Starting phenix.real_space_refine on Sat Mar 7 12:37:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppe_20434/03_2026/6ppe_20434.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppe_20434/03_2026/6ppe_20434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ppe_20434/03_2026/6ppe_20434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppe_20434/03_2026/6ppe_20434.map" model { file = "/net/cci-nas-00/data/ceres_data/6ppe_20434/03_2026/6ppe_20434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppe_20434/03_2026/6ppe_20434.cif" } resolution = 3.19 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= 1.000 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 S 168 5.16 5 C 13762 2.51 5 N 3780 2.21 5 O 4130 1.98 5 H 21896 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43736 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "B" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "C" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "D" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "F" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "G" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "H" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "M" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "O" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Y" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "1" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "3" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.29, per 1000 atoms: 0.17 Number of scatterers: 43736 At special positions: 0 Unit cell: (112.52, 114.84, 128.76, 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) S 168 16.00 O 4130 8.00 N 3780 7.00 C 13762 6.00 H 21896 1.00 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: 3.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5124 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 49 sheets defined 47.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 132 through 158 Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 54 Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 132 through 158 Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 176 through 182 Processing helix chain 'C' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 54 Processing helix chain 'C' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 132 through 158 Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'D' and resid 19 through 26 removed outlier: 3.609A pdb=" N GLU D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 54 Processing helix chain 'D' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 Processing helix chain 'D' and resid 132 through 158 Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 176 through 182 Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 54 Processing helix chain 'E' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 132 through 158 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 54 Processing helix chain 'F' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 132 through 158 Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 176 through 182 Processing helix chain 'G' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 54 Processing helix chain 'G' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 132 through 158 Processing helix chain 'G' and resid 160 through 168 Processing helix chain 'G' and resid 176 through 182 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 132 through 158 Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.609A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.757A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 132 through 158 Processing helix chain 'I' and resid 160 through 168 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 132 through 158 Processing helix chain 'J' and resid 160 through 168 Processing helix chain 'J' and resid 176 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.759A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 105 Processing helix chain 'K' and resid 132 through 158 Processing helix chain 'K' and resid 160 through 168 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 105 Processing helix chain 'L' and resid 132 through 158 Processing helix chain 'L' and resid 160 through 168 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.609A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 132 through 158 Processing helix chain 'M' and resid 160 through 168 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.609A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 105 Processing helix chain 'N' and resid 132 through 158 Processing helix chain 'N' and resid 160 through 168 Processing helix chain 'N' and resid 176 through 182 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE A 59 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE A 90 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 61 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET A 92 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE A 63 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN A 94 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE A 59 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE A 90 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 61 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET A 92 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE A 63 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN A 94 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE A 112 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR A 89 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 131 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 9 Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE B 59 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE B 90 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 61 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET B 92 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE B 63 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN B 94 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE B 59 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE B 90 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 61 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET B 92 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE B 63 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN B 94 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE B 112 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 89 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 125 through 131 Processing sheet with id=AA9, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AB1, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE C 59 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 61 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET C 92 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 63 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN C 94 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE C 59 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 61 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET C 92 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 63 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN C 94 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE C 112 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 89 " --> pdb=" O PHE C 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 125 through 131 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 9 Processing sheet with id=AB5, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE D 59 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D 90 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU D 61 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET D 92 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE D 63 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN D 94 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE D 59 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D 90 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU D 61 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET D 92 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE D 63 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN D 94 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE D 112 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR D 89 " --> pdb=" O PHE D 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 125 through 131 removed outlier: 3.503A pdb=" N TYR D 128 " --> pdb=" O TYR L 128 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR L 128 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AB9, first strand: chain 'E' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE E 59 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E 61 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET E 92 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE E 63 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN E 94 " --> pdb=" O ILE E 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE E 59 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E 61 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET E 92 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE E 63 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN E 94 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE E 112 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR E 89 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 125 through 131 Processing sheet with id=AC3, first strand: chain 'F' and resid 5 through 9 Processing sheet with id=AC4, first strand: chain 'F' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE F 59 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 90 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 61 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET F 92 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE F 63 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN F 94 " --> pdb=" O ILE F 63 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE F 59 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 90 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 61 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET F 92 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE F 63 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN F 94 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N PHE F 112 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR F 89 " --> pdb=" O PHE F 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 125 through 131 Processing sheet with id=AC7, first strand: chain 'G' and resid 5 through 9 Processing sheet with id=AC8, first strand: chain 'G' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE G 59 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU G 61 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET G 92 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE G 63 " --> pdb=" O MET G 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN G 94 " --> pdb=" O ILE G 63 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE G 59 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU G 61 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET G 92 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE G 63 " --> pdb=" O MET G 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN G 94 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE G 112 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR G 89 " --> pdb=" O PHE G 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 125 through 131 Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AD3, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AD6, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AD9, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AE3, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 5 through 9 Processing sheet with id=AE6, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET L 92 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE L 63 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN L 94 " --> pdb=" O ILE L 63 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET L 92 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE L 63 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN L 94 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 5 through 9 Processing sheet with id=AE9, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 5 through 9 Processing sheet with id=AF3, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3690 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: 12.02 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 21868 1.03 - 1.22: 28 1.22 - 1.42: 8979 1.42 - 1.61: 12875 1.61 - 1.80: 308 Bond restraints: 44058 Sorted by residual: bond pdb=" N SER N 97 " pdb=" CA SER N 97 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.17e-02 7.31e+03 3.80e+00 bond pdb=" N SER B 97 " pdb=" CA SER B 97 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.17e-02 7.31e+03 3.79e+00 bond pdb=" N SER G 97 " pdb=" CA SER G 97 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.17e-02 7.31e+03 3.77e+00 bond pdb=" N SER F 97 " pdb=" CA SER F 97 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.17e-02 7.31e+03 3.71e+00 bond pdb=" N SER H 97 " pdb=" CA SER H 97 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.17e-02 7.31e+03 3.63e+00 ... (remaining 44053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 75833 1.30 - 2.59: 3391 2.59 - 3.89: 255 3.89 - 5.18: 139 5.18 - 6.48: 28 Bond angle restraints: 79646 Sorted by residual: angle pdb=" C ALA I 96 " pdb=" N SER I 97 " pdb=" CA SER I 97 " ideal model delta sigma weight residual 121.19 127.67 -6.48 1.59e+00 3.96e-01 1.66e+01 angle pdb=" C ALA G 96 " pdb=" N SER G 97 " pdb=" CA SER G 97 " ideal model delta sigma weight residual 121.19 127.67 -6.48 1.59e+00 3.96e-01 1.66e+01 angle pdb=" C ALA L 96 " pdb=" N SER L 97 " pdb=" CA SER L 97 " ideal model delta sigma weight residual 121.19 127.67 -6.48 1.59e+00 3.96e-01 1.66e+01 angle pdb=" C ALA M 96 " pdb=" N SER M 97 " pdb=" CA SER M 97 " ideal model delta sigma weight residual 121.19 127.66 -6.47 1.59e+00 3.96e-01 1.66e+01 angle pdb=" C ALA H 96 " pdb=" N SER H 97 " pdb=" CA SER H 97 " ideal model delta sigma weight residual 121.19 127.66 -6.47 1.59e+00 3.96e-01 1.66e+01 ... (remaining 79641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 18565 15.41 - 30.83: 1366 30.83 - 46.24: 327 46.24 - 61.66: 294 61.66 - 77.07: 14 Dihedral angle restraints: 20566 sinusoidal: 11466 harmonic: 9100 Sorted by residual: dihedral pdb=" CA ALA D 96 " pdb=" C ALA D 96 " pdb=" N SER D 97 " pdb=" CA SER D 97 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ALA C 96 " pdb=" C ALA C 96 " pdb=" N SER C 97 " pdb=" CA SER C 97 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ALA G 96 " pdb=" C ALA G 96 " pdb=" N SER G 97 " pdb=" CA SER G 97 " ideal model delta harmonic sigma weight residual 180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 20563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1947 0.029 - 0.058: 889 0.058 - 0.087: 341 0.087 - 0.116: 153 0.116 - 0.145: 58 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CA VAL E 3 " pdb=" N VAL E 3 " pdb=" C VAL E 3 " pdb=" CB VAL E 3 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA VAL J 3 " pdb=" N VAL J 3 " pdb=" C VAL J 3 " pdb=" CB VAL J 3 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL K 3 " pdb=" N VAL K 3 " pdb=" C VAL K 3 " pdb=" CB VAL K 3 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 3385 not shown) Planarity restraints: 6580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 176 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO G 177 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 177 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 177 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 176 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO I 177 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO I 177 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 177 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 176 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO J 177 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO J 177 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 177 " 0.017 5.00e-02 4.00e+02 ... (remaining 6577 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 5605 2.27 - 2.85: 101011 2.85 - 3.43: 113604 3.43 - 4.02: 164675 4.02 - 4.60: 253435 Nonbonded interactions: 638330 Sorted by model distance: nonbonded pdb="HE22 GLN E 123 " pdb=" HG1 THR K 133 " model vdw 1.683 2.100 nonbonded pdb=" O MET I 153 " pdb=" HG1 THR I 157 " model vdw 1.712 2.450 nonbonded pdb=" O MET E 153 " pdb=" HG1 THR E 157 " model vdw 1.712 2.450 nonbonded pdb=" O MET G 153 " pdb=" HG1 THR G 157 " model vdw 1.712 2.450 nonbonded pdb=" O MET L 153 " pdb=" HG1 THR L 157 " model vdw 1.712 2.450 ... (remaining 638325 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: 0.05 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' } ncs_group { reference = 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 'X' selection = chain 'Y' selection = chain 'Z' selection = chain '1' selection = chain '2' selection = chain '3' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.530 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 40.000 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 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 : 0.006 0.050 22162 Z= 0.230 Angle : 0.671 6.479 29862 Z= 0.381 Chirality : 0.043 0.145 3388 Planarity : 0.004 0.030 3892 Dihedral : 9.862 77.075 8344 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.12), residues: 2758 helix: -2.12 (0.10), residues: 1358 sheet: 0.30 (0.25), residues: 308 loop : -1.94 (0.15), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 27 TYR 0.008 0.002 TYR J 182 PHE 0.013 0.002 PHE I 17 HIS 0.005 0.001 HIS L 122 Details of bonding type rmsd covalent geometry : bond 0.00571 (22162) covalent geometry : angle 0.67076 (29862) hydrogen bonds : bond 0.26490 ( 1202) hydrogen bonds : angle 7.54371 ( 3690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 758 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.9495 (m-80) cc_final: 0.9258 (m-10) REVERT: A 167 ASP cc_start: 0.9366 (m-30) cc_final: 0.9099 (m-30) REVERT: A 186 ASP cc_start: 0.9386 (m-30) cc_final: 0.9065 (m-30) REVERT: C 186 ASP cc_start: 0.9358 (m-30) cc_final: 0.9121 (m-30) REVERT: D 20 TYR cc_start: 0.9498 (m-80) cc_final: 0.9225 (m-10) REVERT: E 15 ARG cc_start: 0.8905 (ttm170) cc_final: 0.8600 (ttm-80) REVERT: E 186 ASP cc_start: 0.9379 (m-30) cc_final: 0.9120 (m-30) REVERT: G 41 ASN cc_start: 0.9444 (t0) cc_final: 0.9118 (t0) REVERT: H 41 ASN cc_start: 0.8823 (t0) cc_final: 0.8619 (m-40) REVERT: H 118 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.8073 (ptt180) REVERT: I 186 ASP cc_start: 0.9260 (m-30) cc_final: 0.9019 (m-30) REVERT: J 41 ASN cc_start: 0.9380 (t0) cc_final: 0.9169 (t0) REVERT: J 175 SER cc_start: 0.9212 (p) cc_final: 0.8921 (p) REVERT: J 178 GLU cc_start: 0.9259 (mt-10) cc_final: 0.9038 (mt-10) REVERT: J 186 ASP cc_start: 0.9284 (m-30) cc_final: 0.9037 (m-30) REVERT: Y 273 THR cc_start: 0.9144 (t) cc_final: 0.8823 (p) outliers start: 0 outliers final: 0 residues processed: 758 average time/residue: 0.4393 time to fit residues: 470.3778 Evaluate side-chains 488 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN C 193 ASN D 193 ASN E 41 ASN E 193 ASN F 193 ASN G 41 ASN G 193 ASN H 41 ASN H 193 ASN I 41 ASN J 41 ASN K 193 ASN L 193 ASN M 41 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093002 restraints weight = 84272.682| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.18 r_work: 0.3194 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22162 Z= 0.148 Angle : 0.536 5.808 29862 Z= 0.288 Chirality : 0.042 0.150 3388 Planarity : 0.004 0.033 3892 Dihedral : 4.648 26.753 3052 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.86 % Allowed : 8.68 % Favored : 90.46 % 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 are not related in a simple way. whole: 0.16 (0.15), residues: 2758 helix: 1.11 (0.14), residues: 1372 sheet: 0.89 (0.26), residues: 308 loop : -1.47 (0.16), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 118 TYR 0.006 0.001 TYR M 182 PHE 0.008 0.001 PHE K 17 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00328 (22162) covalent geometry : angle 0.53633 (29862) hydrogen bonds : bond 0.04462 ( 1202) hydrogen bonds : angle 4.10924 ( 3690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 523 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9067 (mtp) cc_final: 0.8850 (mtp) REVERT: A 167 ASP cc_start: 0.8815 (m-30) cc_final: 0.8417 (m-30) REVERT: B 15 ARG cc_start: 0.8121 (ttp-170) cc_final: 0.7812 (ttm-80) REVERT: B 80 MET cc_start: 0.9139 (mtp) cc_final: 0.8808 (mtp) REVERT: E 15 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7696 (ttm-80) REVERT: E 74 MET cc_start: 0.8589 (mmm) cc_final: 0.8383 (mmt) REVERT: E 144 LYS cc_start: 0.8685 (mttp) cc_final: 0.8459 (mtpt) REVERT: G 18 ASP cc_start: 0.8461 (p0) cc_final: 0.8130 (p0) REVERT: H 78 ASP cc_start: 0.8596 (m-30) cc_final: 0.8371 (m-30) REVERT: H 120 MET cc_start: 0.9061 (ttt) cc_final: 0.8706 (ttt) REVERT: H 141 GLU cc_start: 0.7848 (tp30) cc_final: 0.7425 (tp30) REVERT: J 171 ASP cc_start: 0.9103 (m-30) cc_final: 0.8848 (m-30) REVERT: K 20 TYR cc_start: 0.9190 (m-80) cc_final: 0.8918 (m-10) REVERT: K 41 ASN cc_start: 0.8661 (m-40) cc_final: 0.8442 (m110) REVERT: K 74 MET cc_start: 0.8744 (tpp) cc_final: 0.8052 (mmt) REVERT: L 15 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.7500 (ttp-170) REVERT: L 74 MET cc_start: 0.8660 (mmm) cc_final: 0.8234 (mmt) REVERT: M 74 MET cc_start: 0.8846 (mmt) cc_final: 0.8367 (mmt) REVERT: M 78 ASP cc_start: 0.8448 (m-30) cc_final: 0.8177 (m-30) REVERT: M 108 LYS cc_start: 0.9014 (tptm) cc_final: 0.8786 (tptt) outliers start: 20 outliers final: 14 residues processed: 538 average time/residue: 0.4025 time to fit residues: 314.0646 Evaluate side-chains 498 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 484 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 217 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN C 41 ASN D 193 ASN E 41 ASN F 64 ASN G 41 ASN H 41 ASN H 193 ASN I 41 ASN J 41 ASN K 41 ASN L 41 ASN L 193 ASN N 41 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.087885 restraints weight = 85840.830| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.18 r_work: 0.3103 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 22162 Z= 0.209 Angle : 0.529 5.407 29862 Z= 0.285 Chirality : 0.042 0.142 3388 Planarity : 0.004 0.037 3892 Dihedral : 4.633 24.068 3052 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.86 % Allowed : 9.15 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2758 helix: 1.85 (0.14), residues: 1372 sheet: 0.97 (0.26), residues: 308 loop : -1.22 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 15 TYR 0.008 0.001 TYR M 182 PHE 0.010 0.001 PHE J 17 HIS 0.006 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00487 (22162) covalent geometry : angle 0.52877 (29862) hydrogen bonds : bond 0.04677 ( 1202) hydrogen bonds : angle 4.08524 ( 3690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 518 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.8999 (ttp) cc_final: 0.8610 (ttt) REVERT: C 153 MET cc_start: 0.8681 (tpp) cc_final: 0.8413 (tpp) REVERT: D 120 MET cc_start: 0.9016 (ttp) cc_final: 0.8728 (ttt) REVERT: E 15 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7724 (ttm-80) REVERT: E 144 LYS cc_start: 0.8662 (mttp) cc_final: 0.8452 (mtpt) REVERT: G 18 ASP cc_start: 0.8487 (p0) cc_final: 0.8152 (p0) REVERT: H 41 ASN cc_start: 0.8516 (t0) cc_final: 0.8282 (t0) REVERT: H 78 ASP cc_start: 0.8618 (m-30) cc_final: 0.8403 (m-30) REVERT: H 80 MET cc_start: 0.9040 (mtp) cc_final: 0.8780 (mtp) REVERT: H 120 MET cc_start: 0.9082 (ttt) cc_final: 0.8748 (ttt) REVERT: H 141 GLU cc_start: 0.8282 (tp30) cc_final: 0.7768 (tp30) REVERT: H 175 SER cc_start: 0.8793 (t) cc_final: 0.8381 (p) REVERT: K 74 MET cc_start: 0.8788 (tpp) cc_final: 0.8258 (mmt) REVERT: K 120 MET cc_start: 0.9103 (ttp) cc_final: 0.8695 (ttt) REVERT: L 8 GLU cc_start: 0.7438 (tt0) cc_final: 0.7185 (tt0) REVERT: L 9 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8193 (mm-40) REVERT: L 74 MET cc_start: 0.8735 (mmm) cc_final: 0.8204 (mmt) REVERT: M 18 ASP cc_start: 0.8259 (p0) cc_final: 0.7867 (p0) REVERT: M 62 TYR cc_start: 0.9244 (m-10) cc_final: 0.9007 (m-10) REVERT: M 74 MET cc_start: 0.8836 (mmt) cc_final: 0.8262 (mmt) REVERT: M 78 ASP cc_start: 0.8688 (m-30) cc_final: 0.8479 (m-30) outliers start: 20 outliers final: 13 residues processed: 531 average time/residue: 0.4217 time to fit residues: 327.3584 Evaluate side-chains 512 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 499 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 181 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN F 64 ASN G 41 ASN H 193 ASN I 41 ASN J 64 ASN L 41 ASN M 41 ASN N 64 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.088519 restraints weight = 85958.793| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.17 r_work: 0.3105 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 22162 Z= 0.162 Angle : 0.494 5.265 29862 Z= 0.263 Chirality : 0.041 0.140 3388 Planarity : 0.004 0.039 3892 Dihedral : 4.546 24.232 3052 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.68 % Allowed : 10.01 % Favored : 89.31 % 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 are not related in a simple way. whole: 1.21 (0.16), residues: 2758 helix: 2.23 (0.14), residues: 1358 sheet: 1.10 (0.24), residues: 336 loop : -1.27 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 15 TYR 0.011 0.001 TYR G 62 PHE 0.008 0.001 PHE J 17 HIS 0.006 0.001 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00371 (22162) covalent geometry : angle 0.49370 (29862) hydrogen bonds : bond 0.03922 ( 1202) hydrogen bonds : angle 3.87965 ( 3690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 517 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.9174 (m-10) cc_final: 0.8939 (m-10) REVERT: B 120 MET cc_start: 0.8983 (ttp) cc_final: 0.8560 (ttt) REVERT: C 153 MET cc_start: 0.8636 (tpp) cc_final: 0.8414 (tpp) REVERT: D 120 MET cc_start: 0.9020 (ttp) cc_final: 0.8705 (ttt) REVERT: E 15 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7804 (ttm-80) REVERT: F 15 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.7981 (ttm-80) REVERT: F 80 MET cc_start: 0.9073 (mtp) cc_final: 0.8848 (mtp) REVERT: G 18 ASP cc_start: 0.8467 (p0) cc_final: 0.8121 (p0) REVERT: H 18 ASP cc_start: 0.8568 (p0) cc_final: 0.8336 (p0) REVERT: H 41 ASN cc_start: 0.8652 (t0) cc_final: 0.8339 (t0) REVERT: H 80 MET cc_start: 0.8951 (mtp) cc_final: 0.8646 (mtp) REVERT: H 120 MET cc_start: 0.9026 (ttt) cc_final: 0.8669 (ttt) REVERT: H 175 SER cc_start: 0.8816 (t) cc_final: 0.8482 (p) REVERT: I 118 ARG cc_start: 0.8446 (ptt180) cc_final: 0.7484 (mtp85) REVERT: I 153 MET cc_start: 0.8614 (tpp) cc_final: 0.8377 (tpp) REVERT: K 74 MET cc_start: 0.8729 (tpp) cc_final: 0.8112 (mmt) REVERT: K 120 MET cc_start: 0.9080 (ttp) cc_final: 0.8679 (ttt) REVERT: L 9 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8073 (mm110) REVERT: M 9 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8772 (mm-40) REVERT: M 18 ASP cc_start: 0.8151 (p0) cc_final: 0.7775 (p0) REVERT: M 62 TYR cc_start: 0.9282 (m-10) cc_final: 0.9082 (m-10) REVERT: M 74 MET cc_start: 0.8722 (mmt) cc_final: 0.8471 (mmt) REVERT: N 25 LYS cc_start: 0.9243 (ttmm) cc_final: 0.8989 (tttm) outliers start: 16 outliers final: 14 residues processed: 531 average time/residue: 0.4086 time to fit residues: 312.5102 Evaluate side-chains 510 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 496 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 85 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 208 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN D 41 ASN D 193 ASN E 64 ASN G 41 ASN H 193 ASN I 41 ASN I 193 ASN J 64 ASN L 41 ASN M 64 ASN N 41 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.086837 restraints weight = 86542.027| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.18 r_work: 0.3086 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22162 Z= 0.200 Angle : 0.509 5.320 29862 Z= 0.273 Chirality : 0.042 0.141 3388 Planarity : 0.004 0.056 3892 Dihedral : 4.560 22.856 3052 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.98 % Allowed : 10.27 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.16), residues: 2758 helix: 2.22 (0.14), residues: 1372 sheet: 1.09 (0.24), residues: 336 loop : -1.14 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 172 TYR 0.008 0.001 TYR L 182 PHE 0.009 0.001 PHE B 17 HIS 0.007 0.001 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00470 (22162) covalent geometry : angle 0.50913 (29862) hydrogen bonds : bond 0.04205 ( 1202) hydrogen bonds : angle 3.94448 ( 3690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 508 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.9174 (m-10) cc_final: 0.8951 (m-10) REVERT: B 120 MET cc_start: 0.8999 (ttp) cc_final: 0.8560 (ttt) REVERT: C 153 MET cc_start: 0.8629 (tpp) cc_final: 0.8407 (tpp) REVERT: F 15 ARG cc_start: 0.8242 (ttp-170) cc_final: 0.7918 (ttm-80) REVERT: G 18 ASP cc_start: 0.8464 (p0) cc_final: 0.8112 (p0) REVERT: H 41 ASN cc_start: 0.8706 (t0) cc_final: 0.8350 (t0) REVERT: H 120 MET cc_start: 0.8979 (ttt) cc_final: 0.8646 (ttt) REVERT: I 118 ARG cc_start: 0.8390 (ptt180) cc_final: 0.7692 (mtp85) REVERT: I 153 MET cc_start: 0.8647 (tpp) cc_final: 0.8430 (tpp) REVERT: K 15 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7692 (ttm-80) REVERT: K 74 MET cc_start: 0.8703 (tpp) cc_final: 0.8024 (mmt) REVERT: K 120 MET cc_start: 0.9079 (ttp) cc_final: 0.8706 (ttt) REVERT: L 9 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8100 (mm110) REVERT: L 80 MET cc_start: 0.9100 (mtp) cc_final: 0.8745 (mtp) REVERT: M 9 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8663 (mm-40) REVERT: M 18 ASP cc_start: 0.8151 (p0) cc_final: 0.7756 (p0) REVERT: M 62 TYR cc_start: 0.9346 (m-10) cc_final: 0.9135 (m-10) REVERT: N 25 LYS cc_start: 0.9283 (ttmm) cc_final: 0.9082 (tttm) outliers start: 23 outliers final: 17 residues processed: 526 average time/residue: 0.4102 time to fit residues: 312.6014 Evaluate side-chains 518 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 501 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 41 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 43 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN D 41 ASN D 193 ASN H 193 ASN L 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.087216 restraints weight = 86479.497| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.18 r_work: 0.3085 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22162 Z= 0.179 Angle : 0.498 5.322 29862 Z= 0.266 Chirality : 0.042 0.139 3388 Planarity : 0.004 0.044 3892 Dihedral : 4.547 23.562 3052 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.90 % Allowed : 10.48 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.16), residues: 2758 helix: 2.16 (0.14), residues: 1400 sheet: 1.08 (0.25), residues: 336 loop : -0.96 (0.17), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 172 TYR 0.008 0.001 TYR L 182 PHE 0.010 0.001 PHE E 17 HIS 0.006 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00418 (22162) covalent geometry : angle 0.49782 (29862) hydrogen bonds : bond 0.03991 ( 1202) hydrogen bonds : angle 3.88560 ( 3690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 516 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.9184 (m-10) cc_final: 0.8950 (m-10) REVERT: B 25 LYS cc_start: 0.9149 (tttp) cc_final: 0.8917 (tttm) REVERT: B 120 MET cc_start: 0.8991 (ttp) cc_final: 0.8571 (ttt) REVERT: F 15 ARG cc_start: 0.8160 (ttp-170) cc_final: 0.7868 (ttm-80) REVERT: F 80 MET cc_start: 0.9153 (mtp) cc_final: 0.8887 (mtp) REVERT: G 18 ASP cc_start: 0.8426 (p0) cc_final: 0.8086 (p0) REVERT: H 25 LYS cc_start: 0.9210 (ttmm) cc_final: 0.8965 (tttm) REVERT: H 41 ASN cc_start: 0.8701 (t0) cc_final: 0.8335 (t0) REVERT: H 120 MET cc_start: 0.8973 (ttt) cc_final: 0.8633 (ttt) REVERT: I 15 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7682 (ttm-80) REVERT: I 118 ARG cc_start: 0.8390 (ptt180) cc_final: 0.7689 (mtp85) REVERT: K 15 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7732 (ttm-80) REVERT: K 74 MET cc_start: 0.8722 (tpp) cc_final: 0.8039 (mmt) REVERT: K 120 MET cc_start: 0.9073 (ttp) cc_final: 0.8710 (ttt) REVERT: K 141 GLU cc_start: 0.8475 (tp30) cc_final: 0.8242 (tp30) REVERT: L 9 GLN cc_start: 0.8246 (mm-40) cc_final: 0.8002 (mm110) REVERT: L 41 ASN cc_start: 0.8457 (m110) cc_final: 0.8152 (m110) REVERT: M 9 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8699 (mm-40) REVERT: M 18 ASP cc_start: 0.8192 (p0) cc_final: 0.7788 (p0) REVERT: M 62 TYR cc_start: 0.9340 (m-10) cc_final: 0.9133 (m-10) REVERT: N 25 LYS cc_start: 0.9293 (ttmm) cc_final: 0.9090 (tttm) outliers start: 21 outliers final: 20 residues processed: 532 average time/residue: 0.4041 time to fit residues: 311.6283 Evaluate side-chains 527 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 507 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 210 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 263 optimal weight: 0.4980 chunk 226 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN D 193 ASN H 193 ASN N 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088135 restraints weight = 85611.682| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.17 r_work: 0.3101 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22162 Z= 0.144 Angle : 0.483 5.194 29862 Z= 0.257 Chirality : 0.041 0.137 3388 Planarity : 0.004 0.045 3892 Dihedral : 4.426 21.935 3052 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.77 % Allowed : 10.27 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.16), residues: 2758 helix: 2.36 (0.14), residues: 1386 sheet: 1.08 (0.25), residues: 336 loop : -0.98 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 172 TYR 0.007 0.001 TYR L 182 PHE 0.009 0.001 PHE E 17 HIS 0.006 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00335 (22162) covalent geometry : angle 0.48347 (29862) hydrogen bonds : bond 0.03709 ( 1202) hydrogen bonds : angle 3.78029 ( 3690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 513 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.9170 (m-10) cc_final: 0.8923 (m-10) REVERT: B 25 LYS cc_start: 0.9154 (tttp) cc_final: 0.8930 (tttm) REVERT: B 120 MET cc_start: 0.8972 (ttp) cc_final: 0.8507 (ttt) REVERT: F 15 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7853 (ttm-80) REVERT: F 80 MET cc_start: 0.9105 (mtp) cc_final: 0.8826 (mtp) REVERT: G 18 ASP cc_start: 0.8412 (p0) cc_final: 0.8048 (p0) REVERT: H 25 LYS cc_start: 0.9207 (ttmm) cc_final: 0.8962 (tttm) REVERT: H 120 MET cc_start: 0.8941 (ttt) cc_final: 0.8613 (ttt) REVERT: I 15 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7666 (ttm-80) REVERT: I 118 ARG cc_start: 0.8311 (ptt180) cc_final: 0.7680 (mtp85) REVERT: K 15 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7721 (ttm-80) REVERT: K 74 MET cc_start: 0.8709 (tpp) cc_final: 0.8052 (mmt) REVERT: K 120 MET cc_start: 0.9063 (ttp) cc_final: 0.8670 (ttt) REVERT: K 141 GLU cc_start: 0.8459 (tp30) cc_final: 0.8220 (tp30) REVERT: L 9 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7973 (mm110) REVERT: L 41 ASN cc_start: 0.8411 (m110) cc_final: 0.8105 (m110) REVERT: M 9 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8688 (mm-40) REVERT: M 18 ASP cc_start: 0.8179 (p0) cc_final: 0.7767 (p0) outliers start: 18 outliers final: 16 residues processed: 528 average time/residue: 0.3953 time to fit residues: 303.5327 Evaluate side-chains 523 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 507 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 137 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 254 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN D 193 ASN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN H 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.097799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.083006 restraints weight = 83838.732| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.97 r_work: 0.2760 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22162 Z= 0.193 Angle : 0.508 5.313 29862 Z= 0.272 Chirality : 0.042 0.137 3388 Planarity : 0.004 0.047 3892 Dihedral : 4.520 23.210 3052 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.90 % Allowed : 10.65 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2758 helix: 2.22 (0.14), residues: 1400 sheet: 0.99 (0.26), residues: 336 loop : -0.90 (0.17), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 172 TYR 0.010 0.001 TYR M 62 PHE 0.008 0.001 PHE E 17 HIS 0.008 0.001 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00453 (22162) covalent geometry : angle 0.50787 (29862) hydrogen bonds : bond 0.04041 ( 1202) hydrogen bonds : angle 3.87411 ( 3690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 514 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.9154 (m-10) cc_final: 0.8940 (m-10) REVERT: B 25 LYS cc_start: 0.9163 (tttp) cc_final: 0.8942 (tttm) REVERT: B 120 MET cc_start: 0.8966 (ttp) cc_final: 0.8543 (ttt) REVERT: E 74 MET cc_start: 0.8513 (mmt) cc_final: 0.8000 (mmt) REVERT: F 15 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7842 (ttm-80) REVERT: F 80 MET cc_start: 0.9077 (mtp) cc_final: 0.8825 (mtp) REVERT: G 18 ASP cc_start: 0.8458 (p0) cc_final: 0.8049 (p0) REVERT: H 120 MET cc_start: 0.8932 (ttt) cc_final: 0.8576 (ttt) REVERT: I 15 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7728 (ttm-80) REVERT: I 118 ARG cc_start: 0.8327 (ptt180) cc_final: 0.7701 (mtp85) REVERT: K 15 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7757 (ttm-80) REVERT: K 74 MET cc_start: 0.8679 (tpp) cc_final: 0.7989 (mmt) REVERT: K 120 MET cc_start: 0.9083 (ttp) cc_final: 0.8705 (ttt) REVERT: K 141 GLU cc_start: 0.8465 (tp30) cc_final: 0.8221 (tp30) REVERT: L 9 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8075 (mm110) REVERT: L 80 MET cc_start: 0.9113 (mtp) cc_final: 0.8722 (mtp) REVERT: M 18 ASP cc_start: 0.8172 (p0) cc_final: 0.7746 (p0) outliers start: 21 outliers final: 20 residues processed: 531 average time/residue: 0.4012 time to fit residues: 310.7596 Evaluate side-chains 528 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 508 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 215 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN H 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.100134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.085203 restraints weight = 82794.086| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.98 r_work: 0.2793 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22162 Z= 0.126 Angle : 0.481 5.146 29862 Z= 0.255 Chirality : 0.041 0.134 3388 Planarity : 0.004 0.045 3892 Dihedral : 4.339 21.360 3052 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.68 % Allowed : 11.12 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.16), residues: 2758 helix: 2.40 (0.14), residues: 1400 sheet: 0.50 (0.20), residues: 518 loop : -0.78 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 172 TYR 0.007 0.001 TYR M 62 PHE 0.008 0.001 PHE E 17 HIS 0.006 0.001 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00295 (22162) covalent geometry : angle 0.48123 (29862) hydrogen bonds : bond 0.03466 ( 1202) hydrogen bonds : angle 3.67058 ( 3690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 518 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.9154 (m-10) cc_final: 0.8888 (m-10) REVERT: B 25 LYS cc_start: 0.9139 (tttp) cc_final: 0.8918 (tttm) REVERT: B 120 MET cc_start: 0.8947 (ttp) cc_final: 0.8496 (ttt) REVERT: F 15 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7777 (ttm-80) REVERT: F 41 ASN cc_start: 0.8212 (m-40) cc_final: 0.7978 (m-40) REVERT: F 80 MET cc_start: 0.9036 (mtp) cc_final: 0.8793 (mtp) REVERT: G 18 ASP cc_start: 0.8417 (p0) cc_final: 0.8030 (p0) REVERT: H 120 MET cc_start: 0.8909 (ttt) cc_final: 0.8522 (ttt) REVERT: I 15 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7709 (ttm-80) REVERT: I 118 ARG cc_start: 0.8335 (ptt180) cc_final: 0.7702 (mtp85) REVERT: J 108 LYS cc_start: 0.9236 (tptt) cc_final: 0.9035 (tptp) REVERT: K 74 MET cc_start: 0.8615 (tpp) cc_final: 0.7953 (mmt) REVERT: K 120 MET cc_start: 0.9074 (ttp) cc_final: 0.8664 (ttt) REVERT: K 141 GLU cc_start: 0.8455 (tp30) cc_final: 0.8210 (tp30) REVERT: L 80 MET cc_start: 0.9079 (mtp) cc_final: 0.8695 (mtp) REVERT: M 9 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8832 (mm-40) REVERT: M 18 ASP cc_start: 0.8153 (p0) cc_final: 0.7712 (p0) REVERT: Q 273 THR cc_start: 0.9336 (t) cc_final: 0.9094 (p) REVERT: X 273 THR cc_start: 0.9297 (t) cc_final: 0.9079 (p) outliers start: 16 outliers final: 13 residues processed: 531 average time/residue: 0.4115 time to fit residues: 314.9685 Evaluate side-chains 526 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 513 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 241 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 202 optimal weight: 0.8980 chunk 234 optimal weight: 0.0030 chunk 196 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN E 64 ASN H 41 ASN H 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.100871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.086035 restraints weight = 82731.489| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.99 r_work: 0.2781 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22162 Z= 0.118 Angle : 0.485 5.139 29862 Z= 0.256 Chirality : 0.041 0.135 3388 Planarity : 0.004 0.053 3892 Dihedral : 4.266 20.808 3052 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.56 % Allowed : 11.42 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.16), residues: 2758 helix: 2.46 (0.14), residues: 1400 sheet: 0.38 (0.21), residues: 490 loop : -0.56 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 172 TYR 0.007 0.001 TYR M 62 PHE 0.007 0.001 PHE E 17 HIS 0.006 0.001 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00276 (22162) covalent geometry : angle 0.48451 (29862) hydrogen bonds : bond 0.03396 ( 1202) hydrogen bonds : angle 3.60680 ( 3690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 514 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LYS cc_start: 0.9111 (tttp) cc_final: 0.8888 (tttm) REVERT: B 120 MET cc_start: 0.8957 (ttp) cc_final: 0.8508 (ttt) REVERT: F 15 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7784 (ttm-80) REVERT: F 41 ASN cc_start: 0.8240 (m-40) cc_final: 0.8006 (m-40) REVERT: F 80 MET cc_start: 0.9033 (mtp) cc_final: 0.8796 (mtp) REVERT: G 18 ASP cc_start: 0.8404 (p0) cc_final: 0.8000 (p0) REVERT: H 41 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8115 (m-40) REVERT: H 120 MET cc_start: 0.8913 (ttt) cc_final: 0.8552 (ttt) REVERT: I 15 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7707 (ttm-80) REVERT: I 118 ARG cc_start: 0.8319 (ptt180) cc_final: 0.7679 (mtp85) REVERT: K 74 MET cc_start: 0.8608 (tpp) cc_final: 0.7943 (mmt) REVERT: K 120 MET cc_start: 0.9068 (ttp) cc_final: 0.8641 (ttt) REVERT: K 141 GLU cc_start: 0.8449 (tp30) cc_final: 0.8200 (tp30) REVERT: L 80 MET cc_start: 0.9090 (mtp) cc_final: 0.8712 (mtp) REVERT: M 9 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8827 (mm-40) REVERT: M 18 ASP cc_start: 0.8118 (p0) cc_final: 0.7669 (p0) REVERT: Q 273 THR cc_start: 0.9331 (t) cc_final: 0.9088 (p) REVERT: X 273 THR cc_start: 0.9288 (t) cc_final: 0.9062 (p) outliers start: 13 outliers final: 10 residues processed: 525 average time/residue: 0.4059 time to fit residues: 307.6178 Evaluate side-chains 518 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 507 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 261 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 265 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN D 193 ASN E 64 ASN H 41 ASN H 193 ASN K 41 ASN L 64 ASN ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.085981 restraints weight = 82865.169| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.99 r_work: 0.2801 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 22162 Z= 0.154 Angle : 0.651 59.163 29862 Z= 0.389 Chirality : 0.041 0.348 3388 Planarity : 0.004 0.053 3892 Dihedral : 4.282 20.808 3052 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.51 % Allowed : 11.80 % Favored : 87.68 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.16), residues: 2758 helix: 2.45 (0.14), residues: 1400 sheet: 0.39 (0.21), residues: 490 loop : -0.56 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 15 TYR 0.006 0.001 TYR L 182 PHE 0.007 0.001 PHE E 17 HIS 0.006 0.001 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00336 (22162) covalent geometry : angle 0.65088 (29862) hydrogen bonds : bond 0.03428 ( 1202) hydrogen bonds : angle 3.60846 ( 3690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10133.64 seconds wall clock time: 172 minutes 23.78 seconds (10343.78 seconds total)