Starting phenix.real_space_refine on Thu Mar 5 04:36:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6si7_10206/03_2026/6si7_10206.cif Found real_map, /net/cci-nas-00/data/ceres_data/6si7_10206/03_2026/6si7_10206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6si7_10206/03_2026/6si7_10206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6si7_10206/03_2026/6si7_10206.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6si7_10206/03_2026/6si7_10206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6si7_10206/03_2026/6si7_10206.map" } resolution = 3.4 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= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 12321 2.51 5 N 3375 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 19476 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "P" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, Q, R Time building chain proxies: 2.16, per 1000 atoms: 0.11 Number of scatterers: 19476 At special positions: 0 Unit cell: (127, 126, 112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3708 8.00 N 3375 7.00 C 12321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 657.7 milliseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4626 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 19 sheets defined 28.1% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS P 22 " --> pdb=" O ALA P 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS P 26 " --> pdb=" O LYS P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL P 69 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR P 70 " --> pdb=" O ALA P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU P 92 " --> pdb=" O ASN P 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE P 95 " --> pdb=" O ASN P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 230 Processing helix chain 'P' and resid 251 through 256 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 74 removed outlier: 4.130A pdb=" N VAL J 69 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE J 95 " --> pdb=" O ASN J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS K 22 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL K 69 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU K 92 " --> pdb=" O ASN K 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE K 95 " --> pdb=" O ASN K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 230 Processing helix chain 'K' and resid 251 through 256 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL L 69 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU L 92 " --> pdb=" O ASN L 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE L 95 " --> pdb=" O ASN L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 230 Processing helix chain 'L' and resid 251 through 256 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL M 69 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 100 removed outlier: 3.778A pdb=" N GLU M 92 " --> pdb=" O ASN M 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE M 95 " --> pdb=" O ASN M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 230 Processing helix chain 'M' and resid 251 through 256 Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL N 69 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU N 92 " --> pdb=" O ASN N 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE N 95 " --> pdb=" O ASN N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 230 Processing helix chain 'N' and resid 251 through 256 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 18 through 29 removed outlier: 4.549A pdb=" N ASN G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 26 removed outlier: 3.880A pdb=" N LYS O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL O 69 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR O 70 " --> pdb=" O ALA O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 100 removed outlier: 3.778A pdb=" N GLU O 92 " --> pdb=" O ASN O 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE O 95 " --> pdb=" O ASN O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 230 Processing helix chain 'O' and resid 251 through 256 Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS Q 22 " --> pdb=" O ALA Q 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS Q 26 " --> pdb=" O LYS Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 74 removed outlier: 4.130A pdb=" N VAL Q 69 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU Q 92 " --> pdb=" O ASN Q 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE Q 95 " --> pdb=" O ASN Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 230 Processing helix chain 'Q' and resid 251 through 256 Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS R 26 " --> pdb=" O LYS R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 74 removed outlier: 4.130A pdb=" N VAL R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU R 92 " --> pdb=" O ASN R 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE R 95 " --> pdb=" O ASN R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 251 through 256 Processing sheet with id=AA1, first strand: chain 'P' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE P 35 " --> pdb=" O ILE P 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL P 123 " --> pdb=" O PHE P 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER P 37 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY P 125 " --> pdb=" O SER P 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE P 34 " --> pdb=" O ILE P 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU P 81 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL P 36 " --> pdb=" O LEU P 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA P 158 " --> pdb=" O ILE P 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR P 130 " --> pdb=" O GLN P 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN P 156 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE P 157 " --> pdb=" O SER P 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER P 178 " --> pdb=" O ILE P 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL P 159 " --> pdb=" O ASN P 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN P 176 " --> pdb=" O VAL P 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU P 161 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER P 174 " --> pdb=" O LEU P 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL P 163 " --> pdb=" O LEU P 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 135 through 142 removed outlier: 4.512A pdb=" N LEU P 154 " --> pdb=" O LYS P 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER P 183 " --> pdb=" O GLN P 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR P 184 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU R 154 " --> pdb=" O LYS R 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER R 183 " --> pdb=" O GLN R 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR R 184 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU Q 154 " --> pdb=" O LYS Q 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER Q 183 " --> pdb=" O GLN Q 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR Q 184 " --> pdb=" O SER Q 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU O 154 " --> pdb=" O LYS O 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER O 183 " --> pdb=" O GLN O 153 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR O 184 " --> pdb=" O SER O 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU N 154 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER N 183 " --> pdb=" O GLN N 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR N 184 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU M 154 " --> pdb=" O LYS M 135 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER M 183 " --> pdb=" O GLN M 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR M 184 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU L 154 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER L 183 " --> pdb=" O GLN L 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 184 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU K 154 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER K 183 " --> pdb=" O GLN K 153 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR K 184 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU J 154 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER J 183 " --> pdb=" O GLN J 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR J 184 " --> pdb=" O SER J 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE J 35 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL J 123 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER J 37 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY J 125 " --> pdb=" O SER J 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE J 34 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU J 81 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL J 36 " --> pdb=" O LEU J 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 42 through 43 removed outlier: 6.509A pdb=" N ALA J 158 " --> pdb=" O ILE J 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR J 130 " --> pdb=" O GLN J 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN J 156 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE J 157 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER J 178 " --> pdb=" O ILE J 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL J 159 " --> pdb=" O ASN J 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN J 176 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU J 161 " --> pdb=" O SER J 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER J 174 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL J 163 " --> pdb=" O LEU J 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE K 35 " --> pdb=" O ILE K 121 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL K 123 " --> pdb=" O PHE K 35 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER K 37 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY K 125 " --> pdb=" O SER K 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE K 34 " --> pdb=" O ILE K 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU K 81 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL K 36 " --> pdb=" O LEU K 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA K 158 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR K 130 " --> pdb=" O GLN K 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN K 156 " --> pdb=" O TYR K 130 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE K 157 " --> pdb=" O SER K 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER K 178 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL K 159 " --> pdb=" O ASN K 176 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN K 176 " --> pdb=" O VAL K 159 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU K 161 " --> pdb=" O SER K 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER K 174 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL K 163 " --> pdb=" O LEU K 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE L 35 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL L 123 " --> pdb=" O PHE L 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER L 37 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY L 125 " --> pdb=" O SER L 37 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE L 34 " --> pdb=" O ILE L 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU L 81 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL L 36 " --> pdb=" O LEU L 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA L 158 " --> pdb=" O ILE L 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR L 130 " --> pdb=" O GLN L 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN L 156 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE L 157 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER L 178 " --> pdb=" O ILE L 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL L 159 " --> pdb=" O ASN L 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN L 176 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU L 161 " --> pdb=" O SER L 174 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER L 174 " --> pdb=" O LEU L 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL L 163 " --> pdb=" O LEU L 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE M 35 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL M 123 " --> pdb=" O PHE M 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER M 37 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY M 125 " --> pdb=" O SER M 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE M 34 " --> pdb=" O ILE M 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU M 81 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL M 36 " --> pdb=" O LEU M 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA M 158 " --> pdb=" O ILE M 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR M 130 " --> pdb=" O GLN M 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN M 156 " --> pdb=" O TYR M 130 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE M 157 " --> pdb=" O SER M 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER M 178 " --> pdb=" O ILE M 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL M 159 " --> pdb=" O ASN M 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN M 176 " --> pdb=" O VAL M 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU M 161 " --> pdb=" O SER M 174 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER M 174 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL M 163 " --> pdb=" O LEU M 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE N 35 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL N 123 " --> pdb=" O PHE N 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER N 37 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY N 125 " --> pdb=" O SER N 37 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE N 34 " --> pdb=" O ILE N 79 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU N 81 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL N 36 " --> pdb=" O LEU N 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA N 158 " --> pdb=" O ILE N 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR N 130 " --> pdb=" O GLN N 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN N 156 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE N 157 " --> pdb=" O SER N 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER N 178 " --> pdb=" O ILE N 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL N 159 " --> pdb=" O ASN N 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN N 176 " --> pdb=" O VAL N 159 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU N 161 " --> pdb=" O SER N 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER N 174 " --> pdb=" O LEU N 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL N 163 " --> pdb=" O LEU N 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE O 35 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL O 123 " --> pdb=" O PHE O 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER O 37 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY O 125 " --> pdb=" O SER O 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE O 34 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU O 81 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL O 36 " --> pdb=" O LEU O 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA O 158 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR O 130 " --> pdb=" O GLN O 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN O 156 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE O 157 " --> pdb=" O SER O 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER O 178 " --> pdb=" O ILE O 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL O 159 " --> pdb=" O ASN O 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN O 176 " --> pdb=" O VAL O 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU O 161 " --> pdb=" O SER O 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER O 174 " --> pdb=" O LEU O 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL O 163 " --> pdb=" O LEU O 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE Q 35 " --> pdb=" O ILE Q 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL Q 123 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER Q 37 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY Q 125 " --> pdb=" O SER Q 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE Q 34 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU Q 81 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL Q 36 " --> pdb=" O LEU Q 81 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 42 through 43 removed outlier: 6.509A pdb=" N ALA Q 158 " --> pdb=" O ILE Q 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR Q 130 " --> pdb=" O GLN Q 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN Q 156 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE Q 157 " --> pdb=" O SER Q 178 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER Q 178 " --> pdb=" O ILE Q 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL Q 159 " --> pdb=" O ASN Q 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN Q 176 " --> pdb=" O VAL Q 159 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU Q 161 " --> pdb=" O SER Q 174 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER Q 174 " --> pdb=" O LEU Q 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL Q 163 " --> pdb=" O LEU Q 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 42 through 43 removed outlier: 6.403A pdb=" N PHE R 35 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL R 123 " --> pdb=" O PHE R 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER R 37 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY R 125 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE R 34 " --> pdb=" O ILE R 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU R 81 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL R 36 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 42 through 43 removed outlier: 6.509A pdb=" N ALA R 158 " --> pdb=" O ILE R 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR R 130 " --> pdb=" O GLN R 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN R 156 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE R 157 " --> pdb=" O SER R 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER R 178 " --> pdb=" O ILE R 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL R 159 " --> pdb=" O ASN R 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN R 176 " --> pdb=" O VAL R 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU R 161 " --> pdb=" O SER R 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER R 174 " --> pdb=" O LEU R 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL R 163 " --> pdb=" O LEU R 172 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2241 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: 3.23 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6397 1.34 - 1.45: 2857 1.45 - 1.57: 10456 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 19845 Sorted by residual: bond pdb=" CA THR E 2 " pdb=" C THR E 2 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.35e-02 5.49e+03 2.12e+00 bond pdb=" CA THR D 2 " pdb=" C THR D 2 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.35e-02 5.49e+03 2.10e+00 bond pdb=" CA THR F 2 " pdb=" C THR F 2 " ideal model delta sigma weight residual 1.526 1.506 0.019 1.35e-02 5.49e+03 2.08e+00 bond pdb=" CA THR A 2 " pdb=" C THR A 2 " ideal model delta sigma weight residual 1.526 1.506 0.019 1.35e-02 5.49e+03 2.08e+00 bond pdb=" CA THR B 2 " pdb=" C THR B 2 " ideal model delta sigma weight residual 1.526 1.506 0.019 1.35e-02 5.49e+03 2.07e+00 ... (remaining 19840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 24429 1.25 - 2.49: 2013 2.49 - 3.74: 346 3.74 - 4.98: 87 4.98 - 6.23: 44 Bond angle restraints: 26919 Sorted by residual: angle pdb=" N THR D 2 " pdb=" CA THR D 2 " pdb=" C THR D 2 " ideal model delta sigma weight residual 111.30 106.28 5.02 1.36e+00 5.41e-01 1.36e+01 angle pdb=" N THR E 2 " pdb=" CA THR E 2 " pdb=" C THR E 2 " ideal model delta sigma weight residual 111.30 106.28 5.02 1.36e+00 5.41e-01 1.36e+01 angle pdb=" N THR F 2 " pdb=" CA THR F 2 " pdb=" C THR F 2 " ideal model delta sigma weight residual 111.30 106.29 5.01 1.36e+00 5.41e-01 1.36e+01 angle pdb=" N THR A 2 " pdb=" CA THR A 2 " pdb=" C THR A 2 " ideal model delta sigma weight residual 111.30 106.29 5.01 1.36e+00 5.41e-01 1.35e+01 angle pdb=" N THR G 2 " pdb=" CA THR G 2 " pdb=" C THR G 2 " ideal model delta sigma weight residual 111.30 106.30 5.00 1.36e+00 5.41e-01 1.35e+01 ... (remaining 26914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 10746 17.63 - 35.27: 990 35.27 - 52.90: 198 52.90 - 70.54: 18 70.54 - 88.17: 27 Dihedral angle restraints: 11979 sinusoidal: 4779 harmonic: 7200 Sorted by residual: dihedral pdb=" CA SER J 126 " pdb=" C SER J 126 " pdb=" N ILE J 127 " pdb=" CA ILE J 127 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA SER Q 126 " pdb=" C SER Q 126 " pdb=" N ILE Q 127 " pdb=" CA ILE Q 127 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA SER N 126 " pdb=" C SER N 126 " pdb=" N ILE N 127 " pdb=" CA ILE N 127 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 11976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1997 0.043 - 0.086: 747 0.086 - 0.129: 204 0.129 - 0.172: 49 0.172 - 0.215: 27 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA VAL R 163 " pdb=" N VAL R 163 " pdb=" C VAL R 163 " pdb=" CB VAL R 163 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA VAL N 163 " pdb=" N VAL N 163 " pdb=" C VAL N 163 " pdb=" CB VAL N 163 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL L 163 " pdb=" N VAL L 163 " pdb=" C VAL L 163 " pdb=" CB VAL L 163 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3021 not shown) Planarity restraints: 3546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY I 1 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C GLY I 1 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY I 1 " -0.017 2.00e-02 2.50e+03 pdb=" N THR I 2 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 1 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C GLY H 1 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY H 1 " -0.017 2.00e-02 2.50e+03 pdb=" N THR H 2 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 1 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C GLY E 1 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY E 1 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 2 " 0.016 2.00e-02 2.50e+03 ... (remaining 3543 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5288 2.79 - 3.32: 18123 3.32 - 3.85: 35588 3.85 - 4.37: 43344 4.37 - 4.90: 72627 Nonbonded interactions: 174970 Sorted by model distance: nonbonded pdb=" OH TYR K 130 " pdb=" OD2 ASP K 155 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR Q 130 " pdb=" OD2 ASP Q 155 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR J 130 " pdb=" OD2 ASP J 155 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR N 130 " pdb=" OD2 ASP N 155 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR P 130 " pdb=" OD2 ASP P 155 " model vdw 2.267 3.040 ... (remaining 174965 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: 0.06 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' } ncs_group { reference = chain 'P' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.120 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.004 0.036 19845 Z= 0.216 Angle : 0.792 6.231 26919 Z= 0.476 Chirality : 0.052 0.215 3024 Planarity : 0.006 0.054 3546 Dihedral : 14.712 88.171 7353 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -4.55 (0.14), residues: 2448 helix: -4.32 (0.08), residues: 657 sheet: -2.79 (0.18), residues: 657 loop : -2.13 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 83 TYR 0.011 0.001 TYR O 143 PHE 0.012 0.002 PHE C 21 TRP 0.006 0.001 TRP J 77 HIS 0.001 0.000 HIS Q 26 Details of bonding type rmsd covalent geometry : bond 0.00448 (19845) covalent geometry : angle 0.79209 (26919) hydrogen bonds : bond 0.26350 ( 765) hydrogen bonds : angle 10.58547 ( 2241) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 126 SER cc_start: 0.8480 (m) cc_final: 0.8257 (m) REVERT: J 153 GLN cc_start: 0.7914 (mt0) cc_final: 0.7627 (mt0) REVERT: J 256 MET cc_start: 0.6516 (mtt) cc_final: 0.6271 (mtp) REVERT: K 256 MET cc_start: 0.6591 (mtt) cc_final: 0.6302 (mtp) REVERT: L 153 GLN cc_start: 0.7989 (mt0) cc_final: 0.7701 (mt0) REVERT: L 256 MET cc_start: 0.6559 (mtt) cc_final: 0.6301 (mtp) REVERT: M 40 ASN cc_start: 0.7731 (t0) cc_final: 0.7488 (t0) REVERT: M 256 MET cc_start: 0.6519 (mtt) cc_final: 0.6244 (mtp) REVERT: N 44 GLU cc_start: 0.7176 (pt0) cc_final: 0.6880 (pt0) REVERT: N 67 MET cc_start: 0.8224 (mtt) cc_final: 0.7384 (mtp) REVERT: N 82 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7189 (tm-30) REVERT: N 126 SER cc_start: 0.8329 (m) cc_final: 0.7954 (m) REVERT: N 153 GLN cc_start: 0.7931 (mt0) cc_final: 0.7729 (mt0) REVERT: N 217 MET cc_start: 0.8052 (tpt) cc_final: 0.7148 (tpt) REVERT: N 256 MET cc_start: 0.6548 (mtt) cc_final: 0.6326 (mtp) REVERT: O 165 ASN cc_start: 0.7581 (t0) cc_final: 0.7295 (t0) REVERT: O 256 MET cc_start: 0.6544 (mtt) cc_final: 0.6248 (mtp) REVERT: Q 153 GLN cc_start: 0.7850 (mt0) cc_final: 0.7584 (mt0) REVERT: Q 256 MET cc_start: 0.6629 (mtt) cc_final: 0.6351 (mtp) REVERT: R 82 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7229 (tm-30) REVERT: R 165 ASN cc_start: 0.7602 (t0) cc_final: 0.7357 (t0) REVERT: R 256 MET cc_start: 0.6611 (mtt) cc_final: 0.6387 (mtm) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.1671 time to fit residues: 129.1105 Evaluate side-chains 336 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN ** P 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN J 133 ASN J 153 GLN J 156 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN K 133 ASN K 153 GLN K 156 GLN ** D 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 ASN L 153 GLN L 156 GLN ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 156 GLN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 ASN N 153 GLN N 156 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN O 88 ASN O 133 ASN O 156 GLN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN Q 47 GLN Q 133 ASN Q 153 GLN Q 156 GLN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN R 156 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.163712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142925 restraints weight = 25345.680| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.74 r_work: 0.3553 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19845 Z= 0.173 Angle : 0.578 8.833 26919 Z= 0.312 Chirality : 0.043 0.151 3024 Planarity : 0.005 0.058 3546 Dihedral : 5.231 21.790 2700 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.06 % Allowed : 13.79 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -3.46 (0.15), residues: 2448 helix: -2.81 (0.13), residues: 702 sheet: -2.28 (0.20), residues: 594 loop : -1.79 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 17 TYR 0.023 0.001 TYR R 21 PHE 0.017 0.001 PHE K 191 TRP 0.005 0.001 TRP Q 77 HIS 0.001 0.000 HIS R 26 Details of bonding type rmsd covalent geometry : bond 0.00371 (19845) covalent geometry : angle 0.57836 (26919) hydrogen bonds : bond 0.04017 ( 765) hydrogen bonds : angle 6.75694 ( 2241) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 407 time to evaluate : 0.735 Fit side-chains REVERT: P 164 VAL cc_start: 0.8936 (t) cc_final: 0.8671 (t) REVERT: P 217 MET cc_start: 0.8600 (tpp) cc_final: 0.8301 (tpt) REVERT: P 256 MET cc_start: 0.6333 (mtt) cc_final: 0.6053 (mtp) REVERT: B 6 GLN cc_start: 0.7394 (pt0) cc_final: 0.7156 (pp30) REVERT: J 35 PHE cc_start: 0.8786 (m-80) cc_final: 0.8536 (m-80) REVERT: J 42 GLN cc_start: 0.8317 (tp40) cc_final: 0.8021 (tt0) REVERT: J 82 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7571 (tm-30) REVERT: J 131 GLU cc_start: 0.6945 (tp30) cc_final: 0.6722 (tp30) REVERT: J 256 MET cc_start: 0.6735 (mtt) cc_final: 0.6383 (mtp) REVERT: K 42 GLN cc_start: 0.8290 (tp40) cc_final: 0.8028 (tt0) REVERT: K 82 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7561 (tm-30) REVERT: K 256 MET cc_start: 0.6626 (mtt) cc_final: 0.6251 (mtp) REVERT: D 29 GLN cc_start: 0.8902 (pt0) cc_final: 0.8663 (pt0) REVERT: D 33 LYS cc_start: 0.7939 (mppt) cc_final: 0.7572 (mmtm) REVERT: L 226 PHE cc_start: 0.9039 (m-10) cc_final: 0.8835 (m-10) REVERT: L 240 GLN cc_start: 0.7654 (mt0) cc_final: 0.7435 (mt0) REVERT: L 256 MET cc_start: 0.6494 (mtt) cc_final: 0.6133 (mtp) REVERT: E 32 TYR cc_start: 0.8376 (m-80) cc_final: 0.8012 (m-80) REVERT: M 256 MET cc_start: 0.6647 (mtt) cc_final: 0.6258 (mtp) REVERT: N 33 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8534 (mtmt) REVERT: N 82 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7518 (tm-30) REVERT: N 143 TYR cc_start: 0.8249 (t80) cc_final: 0.8010 (t80) REVERT: N 256 MET cc_start: 0.6540 (mtt) cc_final: 0.6214 (mtp) REVERT: G 33 LYS cc_start: 0.7750 (mppt) cc_final: 0.7504 (mmtm) REVERT: O 200 LEU cc_start: 0.7981 (tt) cc_final: 0.7539 (tp) REVERT: O 256 MET cc_start: 0.6676 (mtt) cc_final: 0.6318 (mtp) REVERT: H 29 GLN cc_start: 0.8421 (pt0) cc_final: 0.8088 (pt0) REVERT: Q 217 MET cc_start: 0.8575 (tpp) cc_final: 0.8243 (tpt) REVERT: Q 256 MET cc_start: 0.6728 (mtt) cc_final: 0.6408 (mtp) REVERT: I 6 GLN cc_start: 0.7355 (pt0) cc_final: 0.7086 (pp30) REVERT: R 82 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7487 (tm-30) REVERT: R 143 TYR cc_start: 0.8344 (t80) cc_final: 0.8091 (t80) REVERT: R 165 ASN cc_start: 0.8039 (t0) cc_final: 0.7821 (t0) REVERT: R 170 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7561 (mt-10) REVERT: R 200 LEU cc_start: 0.8016 (tt) cc_final: 0.7701 (tp) REVERT: R 217 MET cc_start: 0.8945 (tpt) cc_final: 0.8592 (tpt) REVERT: R 256 MET cc_start: 0.6680 (mtt) cc_final: 0.6260 (mtp) outliers start: 65 outliers final: 23 residues processed: 443 average time/residue: 0.1408 time to fit residues: 96.0897 Evaluate side-chains 360 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 337 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 71 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 196 optimal weight: 0.2980 chunk 171 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 GLN ** P 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 GLN P 247 ASN ** B 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 ASN C 18 ASN K 153 GLN K 247 ASN L 247 ASN ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN M 133 ASN M 247 ASN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 247 ASN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN O 247 ASN H 6 GLN ** H 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141064 restraints weight = 25427.965| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.73 r_work: 0.3521 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19845 Z= 0.166 Angle : 0.556 7.787 26919 Z= 0.295 Chirality : 0.042 0.182 3024 Planarity : 0.005 0.053 3546 Dihedral : 4.991 19.924 2700 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.05 % Allowed : 15.58 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.82 (0.15), residues: 2448 helix: -1.69 (0.15), residues: 738 sheet: -2.35 (0.19), residues: 594 loop : -1.54 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 17 TYR 0.018 0.001 TYR I 32 PHE 0.011 0.001 PHE J 144 TRP 0.006 0.001 TRP P 77 HIS 0.001 0.000 HIS K 26 Details of bonding type rmsd covalent geometry : bond 0.00360 (19845) covalent geometry : angle 0.55570 (26919) hydrogen bonds : bond 0.03529 ( 765) hydrogen bonds : angle 6.32662 ( 2241) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 398 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 2 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8104 (m) REVERT: P 164 VAL cc_start: 0.8995 (t) cc_final: 0.8714 (t) REVERT: P 256 MET cc_start: 0.6385 (mtt) cc_final: 0.6046 (mtp) REVERT: B 2 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.8001 (m) REVERT: B 6 GLN cc_start: 0.7483 (pt0) cc_final: 0.7244 (pp30) REVERT: J 35 PHE cc_start: 0.8800 (m-80) cc_final: 0.8519 (m-80) REVERT: J 200 LEU cc_start: 0.8242 (tt) cc_final: 0.7804 (tp) REVERT: J 256 MET cc_start: 0.6770 (mtt) cc_final: 0.6356 (mtp) REVERT: K 82 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7499 (tm-30) REVERT: K 124 GLU cc_start: 0.7814 (tp30) cc_final: 0.7580 (tp30) REVERT: K 256 MET cc_start: 0.6682 (mtt) cc_final: 0.6259 (mtp) REVERT: D 29 GLN cc_start: 0.8955 (pt0) cc_final: 0.8719 (pt0) REVERT: D 33 LYS cc_start: 0.8011 (mppt) cc_final: 0.7671 (mmtm) REVERT: L 200 LEU cc_start: 0.8217 (tt) cc_final: 0.7911 (tp) REVERT: L 226 PHE cc_start: 0.9035 (m-10) cc_final: 0.8814 (m-10) REVERT: L 256 MET cc_start: 0.6435 (mtt) cc_final: 0.6085 (mtp) REVERT: E 32 TYR cc_start: 0.8453 (m-80) cc_final: 0.8133 (m-80) REVERT: M 82 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7407 (tm-30) REVERT: M 256 MET cc_start: 0.6603 (mtt) cc_final: 0.6240 (mtp) REVERT: N 82 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7398 (tm-30) REVERT: N 143 TYR cc_start: 0.8366 (t80) cc_final: 0.8161 (t80) REVERT: N 256 MET cc_start: 0.6542 (mtt) cc_final: 0.6293 (mtp) REVERT: G 33 LYS cc_start: 0.7753 (mppt) cc_final: 0.7497 (mmtm) REVERT: O 82 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7451 (tm-30) REVERT: O 200 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7958 (tp) REVERT: O 201 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6977 (pt0) REVERT: O 240 GLN cc_start: 0.7657 (mt0) cc_final: 0.7393 (mt0) REVERT: O 256 MET cc_start: 0.6771 (mtt) cc_final: 0.6431 (mtp) REVERT: H 29 GLN cc_start: 0.8488 (pt0) cc_final: 0.8158 (pt0) REVERT: Q 217 MET cc_start: 0.8539 (tpp) cc_final: 0.7750 (tpt) REVERT: Q 256 MET cc_start: 0.6759 (mtt) cc_final: 0.6374 (mtp) REVERT: I 6 GLN cc_start: 0.7343 (pt0) cc_final: 0.7110 (pp30) REVERT: R 82 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7440 (tm-30) REVERT: R 200 LEU cc_start: 0.8133 (tt) cc_final: 0.7712 (tp) REVERT: R 217 MET cc_start: 0.8998 (tpt) cc_final: 0.8718 (tpt) REVERT: R 256 MET cc_start: 0.6639 (mtt) cc_final: 0.6243 (mtp) outliers start: 86 outliers final: 42 residues processed: 444 average time/residue: 0.1358 time to fit residues: 91.7939 Evaluate side-chains 412 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 366 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 114 GLN Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 126 SER Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 200 LEU Chi-restraints excluded: chain O residue 201 GLU Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 169 optimal weight: 0.0270 chunk 75 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 145 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN L 153 GLN ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 9 ASN ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142124 restraints weight = 25276.576| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.75 r_work: 0.3533 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19845 Z= 0.141 Angle : 0.527 8.454 26919 Z= 0.280 Chirality : 0.041 0.138 3024 Planarity : 0.005 0.054 3546 Dihedral : 4.820 19.248 2700 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.05 % Allowed : 16.48 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.24 (0.16), residues: 2448 helix: -0.84 (0.17), residues: 738 sheet: -2.39 (0.19), residues: 594 loop : -1.22 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.020 0.001 TYR H 32 PHE 0.026 0.001 PHE M 191 TRP 0.011 0.001 TRP M 237 HIS 0.001 0.000 HIS N 26 Details of bonding type rmsd covalent geometry : bond 0.00312 (19845) covalent geometry : angle 0.52688 (26919) hydrogen bonds : bond 0.03256 ( 765) hydrogen bonds : angle 6.09907 ( 2241) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 378 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: P 164 VAL cc_start: 0.8970 (t) cc_final: 0.8731 (t) REVERT: P 256 MET cc_start: 0.6342 (mtt) cc_final: 0.6019 (mtp) REVERT: B 6 GLN cc_start: 0.7476 (pt0) cc_final: 0.7261 (pp30) REVERT: J 35 PHE cc_start: 0.8788 (m-80) cc_final: 0.8517 (m-80) REVERT: J 200 LEU cc_start: 0.8138 (tt) cc_final: 0.7745 (tp) REVERT: J 256 MET cc_start: 0.6733 (mtt) cc_final: 0.6422 (mtp) REVERT: K 82 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7390 (tm-30) REVERT: K 185 GLU cc_start: 0.7885 (pt0) cc_final: 0.7604 (tt0) REVERT: K 256 MET cc_start: 0.6655 (mtt) cc_final: 0.6300 (mtp) REVERT: D 33 LYS cc_start: 0.8098 (mppt) cc_final: 0.7761 (mmtm) REVERT: L 200 LEU cc_start: 0.8261 (tt) cc_final: 0.7919 (tp) REVERT: L 201 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6922 (pt0) REVERT: L 240 GLN cc_start: 0.7710 (mt0) cc_final: 0.7465 (mt0) REVERT: L 256 MET cc_start: 0.6471 (mtt) cc_final: 0.6134 (mtp) REVERT: E 32 TYR cc_start: 0.8459 (m-80) cc_final: 0.8045 (m-80) REVERT: E 33 LYS cc_start: 0.7974 (mppt) cc_final: 0.7749 (mmtt) REVERT: M 82 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7388 (tm-30) REVERT: M 217 MET cc_start: 0.8860 (tpt) cc_final: 0.8577 (tpt) REVERT: M 256 MET cc_start: 0.6658 (mtt) cc_final: 0.6329 (mtp) REVERT: N 82 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7422 (tm-30) REVERT: N 143 TYR cc_start: 0.8362 (t80) cc_final: 0.8156 (t80) REVERT: N 201 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: N 210 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7868 (tt0) REVERT: N 217 MET cc_start: 0.8935 (tpt) cc_final: 0.8496 (tpt) REVERT: N 256 MET cc_start: 0.6551 (mtt) cc_final: 0.6270 (mtp) REVERT: G 33 LYS cc_start: 0.7729 (mppt) cc_final: 0.7500 (mmtm) REVERT: O 82 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7435 (tm-30) REVERT: O 200 LEU cc_start: 0.8227 (tt) cc_final: 0.7918 (tp) REVERT: O 240 GLN cc_start: 0.7621 (mt0) cc_final: 0.7358 (mt0) REVERT: O 256 MET cc_start: 0.6708 (mtt) cc_final: 0.6377 (mtp) REVERT: Q 94 LYS cc_start: 0.8654 (mttt) cc_final: 0.8445 (mttm) REVERT: Q 124 GLU cc_start: 0.7623 (tp30) cc_final: 0.7411 (tp30) REVERT: Q 256 MET cc_start: 0.6829 (mtt) cc_final: 0.6456 (mtp) REVERT: R 200 LEU cc_start: 0.8168 (tt) cc_final: 0.7828 (tp) REVERT: R 217 MET cc_start: 0.9021 (tpt) cc_final: 0.8653 (tpp) REVERT: R 256 MET cc_start: 0.6693 (mtt) cc_final: 0.6302 (mtp) outliers start: 86 outliers final: 53 residues processed: 426 average time/residue: 0.1376 time to fit residues: 88.4713 Evaluate side-chains 409 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 354 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 114 GLN Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 126 SER Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 153 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 84 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 chunk 42 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 GLN ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 27 GLN ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139243 restraints weight = 25154.175| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.74 r_work: 0.3498 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19845 Z= 0.173 Angle : 0.542 9.310 26919 Z= 0.289 Chirality : 0.042 0.227 3024 Planarity : 0.005 0.054 3546 Dihedral : 4.816 18.570 2700 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.43 % Allowed : 17.33 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.94 (0.17), residues: 2448 helix: -0.44 (0.18), residues: 729 sheet: -2.39 (0.19), residues: 594 loop : -1.05 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 8 TYR 0.020 0.001 TYR H 32 PHE 0.020 0.002 PHE O 191 TRP 0.009 0.001 TRP M 237 HIS 0.001 0.000 HIS N 26 Details of bonding type rmsd covalent geometry : bond 0.00377 (19845) covalent geometry : angle 0.54196 (26919) hydrogen bonds : bond 0.03322 ( 765) hydrogen bonds : angle 6.09784 ( 2241) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 388 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: P 164 VAL cc_start: 0.9019 (t) cc_final: 0.8780 (t) REVERT: P 256 MET cc_start: 0.6334 (mtt) cc_final: 0.5982 (mtp) REVERT: B 6 GLN cc_start: 0.7614 (pt0) cc_final: 0.7360 (pp30) REVERT: B 32 TYR cc_start: 0.8412 (m-80) cc_final: 0.8179 (m-80) REVERT: B 33 LYS cc_start: 0.8009 (mppt) cc_final: 0.7584 (mmtm) REVERT: J 35 PHE cc_start: 0.8850 (m-80) cc_final: 0.8594 (m-80) REVERT: J 143 TYR cc_start: 0.8030 (t80) cc_final: 0.7787 (t80) REVERT: J 200 LEU cc_start: 0.8346 (tt) cc_final: 0.8027 (tp) REVERT: J 256 MET cc_start: 0.6779 (mtt) cc_final: 0.6360 (mtp) REVERT: K 185 GLU cc_start: 0.7972 (pt0) cc_final: 0.7701 (tt0) REVERT: K 256 MET cc_start: 0.6748 (mtt) cc_final: 0.6347 (mtp) REVERT: D 33 LYS cc_start: 0.8096 (mppt) cc_final: 0.7770 (mmtm) REVERT: L 49 LYS cc_start: 0.9237 (mttm) cc_final: 0.8886 (mttp) REVERT: L 67 MET cc_start: 0.7907 (mtp) cc_final: 0.7624 (mtp) REVERT: L 217 MET cc_start: 0.8435 (mmm) cc_final: 0.7943 (tpp) REVERT: L 240 GLN cc_start: 0.7654 (mt0) cc_final: 0.7429 (mt0) REVERT: L 256 MET cc_start: 0.6583 (mtt) cc_final: 0.6217 (mtp) REVERT: E 32 TYR cc_start: 0.8507 (m-80) cc_final: 0.8160 (m-80) REVERT: M 217 MET cc_start: 0.8932 (tpt) cc_final: 0.8569 (tpt) REVERT: M 256 MET cc_start: 0.6597 (mtt) cc_final: 0.6286 (mtp) REVERT: N 201 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: N 210 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7878 (tt0) REVERT: N 256 MET cc_start: 0.6535 (mtt) cc_final: 0.6261 (mtp) REVERT: G 33 LYS cc_start: 0.7829 (mppt) cc_final: 0.7604 (mmtm) REVERT: O 82 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7445 (tm-30) REVERT: O 210 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8042 (tt0) REVERT: O 240 GLN cc_start: 0.7634 (mt0) cc_final: 0.7305 (mt0) REVERT: O 256 MET cc_start: 0.6754 (mtt) cc_final: 0.6370 (mtp) REVERT: Q 256 MET cc_start: 0.6888 (mtt) cc_final: 0.6548 (mtp) REVERT: R 43 ASP cc_start: 0.8887 (t0) cc_final: 0.8377 (t0) REVERT: R 62 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7847 (mm110) REVERT: R 170 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7723 (mt-10) REVERT: R 200 LEU cc_start: 0.8349 (tt) cc_final: 0.8105 (tp) REVERT: R 201 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7001 (pt0) REVERT: R 234 ARG cc_start: 0.6930 (tpp80) cc_final: 0.6712 (tpp80) REVERT: R 256 MET cc_start: 0.6652 (mtt) cc_final: 0.6257 (mtp) outliers start: 94 outliers final: 68 residues processed: 438 average time/residue: 0.1435 time to fit residues: 94.0467 Evaluate side-chains 430 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 359 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 217 MET Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 126 SER Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain R residue 62 GLN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 201 GLU Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 85 optimal weight: 3.9990 chunk 196 optimal weight: 0.4980 chunk 220 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 151 GLN N 240 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.159076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137889 restraints weight = 25108.212| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.72 r_work: 0.3479 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19845 Z= 0.172 Angle : 0.541 7.677 26919 Z= 0.289 Chirality : 0.042 0.176 3024 Planarity : 0.004 0.051 3546 Dihedral : 4.835 19.004 2700 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.61 % Allowed : 18.13 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.82 (0.17), residues: 2448 helix: -0.20 (0.19), residues: 729 sheet: -2.35 (0.19), residues: 594 loop : -1.07 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 8 TYR 0.021 0.001 TYR H 32 PHE 0.034 0.002 PHE O 144 TRP 0.007 0.001 TRP M 237 HIS 0.001 0.000 HIS Q 26 Details of bonding type rmsd covalent geometry : bond 0.00380 (19845) covalent geometry : angle 0.54072 (26919) hydrogen bonds : bond 0.03270 ( 765) hydrogen bonds : angle 6.10406 ( 2241) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 380 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: P 210 GLU cc_start: 0.8225 (tt0) cc_final: 0.7981 (tt0) REVERT: P 256 MET cc_start: 0.6329 (mtt) cc_final: 0.6004 (mtp) REVERT: B 6 GLN cc_start: 0.7685 (pt0) cc_final: 0.7415 (pp30) REVERT: B 32 TYR cc_start: 0.8444 (m-80) cc_final: 0.8214 (m-80) REVERT: B 33 LYS cc_start: 0.7960 (mppt) cc_final: 0.7566 (mmtm) REVERT: J 35 PHE cc_start: 0.8867 (m-80) cc_final: 0.8634 (m-80) REVERT: J 143 TYR cc_start: 0.8072 (t80) cc_final: 0.7858 (t80) REVERT: J 170 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7226 (mt-10) REVERT: J 200 LEU cc_start: 0.8452 (tt) cc_final: 0.8130 (tp) REVERT: J 256 MET cc_start: 0.6862 (mtt) cc_final: 0.6421 (mtp) REVERT: K 185 GLU cc_start: 0.7948 (pt0) cc_final: 0.7679 (tt0) REVERT: K 256 MET cc_start: 0.6761 (mtt) cc_final: 0.6352 (mtp) REVERT: D 33 LYS cc_start: 0.8025 (mppt) cc_final: 0.7742 (mmtm) REVERT: L 49 LYS cc_start: 0.9280 (mttm) cc_final: 0.8931 (mttp) REVERT: L 217 MET cc_start: 0.8329 (mmm) cc_final: 0.7972 (tpp) REVERT: L 256 MET cc_start: 0.6534 (mtt) cc_final: 0.6187 (mtp) REVERT: E 32 TYR cc_start: 0.8477 (m-80) cc_final: 0.8101 (m-80) REVERT: M 124 GLU cc_start: 0.7627 (tp30) cc_final: 0.7327 (tp30) REVERT: M 217 MET cc_start: 0.8912 (tpt) cc_final: 0.8589 (tpt) REVERT: M 256 MET cc_start: 0.6605 (mtt) cc_final: 0.6287 (mtp) REVERT: N 82 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7484 (tm-30) REVERT: N 124 GLU cc_start: 0.7819 (tp30) cc_final: 0.7565 (tp30) REVERT: N 201 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: N 210 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7868 (tt0) REVERT: N 256 MET cc_start: 0.6558 (mtt) cc_final: 0.6257 (mtp) REVERT: G 33 LYS cc_start: 0.7832 (mppt) cc_final: 0.7615 (mmtm) REVERT: O 82 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7512 (tm-30) REVERT: O 240 GLN cc_start: 0.7638 (mt0) cc_final: 0.7413 (mt0) REVERT: O 256 MET cc_start: 0.6775 (mtt) cc_final: 0.6382 (mtp) REVERT: Q 124 GLU cc_start: 0.7693 (tp30) cc_final: 0.7460 (tp30) REVERT: Q 199 LEU cc_start: 0.8157 (tt) cc_final: 0.7902 (tt) REVERT: Q 256 MET cc_start: 0.6909 (mtt) cc_final: 0.6539 (mtp) REVERT: I 32 TYR cc_start: 0.8355 (m-80) cc_final: 0.8145 (m-80) REVERT: R 43 ASP cc_start: 0.8890 (t0) cc_final: 0.8373 (t0) REVERT: R 62 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7798 (mm110) REVERT: R 170 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7710 (mt-10) REVERT: R 200 LEU cc_start: 0.8258 (tt) cc_final: 0.7981 (tp) REVERT: R 217 MET cc_start: 0.8431 (mmm) cc_final: 0.7918 (tpp) REVERT: R 256 MET cc_start: 0.6700 (mtt) cc_final: 0.6272 (mtp) outliers start: 98 outliers final: 73 residues processed: 436 average time/residue: 0.1434 time to fit residues: 94.4542 Evaluate side-chains 441 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 366 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 217 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain R residue 62 GLN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 201 GLU Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 30 optimal weight: 0.2980 chunk 233 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN K 156 GLN L 151 GLN E 27 GLN M 62 GLN F 27 GLN G 11 ASN G 24 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137934 restraints weight = 25399.106| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.72 r_work: 0.3479 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19845 Z= 0.167 Angle : 0.551 9.996 26919 Z= 0.293 Chirality : 0.042 0.164 3024 Planarity : 0.005 0.054 3546 Dihedral : 4.831 18.572 2700 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.71 % Allowed : 19.35 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.75 (0.17), residues: 2448 helix: -0.14 (0.19), residues: 738 sheet: -2.38 (0.19), residues: 594 loop : -0.99 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 17 TYR 0.023 0.001 TYR H 32 PHE 0.029 0.002 PHE O 144 TRP 0.006 0.001 TRP M 237 HIS 0.001 0.000 HIS N 26 Details of bonding type rmsd covalent geometry : bond 0.00373 (19845) covalent geometry : angle 0.55130 (26919) hydrogen bonds : bond 0.03230 ( 765) hydrogen bonds : angle 6.07635 ( 2241) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 392 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 17 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.7041 (mmt-90) REVERT: P 124 GLU cc_start: 0.7872 (tp30) cc_final: 0.7629 (tp30) REVERT: P 164 VAL cc_start: 0.9022 (t) cc_final: 0.8781 (t) REVERT: P 256 MET cc_start: 0.6339 (mtt) cc_final: 0.6002 (mtp) REVERT: B 6 GLN cc_start: 0.7721 (pt0) cc_final: 0.7429 (pp30) REVERT: B 32 TYR cc_start: 0.8443 (m-80) cc_final: 0.8202 (m-80) REVERT: B 33 LYS cc_start: 0.7949 (mppt) cc_final: 0.7556 (mmtm) REVERT: J 35 PHE cc_start: 0.8852 (m-80) cc_final: 0.8605 (m-80) REVERT: J 256 MET cc_start: 0.6885 (mtt) cc_final: 0.6461 (mtp) REVERT: K 185 GLU cc_start: 0.7939 (pt0) cc_final: 0.7676 (tt0) REVERT: K 256 MET cc_start: 0.6875 (mtt) cc_final: 0.6494 (mtp) REVERT: D 33 LYS cc_start: 0.8021 (mppt) cc_final: 0.7725 (mmtm) REVERT: L 49 LYS cc_start: 0.9272 (mttm) cc_final: 0.8924 (mttp) REVERT: L 142 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7724 (ttt180) REVERT: L 217 MET cc_start: 0.8372 (mmm) cc_final: 0.7945 (tpp) REVERT: L 256 MET cc_start: 0.6677 (mtt) cc_final: 0.6349 (mtp) REVERT: E 32 TYR cc_start: 0.8448 (m-80) cc_final: 0.8072 (m-80) REVERT: E 33 LYS cc_start: 0.8148 (mppt) cc_final: 0.7879 (mmtt) REVERT: M 124 GLU cc_start: 0.7608 (tp30) cc_final: 0.7330 (tp30) REVERT: M 217 MET cc_start: 0.8955 (tpt) cc_final: 0.8602 (tpt) REVERT: M 256 MET cc_start: 0.6665 (mtt) cc_final: 0.6345 (mtp) REVERT: N 201 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7198 (pt0) REVERT: N 210 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7899 (tt0) REVERT: N 256 MET cc_start: 0.6549 (mtt) cc_final: 0.6260 (mtp) REVERT: G 33 LYS cc_start: 0.7927 (mppt) cc_final: 0.7693 (mmtm) REVERT: O 82 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7459 (tm-30) REVERT: O 228 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8439 (mp) REVERT: O 256 MET cc_start: 0.6763 (mtt) cc_final: 0.6379 (mtp) REVERT: Q 124 GLU cc_start: 0.7714 (tp30) cc_final: 0.7456 (tp30) REVERT: Q 199 LEU cc_start: 0.8238 (tt) cc_final: 0.8007 (tt) REVERT: Q 217 MET cc_start: 0.8895 (tpt) cc_final: 0.8189 (tpt) REVERT: Q 221 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7878 (mp0) REVERT: Q 256 MET cc_start: 0.6949 (mtt) cc_final: 0.6601 (mtp) REVERT: I 32 TYR cc_start: 0.8364 (m-80) cc_final: 0.8117 (m-80) REVERT: R 43 ASP cc_start: 0.8888 (t0) cc_final: 0.8614 (t0) REVERT: R 170 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7670 (mt-10) REVERT: R 200 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8064 (tp) REVERT: R 256 MET cc_start: 0.6721 (mtt) cc_final: 0.6302 (mtp) outliers start: 100 outliers final: 74 residues processed: 450 average time/residue: 0.1386 time to fit residues: 93.2337 Evaluate side-chains 451 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 374 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain O residue 228 ILE Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 98 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 201 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 62 GLN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN M 62 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 GLN ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137668 restraints weight = 25299.339| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.72 r_work: 0.3466 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19845 Z= 0.166 Angle : 0.557 9.202 26919 Z= 0.295 Chirality : 0.042 0.202 3024 Planarity : 0.005 0.055 3546 Dihedral : 4.847 18.572 2700 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.33 % Allowed : 20.48 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.17), residues: 2448 helix: 0.04 (0.19), residues: 729 sheet: -2.38 (0.19), residues: 594 loop : -0.97 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 17 TYR 0.023 0.001 TYR H 32 PHE 0.036 0.002 PHE O 144 TRP 0.005 0.001 TRP M 237 HIS 0.001 0.000 HIS N 26 Details of bonding type rmsd covalent geometry : bond 0.00372 (19845) covalent geometry : angle 0.55695 (26919) hydrogen bonds : bond 0.03218 ( 765) hydrogen bonds : angle 6.06267 ( 2241) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 392 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: P 17 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.7047 (mmt-90) REVERT: P 124 GLU cc_start: 0.7823 (tp30) cc_final: 0.7622 (tp30) REVERT: P 164 VAL cc_start: 0.9035 (t) cc_final: 0.8808 (t) REVERT: P 193 PHE cc_start: 0.7868 (m-10) cc_final: 0.7566 (m-10) REVERT: P 256 MET cc_start: 0.6445 (mtt) cc_final: 0.6102 (mtp) REVERT: B 6 GLN cc_start: 0.7697 (pt0) cc_final: 0.7422 (pp30) REVERT: B 32 TYR cc_start: 0.8422 (m-80) cc_final: 0.8182 (m-80) REVERT: B 33 LYS cc_start: 0.7947 (mppt) cc_final: 0.7567 (mmtm) REVERT: J 35 PHE cc_start: 0.8885 (m-80) cc_final: 0.8663 (m-80) REVERT: J 200 LEU cc_start: 0.8582 (tt) cc_final: 0.8092 (tp) REVERT: J 256 MET cc_start: 0.6888 (mtt) cc_final: 0.6461 (mtp) REVERT: K 185 GLU cc_start: 0.7944 (pt0) cc_final: 0.7683 (tt0) REVERT: K 256 MET cc_start: 0.6889 (mtt) cc_final: 0.6490 (mtp) REVERT: D 33 LYS cc_start: 0.8006 (mppt) cc_final: 0.7710 (mmtm) REVERT: L 49 LYS cc_start: 0.9292 (mttm) cc_final: 0.8952 (mttp) REVERT: L 142 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7752 (ttt180) REVERT: L 217 MET cc_start: 0.8366 (mmm) cc_final: 0.8037 (tpp) REVERT: L 256 MET cc_start: 0.6709 (mtt) cc_final: 0.6393 (mtp) REVERT: E 29 GLN cc_start: 0.9100 (pt0) cc_final: 0.8845 (pt0) REVERT: E 32 TYR cc_start: 0.8394 (m-80) cc_final: 0.8120 (m-80) REVERT: M 256 MET cc_start: 0.6699 (mtt) cc_final: 0.6407 (mtp) REVERT: N 82 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7329 (tm-30) REVERT: N 201 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7212 (pt0) REVERT: N 210 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7918 (tt0) REVERT: N 256 MET cc_start: 0.6648 (mtt) cc_final: 0.6376 (mtp) REVERT: O 228 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8340 (mp) REVERT: O 256 MET cc_start: 0.6751 (mtt) cc_final: 0.6376 (mtp) REVERT: Q 124 GLU cc_start: 0.7681 (tp30) cc_final: 0.7447 (tp30) REVERT: Q 217 MET cc_start: 0.8741 (tpt) cc_final: 0.7962 (tpt) REVERT: Q 221 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7817 (mp0) REVERT: Q 256 MET cc_start: 0.6914 (mtt) cc_final: 0.6576 (mtp) REVERT: I 32 TYR cc_start: 0.8284 (m-80) cc_final: 0.8034 (m-80) REVERT: R 170 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7668 (mt-10) REVERT: R 256 MET cc_start: 0.6743 (mtt) cc_final: 0.6329 (mtp) outliers start: 92 outliers final: 79 residues processed: 445 average time/residue: 0.1479 time to fit residues: 97.9922 Evaluate side-chains 452 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 371 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain O residue 228 ILE Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 161 optimal weight: 0.9990 chunk 196 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 40 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: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 GLN P 156 GLN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.158440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137692 restraints weight = 25209.740| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.69 r_work: 0.3484 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19845 Z= 0.169 Angle : 0.577 11.933 26919 Z= 0.302 Chirality : 0.043 0.268 3024 Planarity : 0.005 0.058 3546 Dihedral : 4.899 18.810 2700 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.47 % Allowed : 20.06 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.62 (0.17), residues: 2448 helix: 0.05 (0.19), residues: 729 sheet: -2.35 (0.19), residues: 594 loop : -0.93 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 17 TYR 0.024 0.001 TYR H 32 PHE 0.036 0.002 PHE O 144 TRP 0.005 0.001 TRP Q 237 HIS 0.001 0.000 HIS R 26 Details of bonding type rmsd covalent geometry : bond 0.00378 (19845) covalent geometry : angle 0.57659 (26919) hydrogen bonds : bond 0.03251 ( 765) hydrogen bonds : angle 6.06175 ( 2241) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 392 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9014 (t0) cc_final: 0.8760 (p0) REVERT: P 124 GLU cc_start: 0.7828 (tp30) cc_final: 0.7490 (tp30) REVERT: P 164 VAL cc_start: 0.9051 (t) cc_final: 0.8815 (t) REVERT: P 193 PHE cc_start: 0.7793 (m-10) cc_final: 0.7538 (m-10) REVERT: P 256 MET cc_start: 0.6627 (mtt) cc_final: 0.6301 (mtp) REVERT: B 32 TYR cc_start: 0.8442 (m-80) cc_final: 0.8175 (m-80) REVERT: B 33 LYS cc_start: 0.7927 (mppt) cc_final: 0.7568 (mmtm) REVERT: J 35 PHE cc_start: 0.8833 (m-80) cc_final: 0.8606 (m-80) REVERT: J 200 LEU cc_start: 0.8655 (tt) cc_final: 0.8168 (tp) REVERT: J 256 MET cc_start: 0.6893 (mtt) cc_final: 0.6463 (mtp) REVERT: K 185 GLU cc_start: 0.7930 (pt0) cc_final: 0.7688 (tt0) REVERT: K 256 MET cc_start: 0.6905 (mtt) cc_final: 0.6517 (mtp) REVERT: D 33 LYS cc_start: 0.7958 (mppt) cc_final: 0.7684 (mmtm) REVERT: L 49 LYS cc_start: 0.9270 (mttm) cc_final: 0.8911 (mttp) REVERT: L 256 MET cc_start: 0.6729 (mtt) cc_final: 0.6418 (mtp) REVERT: E 32 TYR cc_start: 0.8397 (m-80) cc_final: 0.8060 (m-80) REVERT: E 33 LYS cc_start: 0.8154 (mppt) cc_final: 0.7877 (mmtt) REVERT: M 256 MET cc_start: 0.6763 (mtt) cc_final: 0.6428 (mtp) REVERT: N 82 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7358 (tm-30) REVERT: N 124 GLU cc_start: 0.7823 (tp30) cc_final: 0.7421 (tp30) REVERT: N 201 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: N 210 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7934 (tt0) REVERT: N 256 MET cc_start: 0.6707 (mtt) cc_final: 0.6422 (mtp) REVERT: O 33 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8579 (mtmm) REVERT: O 228 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8347 (mp) REVERT: O 256 MET cc_start: 0.6763 (mtt) cc_final: 0.6376 (mtp) REVERT: H 6 GLN cc_start: 0.7635 (mp10) cc_final: 0.7254 (mp10) REVERT: Q 124 GLU cc_start: 0.7694 (tp30) cc_final: 0.7438 (tp30) REVERT: Q 256 MET cc_start: 0.6986 (mtt) cc_final: 0.6649 (mtp) REVERT: I 32 TYR cc_start: 0.8255 (m-80) cc_final: 0.8048 (m-80) REVERT: R 170 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7603 (mt-10) REVERT: R 256 MET cc_start: 0.6732 (mtt) cc_final: 0.6317 (mtp) outliers start: 95 outliers final: 85 residues processed: 448 average time/residue: 0.1528 time to fit residues: 102.5512 Evaluate side-chains 457 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 369 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 217 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain O residue 228 ILE Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 98 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 231 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 chunk 183 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137403 restraints weight = 25423.114| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.71 r_work: 0.3478 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19845 Z= 0.180 Angle : 0.594 13.782 26919 Z= 0.310 Chirality : 0.043 0.236 3024 Planarity : 0.005 0.066 3546 Dihedral : 4.986 25.159 2700 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.43 % Allowed : 19.96 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.60 (0.17), residues: 2448 helix: 0.06 (0.19), residues: 729 sheet: -2.33 (0.19), residues: 594 loop : -0.93 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 8 TYR 0.023 0.001 TYR H 32 PHE 0.036 0.002 PHE O 144 TRP 0.004 0.001 TRP O 77 HIS 0.001 0.000 HIS R 26 Details of bonding type rmsd covalent geometry : bond 0.00404 (19845) covalent geometry : angle 0.59396 (26919) hydrogen bonds : bond 0.03327 ( 765) hydrogen bonds : angle 6.09244 ( 2241) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 387 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 164 VAL cc_start: 0.9060 (t) cc_final: 0.8838 (t) REVERT: P 193 PHE cc_start: 0.7808 (m-10) cc_final: 0.7477 (m-10) REVERT: P 256 MET cc_start: 0.6739 (mtt) cc_final: 0.6369 (mtp) REVERT: B 32 TYR cc_start: 0.8460 (m-80) cc_final: 0.8162 (m-80) REVERT: B 33 LYS cc_start: 0.7912 (mppt) cc_final: 0.7569 (mmtm) REVERT: J 200 LEU cc_start: 0.8663 (tt) cc_final: 0.8201 (tp) REVERT: J 256 MET cc_start: 0.7020 (mtt) cc_final: 0.6552 (mtp) REVERT: K 185 GLU cc_start: 0.7921 (pt0) cc_final: 0.7645 (tt0) REVERT: K 256 MET cc_start: 0.6894 (mtt) cc_final: 0.6484 (mtp) REVERT: D 33 LYS cc_start: 0.7980 (mppt) cc_final: 0.7709 (mmtm) REVERT: L 49 LYS cc_start: 0.9262 (mttm) cc_final: 0.8908 (mttp) REVERT: L 256 MET cc_start: 0.6749 (mtt) cc_final: 0.6421 (mtp) REVERT: E 32 TYR cc_start: 0.8463 (m-80) cc_final: 0.8134 (m-80) REVERT: M 82 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7549 (tm-30) REVERT: M 212 VAL cc_start: 0.9334 (p) cc_final: 0.9087 (t) REVERT: M 256 MET cc_start: 0.6758 (mtt) cc_final: 0.6442 (mtp) REVERT: F 6 GLN cc_start: 0.6677 (pp30) cc_final: 0.6418 (pp30) REVERT: N 82 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7390 (tm-30) REVERT: N 124 GLU cc_start: 0.7855 (tp30) cc_final: 0.7366 (tp30) REVERT: N 201 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7175 (pt0) REVERT: N 210 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7914 (tt0) REVERT: N 256 MET cc_start: 0.6854 (mtt) cc_final: 0.6578 (mtp) REVERT: O 33 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8589 (mtmm) REVERT: O 210 GLU cc_start: 0.8055 (tt0) cc_final: 0.7745 (tt0) REVERT: O 228 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8341 (mp) REVERT: O 256 MET cc_start: 0.6749 (mtt) cc_final: 0.6380 (mtp) REVERT: Q 124 GLU cc_start: 0.7743 (tp30) cc_final: 0.7477 (tp30) REVERT: Q 256 MET cc_start: 0.7017 (mtt) cc_final: 0.6669 (mtp) REVERT: I 8 ARG cc_start: 0.7715 (mpt-90) cc_final: 0.7330 (mpt-90) REVERT: I 32 TYR cc_start: 0.8240 (m-80) cc_final: 0.8032 (m-80) REVERT: R 170 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7613 (mt-10) REVERT: R 256 MET cc_start: 0.6762 (mtt) cc_final: 0.6335 (mtp) outliers start: 94 outliers final: 89 residues processed: 442 average time/residue: 0.1483 time to fit residues: 98.1031 Evaluate side-chains 463 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 371 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 217 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain O residue 228 ILE Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 165 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 230 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN E 29 GLN M 156 GLN N 55 ASN O 156 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 ASN ** R 247 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 = 0.3842 r_free = 0.3842 target = 0.159173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138715 restraints weight = 25304.351| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.70 r_work: 0.3481 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19845 Z= 0.157 Angle : 0.598 12.236 26919 Z= 0.311 Chirality : 0.043 0.254 3024 Planarity : 0.005 0.074 3546 Dihedral : 4.995 25.715 2700 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.14 % Allowed : 20.53 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.59 (0.17), residues: 2448 helix: 0.07 (0.19), residues: 729 sheet: -2.32 (0.19), residues: 594 loop : -0.93 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 8 TYR 0.025 0.001 TYR H 32 PHE 0.034 0.001 PHE O 144 TRP 0.004 0.001 TRP M 237 HIS 0.001 0.000 HIS R 26 Details of bonding type rmsd covalent geometry : bond 0.00355 (19845) covalent geometry : angle 0.59816 (26919) hydrogen bonds : bond 0.03258 ( 765) hydrogen bonds : angle 6.04739 ( 2241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4300.48 seconds wall clock time: 75 minutes 26.28 seconds (4526.28 seconds total)