_start: 0.9048 (tt0) cc_final: 0.8718 (tt0) REVERT: D 39 ASP cc_start: 0.8412 (t0) cc_final: 0.7977 (t70) REVERT: D 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8134 (t70) REVERT: D 192 GLN cc_start: 0.9064 (tt0) cc_final: 0.8736 (tt0) REVERT: E 39 ASP cc_start: 0.8403 (t0) cc_final: 0.7971 (t70) REVERT: E 117 ASP cc_start: 0.8446 (t0) cc_final: 0.8136 (t70) REVERT: E 192 GLN cc_start: 0.9057 (tt0) cc_final: 0.8729 (tt0) REVERT: F 39 ASP cc_start: 0.8405 (t0) cc_final: 0.7969 (t70) REVERT: F 117 ASP cc_start: 0.8453 (t0) cc_final: 0.8146 (t70) REVERT: F 192 GLN cc_start: 0.9051 (tt0) cc_final: 0.8732 (tt0) REVERT: G 39 ASP cc_start: 0.8394 (t0) cc_final: 0.7957 (t70) REVERT: G 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8134 (t70) REVERT: G 192 GLN cc_start: 0.9069 (tt0) cc_final: 0.8751 (tt0) REVERT: H 39 ASP cc_start: 0.8412 (t0) cc_final: 0.7979 (t70) REVERT: H 117 ASP cc_start: 0.8434 (t0) cc_final: 0.8121 (t70) REVERT: H 192 GLN cc_start: 0.9048 (tt0) cc_final: 0.8717 (tt0) REVERT: I 39 ASP cc_start: 0.8405 (t0) cc_final: 0.7968 (t70) REVERT: I 117 ASP cc_start: 0.8465 (t0) cc_final: 0.8160 (t70) REVERT: I 192 GLN cc_start: 0.9058 (tt0) cc_final: 0.8740 (tt0) REVERT: J 39 ASP cc_start: 0.8414 (t0) cc_final: 0.7989 (t70) REVERT: J 117 ASP cc_start: 0.8457 (t0) cc_final: 0.8156 (t70) REVERT: J 192 GLN cc_start: 0.9073 (tt0) cc_final: 0.8749 (tt0) REVERT: K 39 ASP cc_start: 0.8401 (t0) cc_final: 0.7966 (t70) REVERT: K 117 ASP cc_start: 0.8453 (t0) cc_final: 0.8152 (t70) REVERT: K 192 GLN cc_start: 0.9060 (tt0) cc_final: 0.8745 (tt0) REVERT: L 39 ASP cc_start: 0.8393 (t0) cc_final: 0.7955 (t70) REVERT: L 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8130 (t70) REVERT: L 192 GLN cc_start: 0.9046 (tt0) cc_final: 0.8720 (tt0) REVERT: M 39 ASP cc_start: 0.8388 (t0) cc_final: 0.7948 (t70) REVERT: M 117 ASP cc_start: 0.8442 (t0) cc_final: 0.8134 (t70) REVERT: M 192 GLN cc_start: 0.9061 (tt0) cc_final: 0.8746 (tt0) REVERT: N 39 ASP cc_start: 0.8397 (t0) cc_final: 0.7965 (t70) REVERT: N 117 ASP cc_start: 0.8451 (t0) cc_final: 0.8132 (t70) REVERT: N 119 SER cc_start: 0.8874 (m) cc_final: 0.8576 (t) REVERT: N 192 GLN cc_start: 0.9063 (tt0) cc_final: 0.8742 (tt0) REVERT: O 39 ASP cc_start: 0.8403 (t0) cc_final: 0.7970 (t70) REVERT: O 117 ASP cc_start: 0.8443 (t0) cc_final: 0.8138 (t70) REVERT: O 192 GLN cc_start: 0.9043 (tt0) cc_final: 0.8711 (tt0) REVERT: P 39 ASP cc_start: 0.8403 (t0) cc_final: 0.7968 (t70) REVERT: P 117 ASP cc_start: 0.8440 (t0) cc_final: 0.8124 (t70) REVERT: P 192 GLN cc_start: 0.9058 (tt0) cc_final: 0.8737 (tt0) REVERT: Q 39 ASP cc_start: 0.8411 (t0) cc_final: 0.7979 (t70) REVERT: Q 117 ASP cc_start: 0.8451 (t0) cc_final: 0.8135 (t70) REVERT: Q 119 SER cc_start: 0.8868 (m) cc_final: 0.8563 (t) REVERT: Q 192 GLN cc_start: 0.9059 (tt0) cc_final: 0.8734 (tt0) REVERT: R 39 ASP cc_start: 0.8395 (t0) cc_final: 0.7956 (t70) REVERT: R 117 ASP cc_start: 0.8435 (t0) cc_final: 0.8120 (t70) REVERT: R 192 GLN cc_start: 0.9055 (tt0) cc_final: 0.8730 (tt0) REVERT: S 39 ASP cc_start: 0.8404 (t0) cc_final: 0.7971 (t70) REVERT: S 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8133 (t70) REVERT: S 192 GLN cc_start: 0.9045 (tt0) cc_final: 0.8717 (tt0) REVERT: T 39 ASP cc_start: 0.8399 (t0) cc_final: 0.7963 (t70) REVERT: T 117 ASP cc_start: 0.8439 (t0) cc_final: 0.8123 (t70) REVERT: T 192 GLN cc_start: 0.9058 (tt0) cc_final: 0.8733 (tt0) REVERT: U 39 ASP cc_start: 0.8408 (t0) cc_final: 0.7973 (t70) REVERT: U 117 ASP cc_start: 0.8439 (t0) cc_final: 0.8128 (t70) REVERT: U 192 GLN cc_start: 0.9058 (tt0) cc_final: 0.8732 (tt0) REVERT: V 39 ASP cc_start: 0.8402 (t0) cc_final: 0.7960 (t70) REVERT: V 117 ASP cc_start: 0.8443 (t0) cc_final: 0.8129 (t70) REVERT: V 119 SER cc_start: 0.8887 (m) cc_final: 0.8571 (t) REVERT: V 192 GLN cc_start: 0.9067 (tt0) cc_final: 0.8755 (tt0) REVERT: W 39 ASP cc_start: 0.8412 (t0) cc_final: 0.7973 (t70) REVERT: W 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8132 (t70) REVERT: W 192 GLN cc_start: 0.9047 (tt0) cc_final: 0.8718 (tt0) REVERT: X 39 ASP cc_start: 0.8377 (t0) cc_final: 0.7937 (t70) REVERT: X 117 ASP cc_start: 0.8443 (t0) cc_final: 0.8125 (t70) REVERT: X 119 SER cc_start: 0.8857 (m) cc_final: 0.8559 (t) REVERT: X 192 GLN cc_start: 0.9048 (tt0) cc_final: 0.8721 (tt0) outliers start: 64 outliers final: 40 residues processed: 866 average time/residue: 0.2846 time to fit residues: 370.8862 Evaluate side-chains 808 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 768 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 152 HIS Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 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 152 HIS Chi-restraints excluded: chain L residue 152 HIS Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 152 HIS Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 152 HIS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 413 optimal weight: 6.9990 chunk 365 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 267 optimal weight: 6.9990 chunk 321 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 89 GLN M 89 GLN N 89 GLN O 89 GLN P 89 GLN Q 89 GLN R 89 GLN S 89 GLN T 89 GLN U 89 GLN V 89 GLN W 89 GLN X 89 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.083394 restraints weight = 42365.052| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.98 r_work: 0.2644 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 35976 Z= 0.271 Angle : 0.593 5.452 48912 Z= 0.316 Chirality : 0.048 0.173 5592 Planarity : 0.004 0.032 6504 Dihedral : 5.015 17.160 5088 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.62 % Allowed : 11.07 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.13), residues: 4512 helix: 2.26 (0.12), residues: 1872 sheet: 0.36 (0.13), residues: 1488 loop : -0.85 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 162 TYR 0.010 0.002 TYR T 45 PHE 0.012 0.002 PHE K 104 HIS 0.006 0.002 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00649 (35976) covalent geometry : angle 0.59265 (48912) hydrogen bonds : bond 0.04623 ( 2184) hydrogen bonds : angle 3.92169 ( 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 782 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 723 time to evaluate : 1.456 Fit side-chains REVERT: A 39 ASP cc_start: 0.8515 (t0) cc_final: 0.8092 (t70) REVERT: A 117 ASP cc_start: 0.8491 (t0) cc_final: 0.8193 (t70) REVERT: B 39 ASP cc_start: 0.8503 (t0) cc_final: 0.8087 (t70) REVERT: B 117 ASP cc_start: 0.8493 (t0) cc_final: 0.8198 (t70) REVERT: C 39 ASP cc_start: 0.8510 (t0) cc_final: 0.8097 (t70) REVERT: C 117 ASP cc_start: 0.8488 (t0) cc_final: 0.8193 (t70) REVERT: D 39 ASP cc_start: 0.8509 (t0) cc_final: 0.8092 (t70) REVERT: D 117 ASP cc_start: 0.8504 (t0) cc_final: 0.8207 (t70) REVERT: E 39 ASP cc_start: 0.8507 (t0) cc_final: 0.8091 (t70) REVERT: E 117 ASP cc_start: 0.8510 (t0) cc_final: 0.8218 (t70) REVERT: F 39 ASP cc_start: 0.8485 (t0) cc_final: 0.8066 (t70) REVERT: F 117 ASP cc_start: 0.8507 (t0) cc_final: 0.8210 (t70) REVERT: G 39 ASP cc_start: 0.8499 (t0) cc_final: 0.8084 (t70) REVERT: G 117 ASP cc_start: 0.8499 (t0) cc_final: 0.8203 (t70) REVERT: H 39 ASP cc_start: 0.8516 (t0) cc_final: 0.8099 (t70) REVERT: H 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8202 (t70) REVERT: I 39 ASP cc_start: 0.8512 (t0) cc_final: 0.8092 (t70) REVERT: I 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8214 (t70) REVERT: J 39 ASP cc_start: 0.8498 (t0) cc_final: 0.8085 (t70) REVERT: J 117 ASP cc_start: 0.8493 (t0) cc_final: 0.8197 (t70) REVERT: K 39 ASP cc_start: 0.8503 (t0) cc_final: 0.8088 (t70) REVERT: K 117 ASP cc_start: 0.8495 (t0) cc_final: 0.8194 (t70) REVERT: L 39 ASP cc_start: 0.8493 (t0) cc_final: 0.8071 (t70) REVERT: L 117 ASP cc_start: 0.8501 (t0) cc_final: 0.8208 (t70) REVERT: M 39 ASP cc_start: 0.8499 (t0) cc_final: 0.8082 (t70) REVERT: M 117 ASP cc_start: 0.8506 (t0) cc_final: 0.8209 (t70) REVERT: N 39 ASP cc_start: 0.8504 (t0) cc_final: 0.8090 (t70) REVERT: N 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8216 (t70) REVERT: O 39 ASP cc_start: 0.8501 (t0) cc_final: 0.8088 (t70) REVERT: O 117 ASP cc_start: 0.8495 (t0) cc_final: 0.8198 (t70) REVERT: P 39 ASP cc_start: 0.8495 (t0) cc_final: 0.8073 (t70) REVERT: P 117 ASP cc_start: 0.8500 (t0) cc_final: 0.8208 (t70) REVERT: Q 39 ASP cc_start: 0.8510 (t0) cc_final: 0.8088 (t70) REVERT: Q 117 ASP cc_start: 0.8508 (t0) cc_final: 0.8214 (t70) REVERT: R 39 ASP cc_start: 0.8502 (t0) cc_final: 0.8081 (t70) REVERT: R 117 ASP cc_start: 0.8494 (t0) cc_final: 0.8201 (t70) REVERT: S 39 ASP cc_start: 0.8502 (t0) cc_final: 0.8086 (t70) REVERT: S 117 ASP cc_start: 0.8506 (t0) cc_final: 0.8211 (t70) REVERT: T 39 ASP cc_start: 0.8501 (t0) cc_final: 0.8083 (t70) REVERT: T 117 ASP cc_start: 0.8504 (t0) cc_final: 0.8212 (t70) REVERT: U 39 ASP cc_start: 0.8515 (t0) cc_final: 0.8097 (t70) REVERT: U 117 ASP cc_start: 0.8515 (t0) cc_final: 0.8223 (t70) REVERT: V 39 ASP cc_start: 0.8499 (t0) cc_final: 0.8078 (t70) REVERT: V 117 ASP cc_start: 0.8505 (t0) cc_final: 0.8207 (t70) REVERT: W 39 ASP cc_start: 0.8514 (t0) cc_final: 0.8096 (t70) REVERT: W 117 ASP cc_start: 0.8499 (t0) cc_final: 0.8207 (t70) REVERT: X 39 ASP cc_start: 0.8493 (t0) cc_final: 0.8073 (t70) REVERT: X 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8201 (t70) outliers start: 59 outliers final: 55 residues processed: 782 average time/residue: 0.2974 time to fit residues: 344.6420 Evaluate side-chains 669 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 614 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR 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 127 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 127 THR 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 127 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 152 HIS Chi-restraints excluded: chain I residue 127 THR 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 127 THR 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 127 THR Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 152 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 152 HIS 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 127 THR 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 127 THR Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 123 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 385 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 89 GLN B 192 GLN C 89 GLN C 192 GLN D 89 GLN D 192 GLN E 89 GLN E 192 GLN F 89 GLN F 192 GLN G 89 GLN G 192 GLN H 89 GLN H 192 GLN I 89 GLN I 192 GLN J 89 GLN J 192 GLN K 89 GLN K 192 GLN L 89 GLN L 192 GLN M 89 GLN M 192 GLN N 89 GLN N 192 GLN O 89 GLN O 192 GLN P 89 GLN P 192 GLN Q 192 GLN R 89 GLN R 192 GLN S 89 GLN S 192 GLN T 89 GLN T 192 GLN U 89 GLN U 192 GLN V 89 GLN V 192 GLN W 89 GLN W 192 GLN X 89 GLN X 192 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.111153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.086090 restraints weight = 42625.858| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.99 r_work: 0.2635 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2991 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= 0.143 Angle : 0.499 5.969 48912 Z= 0.266 Chirality : 0.044 0.134 5592 Planarity : 0.004 0.031 6504 Dihedral : 4.639 16.318 5088 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.75 % Allowed : 11.79 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.13), residues: 4512 helix: 2.52 (0.12), residues: 1872 sheet: 0.29 (0.13), residues: 1488 loop : -0.83 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.006 0.001 TYR N 45 PHE 0.009 0.002 PHE R 104 HIS 0.005 0.001 HIS I 176 Details of bonding type rmsd covalent geometry : bond 0.00334 (35976) covalent geometry : angle 0.49912 (48912) hydrogen bonds : bond 0.03528 ( 2184) hydrogen bonds : angle 3.70664 ( 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 872 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 808 time to evaluate : 1.182 Fit side-chains REVERT: A 39 ASP cc_start: 0.8433 (t0) cc_final: 0.8023 (t70) REVERT: A 117 ASP cc_start: 0.8460 (t0) cc_final: 0.8166 (t70) REVERT: B 39 ASP cc_start: 0.8444 (t0) cc_final: 0.8021 (t70) REVERT: B 117 ASP cc_start: 0.8476 (t0) cc_final: 0.8183 (t70) REVERT: C 39 ASP cc_start: 0.8430 (t0) cc_final: 0.8004 (t70) REVERT: C 117 ASP cc_start: 0.8481 (t0) cc_final: 0.8188 (t70) REVERT: D 39 ASP cc_start: 0.8435 (t0) cc_final: 0.8010 (t70) REVERT: D 117 ASP cc_start: 0.8473 (t0) cc_final: 0.8181 (t70) REVERT: E 39 ASP cc_start: 0.8436 (t0) cc_final: 0.8007 (t70) REVERT: E 117 ASP cc_start: 0.8473 (t0) cc_final: 0.8181 (t70) REVERT: F 39 ASP cc_start: 0.8421 (t0) cc_final: 0.7993 (t70) REVERT: F 117 ASP cc_start: 0.8474 (t0) cc_final: 0.8181 (t70) REVERT: G 39 ASP cc_start: 0.8411 (t0) cc_final: 0.7987 (t70) REVERT: G 117 ASP cc_start: 0.8480 (t0) cc_final: 0.8185 (t70) REVERT: H 39 ASP cc_start: 0.8432 (t0) cc_final: 0.8007 (t70) REVERT: H 117 ASP cc_start: 0.8467 (t0) cc_final: 0.8172 (t70) REVERT: I 39 ASP cc_start: 0.8420 (t0) cc_final: 0.7993 (t70) REVERT: I 117 ASP cc_start: 0.8474 (t0) cc_final: 0.8180 (t70) REVERT: J 39 ASP cc_start: 0.8453 (t0) cc_final: 0.8028 (t70) REVERT: J 117 ASP cc_start: 0.8466 (t0) cc_final: 0.8176 (t70) REVERT: K 39 ASP cc_start: 0.8440 (t0) cc_final: 0.8014 (t70) REVERT: K 117 ASP cc_start: 0.8462 (t0) cc_final: 0.8172 (t70) REVERT: L 39 ASP cc_start: 0.8412 (t0) cc_final: 0.7979 (t70) REVERT: L 117 ASP cc_start: 0.8478 (t0) cc_final: 0.8187 (t70) REVERT: M 39 ASP cc_start: 0.8443 (t0) cc_final: 0.8023 (t70) REVERT: M 117 ASP cc_start: 0.8486 (t0) cc_final: 0.8192 (t70) REVERT: N 39 ASP cc_start: 0.8430 (t0) cc_final: 0.8003 (t70) REVERT: N 117 ASP cc_start: 0.8491 (t0) cc_final: 0.8199 (t70) REVERT: O 39 ASP cc_start: 0.8427 (t0) cc_final: 0.8005 (t70) REVERT: O 117 ASP cc_start: 0.8472 (t0) cc_final: 0.8183 (t70) REVERT: P 39 ASP cc_start: 0.8425 (t0) cc_final: 0.7994 (t70) REVERT: P 117 ASP cc_start: 0.8474 (t0) cc_final: 0.8180 (t70) REVERT: Q 39 ASP cc_start: 0.8422 (t0) cc_final: 0.8006 (t70) REVERT: Q 117 ASP cc_start: 0.8482 (t0) cc_final: 0.8188 (t70) REVERT: R 39 ASP cc_start: 0.8409 (t0) cc_final: 0.7979 (t70) REVERT: R 117 ASP cc_start: 0.8479 (t0) cc_final: 0.8186 (t70) REVERT: S 39 ASP cc_start: 0.8423 (t0) cc_final: 0.7995 (t70) REVERT: S 117 ASP cc_start: 0.8475 (t0) cc_final: 0.8181 (t70) REVERT: T 39 ASP cc_start: 0.8434 (t0) cc_final: 0.8008 (t70) REVERT: T 117 ASP cc_start: 0.8488 (t0) cc_final: 0.8193 (t70) REVERT: U 39 ASP cc_start: 0.8421 (t0) cc_final: 0.7996 (t70) REVERT: U 117 ASP cc_start: 0.8467 (t0) cc_final: 0.8175 (t70) REVERT: V 39 ASP cc_start: 0.8415 (t0) cc_final: 0.7988 (t70) REVERT: V 117 ASP cc_start: 0.8478 (t0) cc_final: 0.8183 (t70) REVERT: W 39 ASP cc_start: 0.8428 (t0) cc_final: 0.8006 (t70) REVERT: W 117 ASP cc_start: 0.8471 (t0) cc_final: 0.8177 (t70) REVERT: X 39 ASP cc_start: 0.8413 (t0) cc_final: 0.7985 (t70) REVERT: X 117 ASP cc_start: 0.8476 (t0) cc_final: 0.8180 (t70) outliers start: 64 outliers final: 57 residues processed: 856 average time/residue: 0.2565 time to fit residues: 330.1025 Evaluate side-chains 704 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 647 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 71 GLU 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 127 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 127 THR 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 127 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 127 THR 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 127 THR Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 152 HIS 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 127 THR Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 152 HIS Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 133 LEU Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain V residue 127 THR 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 71 GLU Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 152 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 439 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 370 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 318 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 89 GLN B 192 GLN C 89 GLN C 192 GLN D 89 GLN D 192 GLN E 89 GLN E 192 GLN F 89 GLN F 192 GLN G 89 GLN G 192 GLN H 89 GLN H 192 GLN I 89 GLN I 192 GLN J 89 GLN J 192 GLN K 89 GLN K 192 GLN L 89 GLN L 192 GLN M 89 GLN M 192 GLN N 89 GLN N 192 GLN O 89 GLN O 192 GLN P 89 GLN P 192 GLN Q 192 GLN R 89 GLN R 192 GLN S 89 GLN S 192 GLN T 89 GLN T 192 GLN U 89 GLN U 192 GLN V 89 GLN V 192 GLN W 89 GLN W 192 GLN X 89 GLN X 192 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.084139 restraints weight = 42373.567| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.97 r_work: 0.2604 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 35976 Z= 0.235 Angle : 0.562 6.172 48912 Z= 0.299 Chirality : 0.047 0.140 5592 Planarity : 0.004 0.032 6504 Dihedral : 4.862 16.788 5088 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.45 % Allowed : 12.36 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.13), residues: 4512 helix: 2.36 (0.12), residues: 1872 sheet: 0.26 (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 L 162 TYR 0.010 0.002 TYR N 45 PHE 0.011 0.002 PHE S 104 HIS 0.006 0.002 HIS Q 176 Details of bonding type rmsd covalent geometry : bond 0.00560 (35976) covalent geometry : angle 0.56199 (48912) hydrogen bonds : bond 0.04323 ( 2184) hydrogen bonds : angle 3.86337 ( 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 687 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 634 time to evaluate : 1.363 Fit side-chains REVERT: A 39 ASP cc_start: 0.8494 (t0) cc_final: 0.8065 (t70) REVERT: A 117 ASP cc_start: 0.8491 (t0) cc_final: 0.8200 (t70) REVERT: B 39 ASP cc_start: 0.8495 (t0) cc_final: 0.8073 (t70) REVERT: B 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8205 (t70) REVERT: C 39 ASP cc_start: 0.8498 (t0) cc_final: 0.8080 (t70) REVERT: C 117 ASP cc_start: 0.8495 (t0) cc_final: 0.8202 (t70) REVERT: D 39 ASP cc_start: 0.8497 (t0) cc_final: 0.8077 (t70) REVERT: D 117 ASP cc_start: 0.8509 (t0) cc_final: 0.8221 (t70) REVERT: E 39 ASP cc_start: 0.8496 (t0) cc_final: 0.8072 (t70) REVERT: E 117 ASP cc_start: 0.8511 (t0) cc_final: 0.8222 (t70) REVERT: F 39 ASP cc_start: 0.8476 (t0) cc_final: 0.8054 (t70) REVERT: F 117 ASP cc_start: 0.8489 (t0) cc_final: 0.8194 (t70) REVERT: G 39 ASP cc_start: 0.8486 (t0) cc_final: 0.8067 (t70) REVERT: G 117 ASP cc_start: 0.8498 (t0) cc_final: 0.8206 (t70) REVERT: H 39 ASP cc_start: 0.8499 (t0) cc_final: 0.8075 (t70) REVERT: H 117 ASP cc_start: 0.8495 (t0) cc_final: 0.8203 (t70) REVERT: I 39 ASP cc_start: 0.8480 (t0) cc_final: 0.8056 (t70) REVERT: I 117 ASP cc_start: 0.8500 (t0) cc_final: 0.8204 (t70) REVERT: J 39 ASP cc_start: 0.8494 (t0) cc_final: 0.8067 (t70) REVERT: J 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8204 (t70) REVERT: K 39 ASP cc_start: 0.8487 (t0) cc_final: 0.8067 (t70) REVERT: K 117 ASP cc_start: 0.8490 (t0) cc_final: 0.8195 (t70) REVERT: L 39 ASP cc_start: 0.8471 (t0) cc_final: 0.8044 (t70) REVERT: L 117 ASP cc_start: 0.8485 (t0) cc_final: 0.8195 (t70) REVERT: M 39 ASP cc_start: 0.8486 (t0) cc_final: 0.8060 (t70) REVERT: M 117 ASP cc_start: 0.8497 (t0) cc_final: 0.8204 (t70) REVERT: N 39 ASP cc_start: 0.8484 (t0) cc_final: 0.8063 (t70) REVERT: N 117 ASP cc_start: 0.8505 (t0) cc_final: 0.8214 (t70) REVERT: O 39 ASP cc_start: 0.8481 (t0) cc_final: 0.8064 (t70) REVERT: O 117 ASP cc_start: 0.8498 (t0) cc_final: 0.8214 (t70) REVERT: P 39 ASP cc_start: 0.8476 (t0) cc_final: 0.8045 (t70) REVERT: P 117 ASP cc_start: 0.8490 (t0) cc_final: 0.8198 (t70) REVERT: Q 39 ASP cc_start: 0.8469 (t0) cc_final: 0.8045 (t70) REVERT: Q 117 ASP cc_start: 0.8504 (t0) cc_final: 0.8213 (t70) REVERT: R 39 ASP cc_start: 0.8461 (t0) cc_final: 0.8036 (t70) REVERT: R 117 ASP cc_start: 0.8487 (t0) cc_final: 0.8199 (t70) REVERT: S 39 ASP cc_start: 0.8494 (t0) cc_final: 0.8065 (t70) REVERT: S 117 ASP cc_start: 0.8506 (t0) cc_final: 0.8215 (t70) REVERT: T 39 ASP cc_start: 0.8485 (t0) cc_final: 0.8060 (t70) REVERT: T 117 ASP cc_start: 0.8496 (t0) cc_final: 0.8204 (t70) REVERT: U 39 ASP cc_start: 0.8483 (t0) cc_final: 0.8060 (t70) REVERT: U 117 ASP cc_start: 0.8501 (t0) cc_final: 0.8212 (t70) REVERT: V 39 ASP cc_start: 0.8487 (t0) cc_final: 0.8058 (t70) REVERT: V 117 ASP cc_start: 0.8490 (t0) cc_final: 0.8198 (t70) REVERT: W 39 ASP cc_start: 0.8485 (t0) cc_final: 0.8059 (t70) REVERT: W 117 ASP cc_start: 0.8504 (t0) cc_final: 0.8213 (t70) REVERT: X 39 ASP cc_start: 0.8470 (t0) cc_final: 0.8051 (t70) REVERT: X 117 ASP cc_start: 0.8490 (t0) cc_final: 0.8199 (t70) outliers start: 53 outliers final: 53 residues processed: 687 average time/residue: 0.2861 time to fit residues: 287.9672 Evaluate side-chains 660 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 607 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 127 THR 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 127 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 152 HIS Chi-restraints excluded: chain L residue 127 THR 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 127 THR Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 152 HIS 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 127 THR Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 152 HIS Chi-restraints excluded: chain T residue 127 THR 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 127 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 86 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 405 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 450 optimal weight: 0.5980 chunk 436 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 362 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 89 GLN B 192 GLN C 89 GLN C 192 GLN D 89 GLN D 192 GLN E 89 GLN E 192 GLN F 89 GLN F 192 GLN G 89 GLN G 192 GLN H 89 GLN H 192 GLN I 89 GLN I 192 GLN J 89 GLN J 192 GLN K 89 GLN K 192 GLN L 89 GLN L 192 GLN M 89 GLN M 192 GLN N 89 GLN N 192 GLN O 89 GLN O 192 GLN P 89 GLN P 192 GLN Q 192 GLN R 89 GLN R 192 GLN S 89 GLN S 192 GLN T 89 GLN T 192 GLN U 89 GLN U 192 GLN V 89 GLN V 192 GLN W 89 GLN W 192 GLN X 89 GLN X 192 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.114156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.089993 restraints weight = 42395.910| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.93 r_work: 0.2663 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 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 : 0.003 0.023 35976 Z= 0.111 Angle : 0.476 6.121 48912 Z= 0.253 Chirality : 0.044 0.132 5592 Planarity : 0.004 0.031 6504 Dihedral : 4.463 15.706 5088 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.79 % Allowed : 13.02 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.13), residues: 4512 helix: 2.59 (0.12), residues: 1872 sheet: 0.18 (0.13), residues: 1488 loop : -0.84 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 95 TYR 0.006 0.001 TYR D 145 PHE 0.009 0.001 PHE F 104 HIS 0.005 0.001 HIS T 176 Details of bonding type rmsd covalent geometry : bond 0.00253 (35976) covalent geometry : angle 0.47584 (48912) hydrogen bonds : bond 0.03128 ( 2184) hydrogen bonds : angle 3.67426 ( 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 828 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 799 time to evaluate : 1.494 Fit side-chains REVERT: A 39 ASP cc_start: 0.8436 (t0) cc_final: 0.8016 (t70) REVERT: A 117 ASP cc_start: 0.8420 (t0) cc_final: 0.8138 (t70) REVERT: B 39 ASP cc_start: 0.8449 (t0) cc_final: 0.8005 (t70) REVERT: B 117 ASP cc_start: 0.8424 (t0) cc_final: 0.8150 (t70) REVERT: C 39 ASP cc_start: 0.8423 (t0) cc_final: 0.7977 (t70) REVERT: C 117 ASP cc_start: 0.8408 (t0) cc_final: 0.8129 (t70) REVERT: D 39 ASP cc_start: 0.8446 (t0) cc_final: 0.8027 (t70) REVERT: D 117 ASP cc_start: 0.8415 (t0) cc_final: 0.8136 (t70) REVERT: E 39 ASP cc_start: 0.8442 (t0) cc_final: 0.7998 (t70) REVERT: E 117 ASP cc_start: 0.8419 (t0) cc_final: 0.8139 (t70) REVERT: F 39 ASP cc_start: 0.8424 (t0) cc_final: 0.7979 (t70) REVERT: F 117 ASP cc_start: 0.8419 (t0) cc_final: 0.8144 (t70) REVERT: G 39 ASP cc_start: 0.8430 (t0) cc_final: 0.7985 (t70) REVERT: G 117 ASP cc_start: 0.8426 (t0) cc_final: 0.8141 (t70) REVERT: H 39 ASP cc_start: 0.8425 (t0) cc_final: 0.7986 (t70) REVERT: H 117 ASP cc_start: 0.8412 (t0) cc_final: 0.8133 (t70) REVERT: I 39 ASP cc_start: 0.8441 (t0) cc_final: 0.7994 (t70) REVERT: I 117 ASP cc_start: 0.8418 (t0) cc_final: 0.8143 (t70) REVERT: J 39 ASP cc_start: 0.8437 (t0) cc_final: 0.7992 (t70) REVERT: J 117 ASP cc_start: 0.8419 (t0) cc_final: 0.8138 (t70) REVERT: K 39 ASP cc_start: 0.8434 (t0) cc_final: 0.7986 (t70) REVERT: K 117 ASP cc_start: 0.8419 (t0) cc_final: 0.8144 (t70) REVERT: L 39 ASP cc_start: 0.8433 (t0) cc_final: 0.7991 (t70) REVERT: L 117 ASP cc_start: 0.8425 (t0) cc_final: 0.8141 (t70) REVERT: M 39 ASP cc_start: 0.8451 (t0) cc_final: 0.8003 (t70) REVERT: M 117 ASP cc_start: 0.8429 (t0) cc_final: 0.8145 (t70) REVERT: N 39 ASP cc_start: 0.8415 (t0) cc_final: 0.7974 (t70) REVERT: N 117 ASP cc_start: 0.8435 (t0) cc_final: 0.8150 (t70) REVERT: O 39 ASP cc_start: 0.8416 (t0) cc_final: 0.7973 (t70) REVERT: O 117 ASP cc_start: 0.8414 (t0) cc_final: 0.8141 (t70) REVERT: P 39 ASP cc_start: 0.8444 (t0) cc_final: 0.7999 (t70) REVERT: P 117 ASP cc_start: 0.8424 (t0) cc_final: 0.8140 (t70) REVERT: Q 39 ASP cc_start: 0.8431 (t0) cc_final: 0.8008 (t70) REVERT: Q 117 ASP cc_start: 0.8419 (t0) cc_final: 0.8137 (t70) REVERT: R 39 ASP cc_start: 0.8423 (t0) cc_final: 0.7982 (t70) REVERT: R 117 ASP cc_start: 0.8430 (t0) cc_final: 0.8145 (t70) REVERT: S 39 ASP cc_start: 0.8430 (t0) cc_final: 0.7986 (t70) REVERT: S 117 ASP cc_start: 0.8422 (t0) cc_final: 0.8141 (t70) REVERT: T 39 ASP cc_start: 0.8444 (t0) cc_final: 0.8002 (t70) REVERT: T 117 ASP cc_start: 0.8430 (t0) cc_final: 0.8144 (t70) REVERT: U 39 ASP cc_start: 0.8441 (t0) cc_final: 0.7999 (t70) REVERT: U 117 ASP cc_start: 0.8413 (t0) cc_final: 0.8135 (t70) REVERT: V 39 ASP cc_start: 0.8425 (t0) cc_final: 0.7978 (t70) REVERT: V 117 ASP cc_start: 0.8436 (t0) cc_final: 0.8151 (t70) REVERT: W 39 ASP cc_start: 0.8445 (t0) cc_final: 0.7999 (t70) REVERT: W 117 ASP cc_start: 0.8422 (t0) cc_final: 0.8144 (t70) REVERT: X 39 ASP cc_start: 0.8424 (t0) cc_final: 0.8001 (t70) REVERT: X 117 ASP cc_start: 0.8429 (t0) cc_final: 0.8144 (t70) outliers start: 29 outliers final: 29 residues processed: 816 average time/residue: 0.2621 time to fit residues: 320.6001 Evaluate side-chains 682 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 653 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain R 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 U residue 133 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 133 LEU Chi-restraints excluded: chain W residue 133 LEU 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: 6.9990 chunk 202 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 446 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 369 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 341 optimal weight: 0.5980 chunk 159 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 89 GLN B 192 GLN C 89 GLN C 192 GLN D 89 GLN D 192 GLN E 89 GLN E 192 GLN F 89 GLN F 192 GLN G 89 GLN G 192 GLN H 89 GLN H 192 GLN I 89 GLN I 192 GLN J 89 GLN J 192 GLN K 89 GLN K 192 GLN L 89 GLN L 192 GLN M 89 GLN M 192 GLN N 89 GLN N 192 GLN O 89 GLN O 192 GLN P 89 GLN P 192 GLN Q 192 GLN R 89 GLN R 192 GLN S 89 GLN S 192 GLN T 89 GLN T 192 GLN U 89 GLN U 192 GLN V 89 GLN V 192 GLN W 89 GLN W 192 GLN X 89 GLN X 192 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.086301 restraints weight = 42188.235| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.92 r_work: 0.2666 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 35976 Z= 0.191 Angle : 0.534 5.791 48912 Z= 0.285 Chirality : 0.046 0.138 5592 Planarity : 0.004 0.032 6504 Dihedral : 4.656 16.245 5088 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.82 % Allowed : 12.99 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.13), residues: 4512 helix: 2.43 (0.12), residues: 1872 sheet: 0.20 (0.13), residues: 1488 loop : -0.80 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 95 TYR 0.008 0.002 TYR D 45 PHE 0.010 0.002 PHE J 104 HIS 0.005 0.001 HIS U 176 Details of bonding type rmsd covalent geometry : bond 0.00454 (35976) covalent geometry : angle 0.53405 (48912) hydrogen bonds : bond 0.03968 ( 2184) hydrogen bonds : angle 3.76305 ( 6048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8819.22 seconds wall clock time: 151 minutes 27.99 seconds (9087.99 seconds total)